bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural Genetic Variation Caused by Transposable Elements in Humans
Authors: Bennett E Andrew , Coleman Laura E , Tsui Circe , Pittard W Stephen , Devine Scott E 
Published: October 2004

Abstract
Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25–35% of ∼2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.
A Workshop Report on Wheat Genome Sequencing
Authors: Gill Bikram S , Appels Rudi , Botha-Oberholster Anna-Maria , Buell C Robin , Bennetzen Jeffrey L , Chalhoub Boulos , Chumley Forrest , Dvořák Jan , Iwanaga Masaru , Keller Beat , Li Wanlong , McCombie W Richard , Ogihara Yasunari , Quetier Francis , Sasaki Takuji 
Published: October 2004

Abstract
Sponsored by the National Science Foundation and the U.S. Department of Agriculture, a wheat genome sequencing workshop was held November 10–11, 2003, in Washington, DC. It brought together 63 scientists of diverse research interests and institutions, including 45 from the United States and 18 from a dozen foreign countries (see list of participants at http://www.ksu.edu/igrow). The objectives of the workshop were to discuss the status of wheat genomics, obtain feedback from ongoing genome sequencing projects, and develop strategies for sequencing the wheat genome. The purpose of this report is to convey the information discussed at the workshop and provide the basis for an ongoing dialogue, bringing forth comments and suggestions from the genetics community.
Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4
Authors:   Miftahudin, Ross K , Ma X-F , Mahmoud A A , Layton J , Milla M A Rodriguez , Chikmawati T , Ramalingam J , Feril O , Pathan M S , Momirovic G Surlan , Kim S , Chema K , Fang P , Haule L , Struxness H , Birkes J , Yaghoubian C , Skinner R , McAllister J , Nguyen V , Qi L L , Echalier B , Gill B S , Linkiewicz A M , Dubcovsky J , Akhunov E D , Dvořák J , Dilbirligi M , Gill K S , Peng J H , Lapitan N L V , Bermudez-Kandianis C E , Sorrells M E , Hossain K G , Kalavacharla V , Kianian S F , Lazo G R , Chao S , Anderson O D , Gonzalez-Hernandez J , Conley E J , Anderson J A , Choi D-W , Fenton R D , Close T J , McGuire P E , Qualset C O , Nguyen H T , Gustafson J P 
Published: October 2004

Abstract
A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.
A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With Rice
Authors: Linkiewicz A M , Qi L L , Gill B S , Ratnasiri A , Echalier B , Chao S , Lazo G R , Hummel D D , Anderson O D , Akhunov E D , Dvořák J , Pathan M S , Nguyen H T , Peng J H , Lapitan N L V ,   Miftahudin, Gustafson J P , La Rota C M , Sorrells M E , Hossain K G , Kalavacharla V , Kianian S F , Sandhu D , Bondareva S N , Gill K S , Conley E J , Anderson J A , Fenton R D , Close T J , McGuire P E , Qualset C O , Dubcovsky J 
Published: October 2004

Abstract
We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible for these differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci, and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. Good overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).
Deletion Mapping of Homoeologous Group 6-Specific Wheat Expressed Sequence Tags
Authors: Randhawa H S , Dilbirligi M , Sidhu D , Erayman M , Sandhu D , Bondareva S , Chao S , Lazo G R , Anderson O D ,   Miftahudin, Gustafson J P , Echalier B , Qi L L , Gill B S , Akhunov E D , Dvořák J , Linkiewicz A M , Ratnasiri A , Dubcovsky J , Bermudez-Kandianis C E , Greene R A , Sorrells M E , Conley E J , Anderson J A , Peng J H , Lapitan N L V , Hossain K G , Kalavacharla V , Kianian S F , Pathan M S , Nguyen H T , Endo T R , Close T J , McGuire P E , Qualset C O , Gill K S 
Published: October 2004

Abstract
To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1–6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.
A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7
Authors: Hossain K G , Kalavacharla V , Lazo G R , Hegstad J , Wentz M J , Kianian P M A , Simons K , Gehlhar S , Rust J L , Syamala R R , Obeori K , Bhamidimarri S , Karunadharma P , Chao S , Anderson O D , Qi L L , Echalier B , Gill B S , Linkiewicz A M , Ratnasiri A , Dubcovsky J , Akhunov E D , Dvořák J ,   Miftahudin, Ross K , Gustafson J P , Radhawa H S , Dilbirligi M , Gill K S , Peng J H , Lapitan N L V , Greene R A , Bermudez-Kandianis C E , Sorrells M E , Feril O , Pathan M S , Nguyen H T , Gonzalez-Hernandez J L , Conley E J , Anderson J A , Choi D W , Fenton D , Close T J , McGuire P E , Qualset C O , Kianian S F 
Published: October 2004

Abstract
The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.
A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat
Authors: Qi L L , Echalier B , Chao S , Lazo G R , Butler G E , Anderson O D , Akhunov E D , Dvořák J , Linkiewicz A M , Ratnasiri A , Dubcovsky J , Bermudez-Kandianis C E , Greene R A , Kantety R , La Rota C M , Munkvold J D , Sorrells S F , Sorrells M E , Dilbirligi M , Sidhu D , Erayman M , Randhawa H S , Sandhu D , Bondareva S N , Gill K S , Mahmoud A A , Ma X-F ,   Miftahudin, Gustafson J P , Conley E J , Nduati V , Gonzalez-Hernandez J L , Anderson J A , Peng J H , Lapitan N L V , Hossain K G , Kalavacharla V , Kianian S F , Pathan M S , Zhang D S , Nguyen H T , Choi D-W , Fenton R D , Close T J , McGuire P E , Qualset C O , Gill B S 
Published: October 2004

Abstract
Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.
Chronology and Sequence of Eruption of the Permanent Teeth in Patients with Complete Unilateral Cleft Lip and Palate
Authors: Carrara Cleide Felíciode Carvalho , Lima JoséEduardode Oliveira , Carrara Carlos Eduardo , Vono Bernardo Gonzalez 
Published: October 2004

Objective To establish the chronology and sequence of eruption of the permanent teeth in subjects with complete unilateral cleft lip and palate. Design Cross-sectional. Data on children presenting complete cleft lip and palate were evaluated. Setting The study was carried out at the Hospital for Rehabilitation of Craniofacial Anomalies, Bauru, Sao Paulo, Brazil. Sample The sample comprised 477 patients with complete unilateral cleft lip and palate, aged 5 to 14 years. Of these patients, 166 were girls and 311 were boys. Results The girls presented, for all maxillary and mandibular teeth, a smaller mean age of eruption than the boys. The maxillary lateral incisor and cuspid adjacent to the cleft presented significantly higher mean ages of eruption than their homologous teeth on the noncleft side.
Cleft Lip and Palate in Jordan: Birth Prevalence Rate
Authors: Al Omari F. , Al-Omari I. K. 
Published: October 2004

Objective and Design A retrospective investigation was conducted to determine the prevalence rate of Jordanian children born with oral clefts from 1991 to 2001. Setting Hospital surgical records from two main sources were used to identify all children born with orofacial clefting. Information about date of birth, sex, cleft types, and associated major anomalies and syndromes were recorded. Results The overall prevalence rate for live births with cleft lip, cleft palate, or both was 1.39 per 1000 live births. Thirty percent of the clefts identified affected the lip, 22 percent affected the palate, and 48 percent involved the clefts of the lip and palate. In general, higher prevalence rates were found for boys than girls (55% boys versus 45% girls). There was a statistically significant sex difference between the cleft types. Clefts of the isolated palate, however, were more common in girls. Eighteen percent of patients with cleft were associated with major anomalies or syndromes. Conclusions The reported prevalence rate for orofacial clefts among Jordanians is similar to the previously reported prevalence rate in white Caucasians. Results and future recommendations are discussed.
The Effect of Infant Orthopedics on the Occlusion of the Deciduous Dentition in Children with Complete Unilateral Cleft Lip and Palate (Dutchcleft)
Authors: Bongaarts Catharina A. M. , Kuijpers-Jagtman Anne M. , van't Hof Martin A. , Prahl-Andersen Birte 
Published: October 2004

Objective Evaluation of the effect of infant orthopedics (IO) on the occlusion of the deciduous dentition in patients with unilateral cleft lip and palate (UCLP). Design Prospective, two-arm, randomized, controlled clinical trial with three participating cleft palate centers (Dutchcleft). Setting Cleft Palate Centers of the University Medical Center Nijmegen, Academic Center of Dentistry Amsterdam, and Dijkzigt University Hospital Rotterdam, The Netherlands. Patients Children with complete UCLP (n = 54) were included. Interventions In a concealed allocation procedure, half of the patients was randomized to wear a plate till surgical closure of the soft palate (IO+), and the other half (IO−) did not have a plate. Mean Outcome Measures Dental arch relationships were assessed at 4 and 6 years of age with the 5-year-old index; the Huddart-score; and measurements of overjet, overbite, and sagittal occlusion. Results There were no significant differences found between the IO+ and IO− groups for the 5-year-old index; the Huddart-score; and overjet, overbite, and sagittal occlusion. Conclusions IO had no observable effect on the occlusion in the deciduous dentition at 4 and 6 years of age. Considering the occlusion only, there is no need to perform IO in children with UCLP.
Development of a prototype MSPC software package for on‐line process monitoring and statistical quality control
Authors: Stavropoulos Y. , Kiparissides C. 
Published: October 2004

AbstractMultivariate statistical process control concepts and methods have become very important for the development of effective quality assurance and statistical process control schemes for process industries. In the present article, the development of a prototype Multivariate Statistical Process Control (MSPC) software package is described and its application to two polymerization processes is demonstrated. © 2001 John Wiley & Sons, Inc. Comput Appl Eng Educ 9: 157–170, 2001
Air Products hydrogen liquefaction project: Building a Web‐based simulation of an industrial process
Authors: Kuriyan K. , Muench W. , Reklaitis G.V. 
Published: October 2004

AbstractIn this paper we present a Web‐based simulation drawn from a hydrogen liquefaction process operated by Air Products. We describe the software architecture that connects Web‐based clients to a simulation server and discuss some implementation issues. © 2001 John Wiley & Sons, Inc. Comput Appl Eng Educ 9: 180–191, 2001
Selective antibodies to methadone enantiomers: Synthesis of (R)‐ and (R,S)‐methadone conjugates and determination by an immunoenzymatic method in human serum
Authors: Chikhi‐Chorfi Nassima , Galons Hervé , Pham‐Huy Chuong , Thevenin Marc , Warnet Jean‐Michel , Claude Jean‐Roger 
Published: October 2004

AbstractSelective antibodies to (R)‐methadone (Mtd) and to its racemate were produced in rabbits by immunization with conjugates of (R)‐ or (R,S)‐hemisuccinyl‐methadol‐bovine serum albumin, respectively. A hapten was first prepared by reduction of (R)‐ or (R,S)‐Mtd with sodium borohydride, followed by esterification with succinic anhydride. The conjugation of hapten with albumin was achieved by the mixed anhydride method. After immunization of rabbits, the titers and specificity of each antibody were determined by ELISA. The antibodies obtained were tested with (R)‐, (S)‐, (R,S)‐Mtd, its major metabolite (EDDP), and some drugs of abuse (morphine, codeine, cocaine). The sensitivities of antibodies to (R)‐ and (R,S)‐Mtd were about 1 and 2 ng/ml, respectively. Selective (R)‐antibodies recognized (R)‐Mtd about 40 times more avidly than the (S)‐isomer, while an antiserum against (R,S)‐Mtd recognized (R)‐ and (S)‐isomers to about the same degree. Both selective antibodies showed little interference (about 0.5%) with EDDP metabolite and no crossreactivity with morphine, codeine, and cocaine. These two selective antibodies were used to develop an immunoenzymatic method (ELISA) for the determination of (R)‐ and (R,S)‐Mtd in serum samples of patients under maintenance treatment for narcotic addiction. Chirality 13:187–192, 2001. © 2001 Wiley‐Liss, Inc.
Molecular structure of dynein and motility of a giant sperm axoneme provided with only the outer dynein arm
Authors: Mencarelli Caterina , Lupetti Pietro , Rosetto Marco , Mercati David , Heuser John E. , Dallai Romano 
Published: October 2004

AbstractThe peculiar sperm axoneme of the dipteran Asphondylia ruebsaameni is characterized by an extraordinarily high number of microtubule doublets (up to 2,500) arranged in double parallel spirals. Doublets of the inner row of each spiral are tilted, so that their outer arms point towards the B‐tubule of the next doublet in the outer row. Doublets are provided with only the outer arm, and no structure related to the central pair/radial spoke complex is present. When analyzed by quick‐freeze, deep‐etch electron microscopy, the structure of the dynein arms was shown to share the same organization described in other organisms; however, it appears to be somewhat more complex than that previously found in a related dipteran species, Monarthropalpus flavus, since the foot region of the arms displays a globular extra‐domain that is intercalated between adjacent arms. Treatment of demembranated sperm with ATP and vanadate induced conformational changes in the dynein arms. SDS‐page suggested the presence of a single dynein high molecular weight band or, in the gels with the best electrophoretic resolution, of two very closely spaced bands. This polypeptide positively reacted with a polyclonal antibody raised against a specific amino acid sequence located in the phosphate‐binding loop of the dynein catalytic site. Dynein heavy chain‐related DNA sequences corresponding to the catalytic phosphate‐binding region were amplified by RT‐PCR. Two distinct fragments (Asph‐ax1 and Asph‐ax2) encoding axonemal dynein sequences were identified. Southern blot analysis performed on genomic DNA using these sequences as a probe showed that they are part of different genes. An intron was identified in the Asph‐ax1 fragment at a position corresponding to the site of a nucleotide deletion in the putative pseudogene of Monarthropalpus. Asphondylia spermatozoa exhibited in vivo a whirling movement both in the deferent duct and in the spermatheca, but they were unable to undergo processive movement in vitro. They propagated a three‐dimensional wave only when constrained in a bent configuration by some mechanical means. The phylogenetic relationships between the two dipteran species, Monarthopalpus and Asphondylia, based on these biochemical and molecular data are also discussed. Cell Motil. Cytoskeleton 50:129–146, 2001. © 2001 Wiley‐Liss, Inc.
Expression of the 53 kD forked protein rescues F‐actin bundle formation and mutant bristle phenotypes in Drosophila
Authors: Grieshaber S. S. , Lankenau D. H. , Talbot T. , Holland S. , Petersen N. S. 
Published: October 2004

Abstractforked mutations affect bristle development in Drosophila pupae, resulting in short, thick, gnarled bristles in the adult. The forked proteins are components of 200–300‐μm‐long actin fiber bundles that are present transiently during pupal development [Petersen et al., 1994: Genetics 136:173–182]. These bundles are composed of segments of 3–10 μm long, and forked protein is localized along the actin fiber bundle segments and accumulates at the junctions connecting them longitudinally. In the forked mutants, f36a and fhd, F‐actin bundles are greatly reduced in number and size, and bundle segmentation is absent. The p‐element, P{w+, falter} contains a 5.3‐kb fragment of the forked gene that encodes the 53‐kD forked protein [Lankenau et al., 1996: Mol Cell Biol 16:3535–3544]. Expression of only the 53‐kD forked protein is sufficient to rescue the actin bundle and bristle phenotypes of f36a and fhd mutant flies. The 5.3‐kb forked sequence, although smaller than the 13‐kb region previously shown to rescue forked mutants [Petersen et al., 1994: Genetics 136:173–182], does contain the core forked sequence that encodes actin binding and bundling domains in cultured mammalian cells [Grieshaber and Petersen, 1999: J Cell Sci 112:2203–2211]. These data show that the 53‐kD forked protein is sufficient for normal bristle development and that the domains shown previously to be important for actin bundling in cell culture may be all that are required for normal actin bundle formation in developing Drosophila bristles. Cell Motil. Cytoskeleton 50:198–206, 2001. © 2001 Wiley‐Liss, Inc.