bluuebunny/crossref_metadata_2025_split huggingface dataset:
In VitroFertilisation: Regulation
Authors: Pynes Christopher A 
Published: September 2010

AbstractIn vitrofertilisation (IVF) is a fertility treatment, sometimes referred to more generically as an assisted reproductive technology (ART), designed to help couples who cannot get pregnant in the normal manner, establish a pregnancy. IVF treatment requires the creation of multiple pre‐embryos for implantation into the patient's uterus. The development of IVF techniques has prompted the use of several regulatory models, such as free market approaches, industry self‐regulation, laissez‐faire legislation and prohibitive licensing systems. Each regulatory model has strengths and weaknesses in dealing with different types of moral concerns within the IVF debate, including reproductive autonomy, safety and dignity of the unborn, the creation and destruction of waste embryos, surrogacy and ownership issues. With varying models of regulation and conflicting moral views on the matter, international harmonisation of IVF regulations is unlikely.Key Concepts:Assisted reproductive technology (ART) is a general term used to describe a variety of fertility treatments fromin vitrofertilisation to sperm donation where the ultimate goal is to achieve pregnancy. There is currently no strict definition.Conflicts of interest occur when an individual or group has multiple interests in a particular act or behaviour, which could unjustly influence the act or behaviour; common examples occur in law, medicine, business, politics and journalism.Industry self‐regulation is where an industry or profession attempts to set up regulations to prevent, what the industry might think is, excessive governmental regulation of the industry. The auto industry in the USA is a prime example.In vitrofertilisation literally mean ‘within the glass’ fertilisation and occurs when an ovum is fertilised outside the body in a glass or plastic container like a Petri dish or test‐tube. Hence, the phrase ‘test‐tube’ baby.Laissez‐faire approaches to regulation refer to a ‘let it be’ attitude and is typically associated with free markets and less government involvement.Pre‐embryos are fertilised ova up to 14 days old before they are implanted into a uterus.Procreative (medical) tourism is the practice of travelling to a country other than one's own home country where a particular medical practice, in this case an ART of some kind, is legally permissible.
Neural Networks
Authors: Wu Cathy H , McLarty Jerry W , Liao Li 
Published: September 2010

AbstractArtificial neural networks are a form of machine learning, inspired by biological neural networks, which can be trained by examples to recognise patterns, classify data and make predictions. They have been used in a wide variety of problems in the fields of life sciences, such as predicting protein secondary structures, classifying protein families and identifying single nucleotide polymorphism. Problems in life sciences in general and in bioinformatics in particular present challenges to the design and training of neural networks and to the interpretation of networks outputs as well, including complex structured data and limited amount of training examples. In addressing these issues and limitations, significant progress has been made, including ways to design the neural networks to incorporate prior knowledge, to make automatic formulation of network architecture for optimal performance and to construct hybrid systems to leverage advantages of various learning methods.Key Concepts:Artificial neural networks are a means of mapping input data to output data in such a manner as to perform complex functions such as pattern recognition, classification, prediction and knowledge extraction, that are increasingly useful in bioinformatics applications.There are numerous kinds of neural networks, classified by their architecture (number of layers, number of processing units, interconnections, etc.) and how they are trained to perform.Neural networks have been successfully applied to numerous areas of genomic and proteomic research; the number of such applications has grown explosively in the past few years.One of the most difficult challenges in constructing and training neural networks is often in determining the content and features of data to be used for training and ultimately using the neural networks, that is feature extraction, preprocessing.Hybrid systems, which combine neural networks with other artificial intelligence and statistical techniques, are a promising area of research.
Mammalian Phylogeny
Authors: Phillips Matthew J , Penny David 
Published: September 2010

Abstract

Living mammals can be divided into three subclasses (monotremes, marsupials and placentals) and within these, about 27 orders. Final resolution of the relationships between the orders is only now being achieved with the increased availability of
deoxyribonucleic acid
(DNA) sequences. Highlights include the deep division of placental mammals into African (Afrotheria), South American (Xenarthra) and northern hemisphere (Boreoeutheria) super‐orders, and the finding that the once considered primitive ‘Insectivora’ and ‘Edentata’ clades, in fact, have members distributed widely among these super‐orders. Another surprise finding from DNA studies has been that whale origins lie among the even‐toed ungulates (Artiodactyla). Our order, Primates is most closely related to the flying lemurs and next, the tree shrews. With the mammal phylogeny becoming well resolved, it is increasingly being used as a framework for inferring evolutionary and ecological processes, such as adaptive radiation.

Key Concepts:

A phylogeny describes the relationships of organisms with respect to their shared ancestry.

In the context of phylogenetics, molecular data refer to the genotype (DNA) and its direct translations (e.g. protein sequences).

Morphology refers to an organism's structural phenotype, sometimes limited to anatomy, but often also incorporating physiology.

Homoplasy describes character states that are similar for reasons other than shared ancestry, such as due to convergent or parallel evolution.

Retroposons are DNA sequences that can use the protein, reverse transcriptase to copy themselves and insert into new positions in the genome.

Molecular dating employs DNA or protein sequence differences between organisms to provide evolutionary time scales, with independent (especially fossil) information used to convert molecular differences into time.

Adaptive radiation describes the (often) rapid diversification of closely related species into a wide variety of ecological niches.
Pulmonary Disorders: Hereditary
Authors: Marciniak Stefan J , Lomas David A 
Published: September 2010

AbstractHereditary lung diseases can affect the airways (asthma, COPD, cystic fibrosis and primary ciliary dyskinesia), parenchyma (pulmonary fibrosis, Birt Hogg Dube syndrome and tuberous sclerosis) and vasculature (hereditary heamorrhagic telangiectasia) of the lung. Such conditions include simple monogenic disorders such as Kartagener syndrome andα1‐antitrypsin, wherein mutations of critical genes are sufficient to induce well‐defined disease phenotypes. However, many are complex genetic traits in which inheritance subtly affects pathogenesis, for example asthma and idiopathic pulmonary fibrosis. A greater understanding of the genetic basis of pulmonary conditions has provided new insights into their underlying pathophysiology and helped in some cases to shed light on more common sporadic forms. Importantly, the identification of causative genes has also enabled prenatal diagnosis and genetic counselling to be introduced for many diseases.Key Concepts:Common diseases frequently have a genetic component, which with the advent of genome‐wide association studies can now be elucidated.The study of rare monogenic disorders can provide important mechanistic clues to the pathogensis of more common sporadic disease.Pulmonary manifestations can be the presenting feature of several important inherited diseases.
Porphyrias: Genetics
Authors: Elder George H 
Published: September 2010

Abstract

The porphyrias are a group of eight disorders of haem biosynthesis characterised by overproduction of haem precursors secondary to partial enzyme deficiencies or, in one porphyria, gain‐of‐function of the rate‐controlling enzyme of the pathway in erythroid cells. Patients suffer from acute neurovisceral attacks, always associated with overproduction of porphyrin precursors, skin lesions caused by photosensitisation by porphyrins or both together. All are inherited, apart from sporadic porphyria cutanea tarda. The three porphyrias in which acute attacks occur (acute intermittent porphyria, hereditary coproporphyria and variegate porphyria) and familial porphyria cutanea tarda are low penetrance autosomal dominant disorders and one is an X‐linked dominant disorder. All others are autosomal recessive. Most patients with erythropoietic protoporphyria, the commonest inherited cutaneous porphyria, are compound heterozygotes for a deleterious
ferrochelatase
mutation and a low expression
ferrochelatase
allele; the population frequency of the latter is a major determinant of the prevalence of erythropoietic protoporphyria.

Key Concepts:

The porphyrias are disorders of haem biosynthesis.

Each of the eight porphyrias is caused by an abnormality of a different enzyme of haem biosynthesis.

Each enzyme abnormality leads to overproduction of haem precursors in a specific pattern that defines the disorder.

Overproduction of porphyrin precursors leads to acute neurovisceral attacks which characterise the three autosomal dominant acute porphyrias and one rare recessive porphyria.

Overproduction of porphyrins leads to photosensitisation of the skin with either skin fragility and blisters or, when only protoporphyrin accumulates, acute painful photosensitivity.

All autosomal dominant porphyrias have low clinical penetrance.

Most patients with the commonest inherited cutaneous porphyria, erythropoietic protoporphyria, have inherited a low expression ferrochelatase allele
trans
to a deleterious ferrochelatase mutation.

The prevalence of erythropoietic protoporphyria and the proportion of families showing pseudodominant inheritance are determined by the population frequency of the low expression allele.
Autosomal Dominant Polycystic Kidney Disease
Authors: Arnaout M Amin 
Published: September 2010

AbstractAutosomal dominant polycystic disease (ADPKD) is the most common monogenic disease in humans and is among the leading causes of kidney failure. Dominantly inherited germline mutations in 2 genes,PKD1andPKD2followed by a second somatic hit that annuls or reduces the function of the remaining normal allele lead to loss of tube diameter control, cyst formation and eventual kidney failure. The respective gene products,polycystin‐1andpolycystin‐2form a receptor–ion channel complex that transduces mechanical and/or chemical signals into a calcium entry signal that regulates cell polarity, proliferation and movement. Localisation of this complex in the primary cilium has linked this sensory organelle to the regulation of tube size. Here we review the recent advances made in elucidating pathogenesis, diagnosis and management of this disease and the experimental therapies targeting the implicated signalling pathways.Key Concepts:ADPKD presents with tubular dilatations/cysts mainly affecting the kidney, liver and cardiovascular system, reflecting a defect in tube diameter control. Arterial hypertension is common and occurs early. Current therapy is largely conservative.ADPKD is caused by commonly inactivating germline mutations inPKD1orPKD2combined with a second somatic hit that abolishes or reduces function of the remaining normal allele, an event enhanced by the genomic instability associated with the haploid state.Wide variations in onset and progression of the disease are caused by the type of the impaired gene, hypomorphic alleles, mosaicism, combining an inactivating germline mutation with an acquired hypomorphic allele, stochastic fluctuations in expression level of the remaining normal allele and the genetic background.Cerebral aneurysms are more common in ADPKD patients, occur at an earlier age and tend to rupture at a smaller size when compared to the general population.Progressive loss of renal function occurs before standard markers of renal function are abnormal. Measurement of kidney volume in patients with normal renal function using MR imaging (MRI), CT, or ultrasonography is a more sensitive approach for following disease progression at any age.DNA‐based diagnostics are useful when imaging studies are equivocal, in individuals with a negative family history, in the selection of a young transplant donor from an ADPKD family or to facilitate pre‐implantation genetic diagnosis.The gene products ofPKD1andPKD2, polyctytsin‐1 (PC1) and polycystin‐2 (PC2), respectively, localise to primary cilia as well as to other membrane compartments. Defects in primary cilium structure causes cysts, as are mutations in several other ciliogenic genes supporting a critical role of the primary cilium in tube formation and maintenance.PC1 and PC2 form a receptor‐ion channel complex that triggers calcium entry, which normally activates the planar polarity pathway and represses mitogenic pathways thus regulating tube diameter.The abnormal mitogenesis and fluid secretion pathways that contribute to cyst growth are being targeted therapeutically.
Astromicrobiology
Authors: Davila Alfonso F 
Published: September 2010

Abstract

Astrobiology is the scientific discipline that focuses on the origin, evolution and distribution of life in the universe. Most efforts aiming at understanding the origin of life on Earth, and the possibility that life might exist elsewhere, are directed to the study of microorganisms. This is so because on Earth, microorganisms are the most abundant and widespread forms of life, and are seemingly able to colonise virtually every environment that can support life. Furthermore, small and relatively simple cells are more likely to originate first on a planet than large and complex multicellular organisms, and are also more likely to be transported from one planet to another in the process of panspermia. Hence the term Astro(micro)biology. In this article I introduce and summarise the main fields of research in Astro(micro)biology.

Key Concepts:

The study of life in the Universe requires an interdisciplinary approach.

Mars is the prime target for the search for life beyond the Earth.

The primary focus of planetary exploration is concerned with planets having liquid water.

Terrestrial analogue environments share physical, chemical, geological, mineralogical and any other type of environmental similarity with another planetary body.

Meteorites represent the main source of extraterrestrial material available to scientist.

Extrasolar planets are a likely candidate to provide the first evidence of life outside the Earth.
Microbial Inorganic Carbon Fixation
Authors: Sato Takaaki , Atomi Haruyuki 
Published: September 2010

AbstractCarbon dioxide fixation is the biological process through which carbon dioxide is converted to organic compounds. Organisms that fix carbon dioxide provide the organic carbon necessary to support the existence of all heterotrophic life on our planet. This article provides an introduction to the various mechanisms of carbon dioxide fixation utilised by microorganisms. The Calvin–Benson–Bassham cycle is shared among plants, algae and many photo‐ and chemoautotrophic bacteria, and is probably the most well known carbon dioxide‐fixation pathway. However, a number of other pathways exist that are unique to the microbial world and the diverse chemistry and strategies they utilise are fascinating. Among the six carbon‐fixing pathways known at present, three pathways harbouring novel enzymes have just been established in the past few years. With the number and diversity of microorganisms still expanding, the possibilities are high that further novel pathways will be identified in the near future.Key Concepts:Carbon dioxide fixation is the biological process through which carbon dioxide is converted to organic compounds.Organisms that fix carbon dioxide provide the organic carbon necessary to support the existence of all heterotrophic life on our planet.In addition to the Calvin–Benson–Bassham cycle, which is also found in plants and microorganisms harbour a number of unique carbon dioxide‐fixing pathways.
Regeneration in Echinoderms and Ascidians
Authors: Carnevali M Daniela Candia , Burighel Paolo 
Published: September 2010

AbstractThe regenerative potential is expressed to a maximum extent in echinoderms and ascidians. They provide unique and valuable deuterostome models, closely related to vertebrates (man included), for an integrated approach exploring regeneration from tissue repair to asexual cloning. The comparison of results derived from different experimental models of echinoderms and ascidians and employing different approaches,in vivoandin vitro, provides an insight on specificity of regulatory mechanisms and processes governing large‐scale pattern formation and information signalling storage between cells and tissues allowing a living system to reliably regenerate and maintain a complex morphology. Since in these animals, regenerative phenomena involve progenitor cells present in the circulating fluids or in the tissues, the crucial questions opened are those related to (1) stemness properties of responsible cells, in terms of origin and derivation (stem cells or dedifferentiated cells) and (2) activities (proliferation and/or migration), plasticity and differentiation potential (derived cellular phenotypes).Key Concepts:Regeneration is a regulative and conservative developmental process complementary to asexual reproduction.Asexual reproduction (cloning) represents the highest expression of the regenerative potential of an organism.Regeneration processes generally imply the key‐contribution of pluripotential cells (stem cells or reprogrammed cells).Echinoderms utilise regeneration processes at all stages of their life cycle (embryo, larva and adult).Echinoderms can regenerate body parts and even complete individual from a fragment following self‐induced or traumatic amputation processes.In ascidians the potential for asexual development is expressed during colony formation by developing functional individuals from adult tissues.Ascidians are the unique adult chordates able to regenerate completely the ablated nervous system.
Regeneration in Annelids
Authors: Zoran Mark J 
Published: September 2010

AbstractAnnelids, like many other invertebrate animals, replace lost body parts in a process called regeneration. However, the ability to regenerate lost segments is present in some groups and not others, for example leeches do not regenerate lost segments. Anterior and posterior regeneration involves the formation of a bud containing stem cells that differentiate into the new head or tail segments. Annelid regeneration also involves remodelling of surviving body fragments. The ability of annelids to regenerate tail segments appears to be nearly universal among species capable of regeneration. The ability to regenerate head segments, although common, is not universal and can depend on the number of segments lost. The absence and presence of regeneration across annelid groups, including closely related species, suggests that regeneration ability may be an ancient trait that has been lost in some species during annelid evolution. Why regeneration varies among annelid species remains an intriguing question for life scientists.Key Concepts:Annelids vary in their capability for regenerating body segments, including among closely related species.The ability of annelids to regenerate posterior segments appears to be nearly universal.The ability of annelids to regenerate anterior segments, although common, is not universal and is often limited depending on the number of segments lost.Annelid regeneration may involve both epimorphic and morphallactic mechanisms.Multiple losses and gains of regeneration ability have likely occurred during annelid evolution.Why regenerative ability among annelids varies extensively remains unclear.
Neurofibromatosis Type 2 Clinics and Genetics
Authors: Kluwe Lan , Mautner Victor‐F 
Published: September 2010

AbstractNeurofibromatosis type 2 (NF2) is an autosomal dominant disorder characterised by multiple benign tumours of the nervous system. More than 90% of the patients develop bilateral vestibular schwannomas, which are the hallmark of NF2 and lead to progressive hearing loss in adult patients. Spinal tumours are as frequent as bilateral vestibular schwannomas, whereas approximately 1/3 of them cause neurological symptoms. Cranial nonvestibular schwannomas, meningiomas and ependymomas are also frequent in NF2, as well as ophthalmological lesions and peripheral polyneuropathy. With a birth incidence of around 1 in 25 000, the genetic cause for NF2 is the heterozygous inactivation of theNF2tumour suppressor gene on 22q. More than half (50–80%) of NF2 patients are founders who bearde novomutations which are present in a mosaic fashion in at least 25–30% of the patients. NF2 is a complex syndrome and demands interdisciplinal care, experienced specialists, social and psychological support and rehabilitation measures.Key Concepts:NF2 is a tumour suppressor gene syndrome and is characterised by multiple benign cerebral and spinal tumours.Bilateral vestibular schwannomas are the hallmark of NF2.The genetic cause for NF2 is the heterozygotic inactivating mutation of theNF2gene on 22q.Mosaicism is frequent amongde novoNF2 patients (25–30%).NF2 is a complex syndrome and demands interdisciplinal care, experienced specialists, coordinated social and psychological supports and rehabilitation measures.
Pathological Mutations in 5′ Untranslated Regions of Human Genes
Authors: Chatterjee Sangeeta , Berwal Sunil Kumar , Pal Jayanta K 
Published: September 2010

Abstract

The 5′ untranslated region (5′‐UTR) of a messenger
ribonucleic acid
(mRNA) plays a critical role in translation regulation by influencing mRNA stability and translation efficiency. Functional elements in the 5′‐UTR such as internal ribosome entry site (IRES), upstream open reading frames (uORFs) and iron responsive element (IRE) serve to fine tune protein expression in response to cellular requirement. Genetic variations such as mutations and single nucleotide polymorphisms (SNPs) in the 5′‐UTR are associated with a number of human diseases and increased susceptibility to diseases. Such pathological variations disrupt the motifs at the 5′‐UTR and cause diseases such as X‐linked Charcot‐Marie‐Tooth (CMTX) disease, multiple myeloma, hereditary hyperferritinaemia/cataract syndrome (HHCS), familial predisposition to melanoma, Marie Unna hereditary hypotrichosis (MUHH), oesophageal cancer and many others. Genetic and molecular profiling of many diseases has shown that a holistic approach of including the UTRs in regular diagnostic
deoxyribonucleic acid
(DNA) screening would aid in better disease profiling and disease management.

Key Concepts:

5′ Untranslated regions (UTRs) are noncoding regions of messenger RNAs (mRNAs).

The 5′‐UTR is delimited by transcription initiation site at 5′ end and the physiological start codon (AUG) at the 3′ end.

Motifs such as internal ribosome entry site (IRES), upstream open reading frames (uORFs), iron responsive element (IRE) and others are involved in mRNA stability and translation control.

mRNAs encoding regulatory proteins need to be strongly and precisely regulated. These mRNAs are often endowed with longer than average 5′‐UTR, uORFs and stable secondary structures that regulate their translation efficiency.

Mutations are changes in the DNA/genes of an organism which are heritable.

Mutations that disrupt the functional elements of the 5′‐UTR are often associated with diseases.

Single nucleotide polymorphisms (SNPs) in the 5′‐UTR are associated with individual's drug response and disease risk.