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The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: Genetic mapping of the copper toxicosis locus in Bedlington terriers to dog chromosome 10, in a region syntenic to human chromosome region 2p13-p16. Useful knowledge : ||| Genetic mapping definition: Any method used for determining the location of and relative distances between genes on a chromosome. ||| copper definition: A heavy metal trace element with the atomic symbol Cu, atomic number 29, and atomic weight 63.55. ||| toxicosis definition: None ||| locus definition: The position of a gene or a chromosomal marker on a chromosome; also, a stretch of DNA at a particular place on a particular chromosome. The use of locus is sometimes restricted to mean regions of DNA that are expressed. ||| Bedlington terriers definition: A terrier that resembles a lamb, with a pear-shaped head, arched back, and a thick, curly double coat that can be blue, liver, or sandy color. The average height range is 15-17 inches and the average weight range is 18-23 pounds. ||| dog chromosome 10 definition: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification. ||| human definition: Members of the species Homo sapiens. ||| Output:

Genetic mapping of the @@copper toxicosis## locus in Bedlington terriers to dog chromosome 10, in a region syntenic to human chromosome region 2p13-p16.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: Abnormal hepatic copper accumulation is recognized as an inherited disorder in man, mouse, rat and dog. Useful knowledge : ||| Abnormal definition: Deviating in any way from the state, position, structure, condition, behavior, or rule which is considered a norm. ||| hepatic copper definition: Pertaining to, affecting, or associated with the liver. ||| accumulation definition: A state characterized by the gradual increase in entities or substances. ||| inherited definition: Transmitted through genes from parents to offspring. (genome.gov) ||| disorder definition: A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown. ||| man definition: Human males as cultural, psychological, sociological, political, and economic entities. ||| mouse definition: The common mouse species, Mus musculus. ||| rat definition: The common rat, Rattus norvegicus, often used as an experimental organism. ||| dog definition: The domestic dog, Canis familiaris, comprising about 400 breeds, of the carnivore family CANIDAE. They are worldwide in distribution and live in association with people. (Walker's Mammals of the World, 5th ed, p1065) ||| Output:

Abnormal @@hepatic copper accumulation## is recognized as an @@inherited disorder## in man, mouse, rat and dog.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: The major cause of hepatic copper accumulation in man is a dysfunctional ATP7B gene, causing Wilson disease (WD). Useful knowledge : ||| hepatic copper definition: Pertaining to, affecting, or associated with the liver. ||| accumulation definition: A state characterized by the gradual increase in entities or substances. ||| man definition: Human males as cultural, psychological, sociological, political, and economic entities. ||| dysfunctional definition: Used with organs and diseases for disordered function in disease states. ||| ATP7B gene definition: This gene plays a role in ATPase-dependent copper export. ||| Wilson disease definition: A rare autosomal recessive disease characterized by the deposition of copper in the BRAIN; LIVER; CORNEA; and other organs. It is caused by defects in the ATP7B gene encoding copper-transporting ATPase 2 (EC 3.6.3.4), also known as the Wilson disease protein. The overload of copper inevitably leads to progressive liver and neurological dysfunction such as LIVER CIRRHOSIS; TREMOR; ATAXIA and intellectual deterioration. Hepatic dysfunction may precede neurologic dysfunction by several years. ||| WD definition: A rare autosomal recessive disease characterized by the deposition of copper in the BRAIN; LIVER; CORNEA; and other organs. It is caused by defects in the ATP7B gene encoding copper-transporting ATPase 2 (EC 3.6.3.4), also known as the Wilson disease protein. The overload of copper inevitably leads to progressive liver and neurological dysfunction such as LIVER CIRRHOSIS; TREMOR; ATAXIA and intellectual deterioration. Hepatic dysfunction may precede neurologic dysfunction by several years. ||| Output:

The major cause of @@hepatic copper accumulation## in man is a dysfunctional ATP7B gene, causing @@Wilson disease## (@@WD##).

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: Mutations in the ATP7B genes have also been demonstrated in mouse and rat. Useful knowledge : ||| Mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| ATP7B genes definition: This gene plays a role in ATPase-dependent copper export. ||| mouse definition: The common mouse species, Mus musculus. ||| rat definition: The common rat, Rattus norvegicus, often used as an experimental organism. ||| Output:

Mutations in the ATP7B genes have also been demonstrated in mouse and rat.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: The ATP7B gene has been excluded in the much rarer human copper overload disease non-Indian childhood cirrhosis, indicating genetic heterogeneity. Useful knowledge : ||| ATP7B gene definition: This gene plays a role in ATPase-dependent copper export. ||| human definition: Members of the species Homo sapiens. ||| childhood cirrhosis definition: Severe autosomal recessive intrahepatic cholestasis described in aboriginal children from northwestern Quebec. First manifestation as neonatal jaundice, progresses to periportal fibrosis and cirrhosis. ||| genetic heterogeneity definition: The presence of apparently similar characters for which the genetic evidence indicates that different genes or different genetic mechanisms are involved in different pedigrees. In clinical settings genetic heterogeneity refers to the presence of a variety of genetic defects which cause the same disease, often due to mutations at different loci on the same gene, a finding common to many human diseases including ALZHEIMER DISEASE; CYSTIC FIBROSIS; LIPOPROTEIN LIPASE DEFICIENCY, FAMILIAL; and POLYCYSTIC KIDNEY DISEASES. (Rieger, et al., Glossary of Genetics: Classical and Molecular, 5th ed; Segen, Dictionary of Modern Medicine, 1992) ||| Output:

The ATP7B gene has been excluded in the much rarer human @@copper overload## disease @@non-Indian childhood cirrhosis##, indicating genetic heterogeneity.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: By investigating the common autosomal recessive copper toxicosis (CT) in Bedlington terriers, we have identified a new locus involved in progressive liver disease. Useful knowledge : ||| investigating definition: None ||| autosomal definition: Any chromosome other than a sex chromosome. [GOC:mah] ||| CT definition: State bounded on the north by Massachusetts, on the east by Rhode Island, on the south by Long Island Sound, and on the west by New York. ||| Bedlington terriers definition: A terrier that resembles a lamb, with a pear-shaped head, arched back, and a thick, curly double coat that can be blue, liver, or sandy color. The average height range is 15-17 inches and the average weight range is 18-23 pounds. ||| identified definition: The procedure of having an identity established. ||| locus definition: The position of a gene or a chromosomal marker on a chromosome; also, a stretch of DNA at a particular place on a particular chromosome. The use of locus is sometimes restricted to mean regions of DNA that are expressed. ||| progressive definition: Advancing in extent or severity. ||| liver disease definition: Pathological processes of the LIVER. ||| Output:

By investigating the common autosomal recessive @@copper toxicosis## (@@CT##) in Bedlington terriers, we have identified a new locus involved in progressive @@liver disease##.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: We examined whether the WD gene ATP7B was also causative for CT by investigating the chromosomal co-localization of ATP7B and C04107, using fluorescence in situ hybridization (FISH). Useful knowledge : ||| WD gene definition: A rare autosomal recessive disease characterized by the deposition of copper in the BRAIN; LIVER; CORNEA; and other organs. It is caused by defects in the ATP7B gene encoding copper-transporting ATPase 2 (EC 3.6.3.4), also known as the Wilson disease protein. The overload of copper inevitably leads to progressive liver and neurological dysfunction such as LIVER CIRRHOSIS; TREMOR; ATAXIA and intellectual deterioration. Hepatic dysfunction may precede neurologic dysfunction by several years. ||| ATP7B definition: This gene plays a role in ATPase-dependent copper export. ||| causative definition: <p>Definition: A factor, such as a microorganism, chemical substance, or form of radiation, whose presence, excessive presence, or (in deficiency diseases) relative absence is essential, in whole or in part, for the occurrence of a condition.</p><p>Constraint: The use of this participation is limited to observations.</p> ||| CT definition: State bounded on the north by Massachusetts, on the east by Rhode Island, on the south by Long Island Sound, and on the west by New York. ||| investigating definition: None ||| chromosomal co-localization definition: Any process in which a chromosome is transported to, or maintained in, a specific location. [GOC:ai] ||| ATP7B definition: This gene plays a role in ATPase-dependent copper export. ||| fluorescence in situ hybridization ( definition: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| Output:

We examined whether the @@WD## gene ATP7B was also causative for @@CT## by investigating the chromosomal co-localization of ATP7B and C04107, using fluorescence in situ hybridization (FISH).

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: C04107 is an anonymous microsatellite marker closely linked to CT. Useful knowledge : ||| microsatellite marker definition: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs). ||| CT definition: State bounded on the north by Massachusetts, on the east by Rhode Island, on the south by Long Island Sound, and on the west by New York. ||| Output:

C04107 is an anonymous microsatellite marker closely linked to @@CT##.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: However, BAC clones containing ATP7B and C04107 mapped to the canine chromosome regions CFA22q11 and CFA10q26, respectively, demonstrating that WD cannot be homologous to CT. Useful knowledge : ||| BAC clones definition: A group of genetically identical cells all descended from a single common ancestral cell by mitosis in eukaryotes or by binary fission in prokaryotes. Clone cells also include populations of recombinant DNA molecules all carrying the same inserted sequence. (From King & Stansfield, Dictionary of Genetics, 4th ed) ||| ATP7B definition: This gene plays a role in ATPase-dependent copper export. ||| mapped definition: The process of connecting an item or symbol to a code or concept. ||| canine definition: The domestic dog, Canis familiaris, comprising about 400 breeds, of the carnivore family CANIDAE. They are worldwide in distribution and live in association with people. (Walker's Mammals of the World, 5th ed, p1065) ||| chromosome regions definition: Any subdivision of a chromosome along its length. [GOC:dos] ||| WD definition: A rare autosomal recessive disease characterized by the deposition of copper in the BRAIN; LIVER; CORNEA; and other organs. It is caused by defects in the ATP7B gene encoding copper-transporting ATPase 2 (EC 3.6.3.4), also known as the Wilson disease protein. The overload of copper inevitably leads to progressive liver and neurological dysfunction such as LIVER CIRRHOSIS; TREMOR; ATAXIA and intellectual deterioration. Hepatic dysfunction may precede neurologic dysfunction by several years. ||| CT definition: State bounded on the north by Massachusetts, on the east by Rhode Island, on the south by Long Island Sound, and on the west by New York. ||| Output:

However, BAC clones containing ATP7B and C04107 mapped to the canine chromosome regions CFA22q11 and CFA10q26, respectively, demonstrating that @@WD## cannot be homologous to @@CT##.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: The copper transport genes CTR1 and CTR2 were also excluded as candidate genes for CT since they both mapped to canine chromosome region CFA11q22. Useful knowledge : ||| copper transport genes definition: The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai] ||| CTR1 definition: None ||| CTR2 definition: None ||| candidate genes definition: A gene proposed to have a primary role in a disease, based upon its known function in other organisms or model systems or based upon its physical proximity to markers linked to a genetic disease. ||| CT definition: State bounded on the north by Massachusetts, on the east by Rhode Island, on the south by Long Island Sound, and on the west by New York. ||| mapped definition: The process of connecting an item or symbol to a code or concept. ||| canine definition: The domestic dog, Canis familiaris, comprising about 400 breeds, of the carnivore family CANIDAE. They are worldwide in distribution and live in association with people. (Walker's Mammals of the World, 5th ed, p1065) ||| chromosome region definition: Any subdivision of a chromosome along its length. [GOC:dos] ||| Output:

The copper transport genes CTR1 and CTR2 were also excluded as candidate genes for @@CT## since they both mapped to canine chromosome region CFA11q22.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: 2-22. Useful knowledge : ||| Output:

2-22.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: 5. Useful knowledge : ||| Output:

5.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: A transcribed sequence identified from the C04107-containing BAC was found to be homologous to a gene expressed from human chromosome 2p13-p16, a region devoid of any positional candidate genes. Useful knowledge : ||| identified definition: The procedure of having an identity established. ||| homologous definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| gene expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| region definition: The continents and countries situated on those continents; the UNITED STATES and each of the constituent states arranged by region; CANADA and each of its provinces; AUSTRALIA and each of its states; the major bodies of water and major islands on both hemispheres; and selected major cities. ||| positional candidate genes definition: A gene proposed to have a primary role in a disease, based upon its known function in other organisms or model systems or based upon its physical proximity to markers linked to a genetic disease. ||| Output:

A transcribed sequence identified from the C04107-containing BAC was found to be homologous to a gene expressed from human chromosome 2p13-p16, a region devoid of any positional candidate genes.

The task is to label all mentions of diseases in a sentence, by putting them in a specific format. Here are some examples: Input: CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Useful knowledge : ||| CAG expansions definition: Procedures that stimulate nerve elongation over a period of time. They are used in repairing nerve tissue. ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| Machado-Joseph disease definition: A dominantly-inherited ATAXIA first described in people of Azorean and Portuguese descent, and subsequently identified in Brazil, Japan, China, and Australia. This disorder is classified as one of the SPINOCEREBELLAR ATAXIAS (Type 3) and has been associated with a mutation of the MJD1 gene on chromosome 14. Clinical features include progressive ataxia, DYSARTHRIA, postural instability, nystagmus, eyelid retraction, and facial FASCICULATIONS. DYSTONIA is prominent in younger patients (referred to as Type I Machado-Joseph Disease). Type II features ataxia and ocular signs; Type III features MUSCULAR ATROPHY and a sensorimotor neuropathy; and Type IV features extrapyramidal signs combined with a sensorimotor neuropathy. (From Clin Neurosci 1995;3(1):17-22; Ann Neurol 1998 Mar;43(3):288-96) ||| chromosome 14q32.1 definition: A chromosome band present on 14q ||| Output: CAG expansions in a novel gene for @@Machado-Joseph disease## at chromosome 14q32.1. Input: Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Useful knowledge : ||| Deletions definition: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus. ||| DNA sequence definition: The sequence of nucleotide residues along a DNA chain. ||| retinoblastomas definition: A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) ||| mesenchymal tumors definition: A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma. ||| organization definition: None ||| sequence definition: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. ||| encoded protein definition: To assign a code to represent data. ||| Output: Deletions of a DNA sequence in @@retinoblastomas## and @@mesenchymal tumors##: organization of the sequence and its encoded protein. Input: BRCA1 interacts with components of the histone deacetylase complex. Useful knowledge : ||| BRCA1 definition: A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. It encodes a large nuclear protein that is a component of DNA repair pathways. ||| components definition: None ||| histone deacetylase complex definition: A protein complex that possesses histone deacetylase activity. [GOC:mah] ||| Output: BRCA1 interacts with components of the histone deacetylase complex. Input: Both mutations in G6PD A- are necessary to produce the G6PD deficient phenotype. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| G6PD definition: None ||| G6PD definition: None ||| deficient definition: None ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Both mutations in G6PD A- are necessary to produce the @@G6PD deficient## phenotype. Input: Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene. Useful knowledge : ||| Prenatal diagnosis definition: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth. ||| FISH definition: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales. ||| family definition: A social group consisting of parents or parent substitutes and children. ||| Pelizaeus-Merzbacher disease definition: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190) ||| duplication definition: None ||| PLP gene definition: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE). ||| Output: Prenatal diagnosis by FISH in a family with @@Pelizaeus-Merzbacher disease## caused by duplication of PLP gene. Input: The gene for familial Mediterranean fever, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Useful knowledge : ||| gene definition: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. ||| familial Mediterranean fever definition: A group of HEREDITARY AUTOINFLAMMATION DISEASES, characterized by recurrent fever, abdominal pain, headache, rash, PLEURISY; and ARTHRITIS. ORCHITIS; benign MENINGITIS; and AMYLOIDOSIS may also occur. Homozygous or compound heterozygous mutations in marenostrin gene encoding PYRIN result in autosomal recessive transmission; simple heterozygous, autosomal dominant form of the disease also exists with mutations in the same gene. ||| MEFV definition: None ||| expressed definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| leukocyte development definition: White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). ||| response definition: Any act or phenomena, or behavior, constituting a reply or reaction of a living organism or its part to some foregoing stimulus or agent. ||| inflammatory mediators definition: The endogenous compounds that mediate inflammation (AUTACOIDS) and related exogenous compounds including the synthetic prostaglandins (PROSTAGLANDINS, SYNTHETIC). ||| Output: The gene for @@familial Mediterranean fever##, MEFV, is expressed in early leukocyte development and is regulated in response to inflammatory mediators. Input: Prader-Willi syndrome and chromosome 15. Useful knowledge : ||| Prader-Willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| chromosome 15 definition: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification. ||| Output: @@Prader-Willi syndrome## and chromosome 15. Input: Expression and imprinting of MAGEL2 suggest a role in Prader-willi syndrome and the homologous murine imprinting phenotype. Useful knowledge : ||| Expression definition: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| MAGEL2 definition: None ||| Prader-willi syndrome definition: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229) ||| homologous murine definition: A gene from one species which corresponds to a gene in another species and that is related via a common ancestral species. These genes retain a similar sequence and function. ||| imprinting definition: A particular kind of learning characterized by occurrence in very early life, rapidity of acquisition, and relative insusceptibility to forgetting or extinction. Imprinted behavior includes most (or all) behavior commonly called instinctive, but imprinting is used purely descriptively. ||| phenotype definition: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. ||| Output: Expression and imprinting of MAGEL2 suggest a role in @@Prader-willi syndrome## and the homologous murine imprinting phenotype. Input: X linked recessive thrombocytopenia. Useful knowledge : ||| recessive thrombocytopenia definition: A subnormal level of BLOOD PLATELETS. ||| Output: @@X linked recessive thrombocytopenia##. Input: Three novel mutations in five unrelated subjects with hereditary protein S deficiency type I. Useful knowledge : ||| mutations definition: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. ||| subjects definition: Persons who are enrolled in research studies or who are otherwise the subjects of research. ||| hereditary protein S deficiency type I. definition: An inherited coagulation disorder characterized by recurrent venous thrombosis symptoms due to reduced synthesis and/or activity levels of protein S. ||| Output: Three novel mutations in five unrelated subjects with hereditary @@protein S deficiency type I##. Identify all the mentions of diseases in the following sentence, by putting @@ in front and a ## behind each of them Input: Molecular analysis of the APC gene in 205 families: extended genotype-phenotype correlations in FAP and evidence for the role of APC amino acid changes in colorectal cancer predisposition. Useful knowledge : ||| Molecular analysis definition: A laboratory procedure that involves the study of tissues, cells, and fluids using DNA/RNA analysis techniques for the identification of characteristics and abnormalities at the molecular level. ||| APC gene definition: Tumor suppressor genes located in the 5q21 region on the long arm of human chromosome 5. The mutation of these genes is associated with familial adenomatous polyposis (ADENOMATOUS POLYPOSIS COLI) and GARDNER SYNDROME, as well as some sporadic colorectal cancers. ||| families definition: A social group consisting of parents or parent substitutes and children. ||| genotype-phenotype definition: Genetic variants (specific mutations or allelles of genes) and their corresponding phenotypic variations in the trait or the disease which the genes controls. ||| correlations definition: The degree to which two or more quantities or events are linearly associated, a statistical relation between two or more variables such that systematic changes in the value of one variable are accompanied by systematic changes in the others. ||| FAP definition: A polyposis syndrome due to an autosomal dominant mutation of the APC genes (GENES, APC) on CHROMOSOME 5. The syndrome is characterized by the development of hundreds of ADENOMATOUS POLYPS in the COLON and RECTUM of affected individuals by early adulthood. ||| evidence definition: Knowledge on which to base belief. ||| APC definition: A heterogeneous group of immunocompetent cells that mediate the cellular immune response by processing and presenting antigens to the T-cells. Traditional antigen-presenting cells include MACROPHAGES; DENDRITIC CELLS; LANGERHANS CELLS; and B-LYMPHOCYTES. FOLLICULAR DENDRITIC CELLS are not traditional antigen-presenting cells, but because they hold antigen on their cell surface in the form of IMMUNE COMPLEXES for B-cell recognition they are considered so by some authors. ||| amino acid definition: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. ||| colorectal cancer definition: A malignant epithelial neoplasm that arises from the colon or rectum and invades through the muscularis mucosa into the submucosa. The vast majority are adenocarcinomas. ||| predisposition definition: A constitution or condition of the body which makes the tissues react in special ways to certain extrinsic stimuli and thus tends to make the individual more than usually susceptible to certain diseases. ||| Output:

Molecular analysis of the @@APC## gene in 205 families: extended genotype-phenotype correlations in @@FAP## and evidence for the role of @@APC## amino acid changes in @@colorectal cancer## predisposition.