cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104408
title: Supplementary Material for: Integration of chicken genomic resources to enable whole-genome sequencing

description: Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome walking experiments. Second, <i>Hin</i>dIII digestion fingerprints were created for all BACs of the Wageningen chicken BAC library. Third, cytogenetic positions of BACs were assigned by FISH. These integrated resources will facilitate further chromosome-walking experiments and whole-genome sequencing.
DOI: 10.6084/m9.figshare.5104417.v1
title: Supplementary Material for: Systems biology of the 2-cell mouse embryo

description: The transcriptome of the 2-cell mouse embryo was analyzed to provide insight into the molecular networks at play during nuclear reprogramming and embryonic genome activation. Analysis of ESTs from a 2-cell cDNA library identified nearly 4,000 genes, over half of which have not been previously studied. Transcripts of mobile elements, especially those of LTR retrotransposons, are abundantly represented in 2-cell embryos, suggesting their possible role in introducing genomic variation, and epigenetic restructuring of the embryonic genome. Analysis of Gene Ontology of the 2-cell-stage expressed genes outlines the major biological processes that guide the oocyte-to-embryo transition. These results provide a foundation for understanding molecular control at the onset of mammalian development.
DOI: 10.6084/m9.figshare.5104420.v1
title: Supplementary Material for: Identifying differentially expressed genes in the mammalian retina and the retinal pigment epithelium by suppression subtractive hybridization

description: Retina and retinal pigment epithelium (RPE) cells are of neuroectodermal origin with highly specialized functions in light perception. Identification and characterization of genes differentially expressed in these cells will greatly aid our understanding of their functional roles in retinal biology. As a source enriched for gene transcripts from the retina/RPE, we generated a human retina and a bovine RPE cDNA library applying the PCR-based technique of suppression subtractive hybridization (SSH). Sequencing of 1,080 retina and 2,350 RPE SSH clones resulted in the identification of 321 and 343 non-redundant human transcripts, respectively. Of these, only 27 genes were in common between the two cDNA libraries. One transcript expressed exclusively in retina and RPE is the novel gene C4orf11 which is comprised of four exons on chromosome 4q21.2. We report the full-length cloning of two isoforms of C4orf11, 919 bp and 857 bp in length, both of which contain four identical open reading frames (ORFs). While ORFs 1 to 3 show no homologies to known proteins or protein domains, ORF4 reveals 50% sequence identity to RPE-spondin, a hypothetical protein on 8q13.3 with unknown function. We demonstrate that both the retina and the RPE SSH cDNA libraries are excellent resources for identifying known and novel genes exclusively or abundantly expressed in the retina/RPE complex. In combination with other approaches such as microarray analysis or serial analysis of gene expression (SAGE), the availability of highly sensitive and specific SSH cDNA libraries will facilitate the comprehensive description of the retina/RPE transcriptome.
DOI: 10.6084/m9.figshare.5104399
title: Supplementary Material for: Development of a linkage map and QTL scan for growth traits in North American bison

description: PCR protocols incorporating fluorescently labeled multiplexed primer combinations were developed to produce a linkage map for bison. Three hundred fifty eight microsatellite loci spanning all 29 autosomes were genotyped via 83 PCR multiplexes and nine individual amplifications. A total of 292 markers were integrated into an autosomal linkage map for bison. The sex averaged bison map (2,647 cM) was approximately 9% longer than the corresponding USDA MARC map, which covered 2,415 cM. Utilizing weaning, yearling and 17-month weights from two private bison herds, a QTL scan was conducted using the developed linkage map. LOD peaks suggestive of QTL were identified on chromosomes 2, 7, 15, and 24 for weaning weight, chromosomes 4, 14, and 15 for yearling weight and chromosomes 8, 14, and 25 for 17-month weight. Four of the identified chromosomes have conserved synteny with regions harboring growth QTL in cattle.
DOI: 10.6084/m9.figshare.5104405.v1
title: Supplementary Material for: Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome

description: Effective utilization of the domestic cat as an animal model for hereditary and infectious disease requires the development and implementation of high quality gene maps incorporating microsatellites and conserved coding gene markers. Previous feline linkage and radiation hybrid maps have lacked sufficient microsatellite coverage on all chromosomes to make effective use of full genome scans. Here we report the isolation and genomic mapping of 304 novel polymorphic repeat loci in the feline genome. The new loci were mapped in the domestic cat radiation hybrid panel using an automated fluorescent <i>Taq</i>-Man based assay. The addition of these 304 microsatellites brings the total number of microsatellites mapped in the feline genome to 580, and the total number of loci placed onto the RH map to 1,126. Microsatellites now span every autosome with an average spacing of roughly one polymorphic STR every five centimorgans, and full genome coverage of one marker every 2.7 megabases. These loci now provide a useful tool for undertaking full-genome scans to identify genes associated with phenotypes of interest, such as those relating to hereditary disease, coat color, patterning and morphology. These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses.
DOI: 10.6084/m9.figshare.5104399.v1
title: Supplementary Material for: Development of a linkage map and QTL scan for growth traits in North American bison

description: PCR protocols incorporating fluorescently labeled multiplexed primer combinations were developed to produce a linkage map for bison. Three hundred fifty eight microsatellite loci spanning all 29 autosomes were genotyped via 83 PCR multiplexes and nine individual amplifications. A total of 292 markers were integrated into an autosomal linkage map for bison. The sex averaged bison map (2,647 cM) was approximately 9% longer than the corresponding USDA MARC map, which covered 2,415 cM. Utilizing weaning, yearling and 17-month weights from two private bison herds, a QTL scan was conducted using the developed linkage map. LOD peaks suggestive of QTL were identified on chromosomes 2, 7, 15, and 24 for weaning weight, chromosomes 4, 14, and 15 for yearling weight and chromosomes 8, 14, and 25 for 17-month weight. Four of the identified chromosomes have conserved synteny with regions harboring growth QTL in cattle.
DOI: 10.6084/m9.figshare.5104402
title: Supplementary Material for: Generation of a 5.5-Mb BAC/PAC contig of pig chromosome 6q1.2 and its integration with existing RH, genetic and comparative maps

description: We generated a sequence-ready BAC/PAC contig spanning approximately 5.5 Mb on porcine chromosome 6q1.2, which represents a very gene-rich genome region. STS content mapping was used as the main strategy for the assembly of the contig and a total of 6 microsatellite markers, 53 gene-related STS and 116 STS corresponding to BAC and PAC end sequences were analyzed. The contig comprises 316 BAC and PAC clones covering the region between the genes GPI and LIPE. The correct contig assembly was verified by RH-mapping of STS markers and comparative mapping of BAC/PAC end sequences using BLAST searches. The use of microsatellite primer pairs allowed the integration of the physical maps with the genetic map of this region. Comparative mapping of the porcine BAC/PAC contig with respect to the gene-rich region on the human chromosome 19q13.1 map revealed a completely conserved gene order of this segment, however, physical distances differ somewhat between HSA19q13.1 and SSC6q1.2. Three major differences in DNA content between human and pig are found in two large intergenic regions and in one region of a clustered gene family, respectively. While there is a complete conservation of gene order between pig and human, the comparative analysis with respect to the rodent species mouse and rat shows one breakpoint where a genome segment is inverted.
DOI: 10.6084/m9.figshare.5104252
title: Supplementary Material for: Major Contribution of Genomic Copy Number Variation in Syndromic Congenital Heart Disease: The Use of MLPA as the First Genetic Test

description: Congenital heart disease (CHD) is the most common congenital disorder among live births. When associated with extracardiac abnormalities, it is characterized as a syndromic heart disease (syndromic CHD) and corresponds to 25% of all liveborn infants with a heart defect. The etiology in about 65% of the cases still remains unknown, and in about 35% of the patients, it is associated with genetic factors. In the present study, MLPA and SNP-array techniques were used to investigate a group of 47 patients with syndromic CHD. In total, 16 defects (34%) were identified, of which 12 (25.5%) were classified as pathogenic or probably pathogenic. The most frequent abnormalities were 22q11.2 deletion (22q11.2 deletion syndrome) and 7q11.23 deletion (Williams-Beuren syndrome). We also show that rarer malformations may be associated with syndromic CHD, such as 14q32.33 deletion as well as 17q25.3, 15q11.2 (BP1-BP2), 22q13.31, and 12p13.31 (<i>SLC2A3</i>) duplications. The present study demonstrates that CNVs are important causal factors and should be studied in patients with syndromic CHD. Furthermore, the use of MLPA as a first screening test was appropriate, as this less expensive technology detected 11 of the 12 pathogenic abnormalities (91.6%).
DOI: 10.6084/m9.figshare.5104276
title: Supplementary Material for: Visualization of Leukocyte Transendothelial and Interstitial Migration Using Reflected Light Oblique Transillumination in Intravital Video Microscopy

description: Dynamic visualization of the intravascular events leading to the extravasation of leukocytes into tissues by intravital microscopy has significantly expanded our understanding of the underlying molecular processes. In contrast, the detailed observation of leukocyte transendothelial and interstitial migration in vivo has been hampered by the poor image contrast of cells within turbid media that is obtainable by conventional brightfield microscopy. Here we present a microscopic method, termed reflected light oblique transillumination microscopy, that makes use of the optical interference phenomena generated by oblique transillumination to visualize subtle gradients of refractive indices within tissues for enhanced image contrast. Using the mouse cremaster muscle, we demonstrate that this technique makes possible the reliable quantification of extravasated leukocytes as well as the characterization of morphological phenomena of leukocyte transendothelial and interstitial migration.
DOI: 10.6084/m9.figshare.5104249
title: Online Material for Survey on Code Review Use

description: The instrument, raw data and further material for the paper "The Choice of Code Review Process: A Survey on the State of the Practice" by Baum, Leßmann and Schneider.<br>A lime survey export of the instrument can be found in the subdirectory "questions". The preprocessed survey results can be found in "cleansed.csv" in the subdirectory "result_data".
DOI: 10.6084/m9.figshare.5104252.v1
title: Supplementary Material for: Major Contribution of Genomic Copy Number Variation in Syndromic Congenital Heart Disease: The Use of MLPA as the First Genetic Test

description: Congenital heart disease (CHD) is the most common congenital disorder among live births. When associated with extracardiac abnormalities, it is characterized as a syndromic heart disease (syndromic CHD) and corresponds to 25% of all liveborn infants with a heart defect. The etiology in about 65% of the cases still remains unknown, and in about 35% of the patients, it is associated with genetic factors. In the present study, MLPA and SNP-array techniques were used to investigate a group of 47 patients with syndromic CHD. In total, 16 defects (34%) were identified, of which 12 (25.5%) were classified as pathogenic or probably pathogenic. The most frequent abnormalities were 22q11.2 deletion (22q11.2 deletion syndrome) and 7q11.23 deletion (Williams-Beuren syndrome). We also show that rarer malformations may be associated with syndromic CHD, such as 14q32.33 deletion as well as 17q25.3, 15q11.2 (BP1-BP2), 22q13.31, and 12p13.31 (<i>SLC2A3</i>) duplications. The present study demonstrates that CNVs are important causal factors and should be studied in patients with syndromic CHD. Furthermore, the use of MLPA as a first screening test was appropriate, as this less expensive technology detected 11 of the 12 pathogenic abnormalities (91.6%).
DOI: 10.6084/m9.figshare.5104276.v1
title: Supplementary Material for: Visualization of Leukocyte Transendothelial and Interstitial Migration Using Reflected Light Oblique Transillumination in Intravital Video Microscopy

description: Dynamic visualization of the intravascular events leading to the extravasation of leukocytes into tissues by intravital microscopy has significantly expanded our understanding of the underlying molecular processes. In contrast, the detailed observation of leukocyte transendothelial and interstitial migration in vivo has been hampered by the poor image contrast of cells within turbid media that is obtainable by conventional brightfield microscopy. Here we present a microscopic method, termed reflected light oblique transillumination microscopy, that makes use of the optical interference phenomena generated by oblique transillumination to visualize subtle gradients of refractive indices within tissues for enhanced image contrast. Using the mouse cremaster muscle, we demonstrate that this technique makes possible the reliable quantification of extravasated leukocytes as well as the characterization of morphological phenomena of leukocyte transendothelial and interstitial migration.
DOI: 10.6084/m9.figshare.5104249.v1
title: Online Material for Survey on Code Review Use

description: The instrument, raw data and further material for the paper "The Choice of Code Review Process: A Survey on the State of the Practice" by Baum, Leßmann and Schneider.<br>A lime survey export of the instrument can be found in the subdirectory "questions". The preprocessed survey results can be found in "cleansed.csv" in the subdirectory "result_data".
DOI: 10.6084/m9.figshare.5104084
title: Improved detection of DNA-binding proteins via compression technology on PSSM information

description: Improved detection of DNA-binding proteins via compression technology on PSSM information<br>
DOI: 10.6084/m9.figshare.5104084.v1
title: Improved detection of DNA-binding proteins via compression technology on PSSM information

description: Improved detection of DNA-binding proteins via compression technology on PSSM information<br>
DOI: 10.6084/m9.figshare.5103871
title: Statistical code from Injury-mediated decrease in locomotor performance increases predation risk in schooling fish

description: The costs and benefits of group living often depend on the spatial position of individuals within groups and the ability of individuals to occupy preferred positions. For example, models of predation events for moving prey groups predict higher mortality risk for individuals at the periphery and front of groups. We investigated these predictions in sardine (<i>Sardinella aurita</i>) schools under attack from group hunting sailfish (<i>Istiophorus platypterus</i>) in the open ocean. Sailfish approached sardine schools about equally often from the front and rear, but prior to attack there was a chasing period in which sardines attempted to swim away from the predator. Consequently, all sailfish attacks were directed at the rear and peripheral positions of the school, resulting in higher predation risk for individuals at these positions. During attacks, sailfish slash at sardines with their bill causing prey injury including scale removal and tissue damage. Sardines injured in previous attacks were more often found in the rear half of the school than in the front half. Moreover, injured fish had lower tail-beat frequencies and lagged behind uninjured fish. Injuries inflicted by sailfish bills may, therefore, hinder prey swimming speed and drive spatial sorting in prey schools through passive self-assortment. We found only partial support for the theoretical predictions from current predator–prey models, highlighting the importance of incorporating more realistic predator–prey dynamics into these models.This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
DOI: 10.6084/m9.figshare.5103871.v1
title: Statistical code from Injury-mediated decrease in locomotor performance increases predation risk in schooling fish

description: The costs and benefits of group living often depend on the spatial position of individuals within groups and the ability of individuals to occupy preferred positions. For example, models of predation events for moving prey groups predict higher mortality risk for individuals at the periphery and front of groups. We investigated these predictions in sardine (<i>Sardinella aurita</i>) schools under attack from group hunting sailfish (<i>Istiophorus platypterus</i>) in the open ocean. Sailfish approached sardine schools about equally often from the front and rear, but prior to attack there was a chasing period in which sardines attempted to swim away from the predator. Consequently, all sailfish attacks were directed at the rear and peripheral positions of the school, resulting in higher predation risk for individuals at these positions. During attacks, sailfish slash at sardines with their bill causing prey injury including scale removal and tissue damage. Sardines injured in previous attacks were more often found in the rear half of the school than in the front half. Moreover, injured fish had lower tail-beat frequencies and lagged behind uninjured fish. Injuries inflicted by sailfish bills may, therefore, hinder prey swimming speed and drive spatial sorting in prey schools through passive self-assortment. We found only partial support for the theoretical predictions from current predator–prey models, highlighting the importance of incorporating more realistic predator–prey dynamics into these models.This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
DOI: 10.6084/m9.figshare.5103859
title: Data supplement from Injury-mediated decrease in locomotor performance increases predation risk in schooling fish

description: The costs and benefits of group living often depend on the spatial position of individuals within groups and the ability of individuals to occupy preferred positions. For example, models of predation events for moving prey groups predict higher mortality risk for individuals at the periphery and front of groups. We investigated these predictions in sardine (<i>Sardinella aurita</i>) schools under attack from group hunting sailfish (<i>Istiophorus platypterus</i>) in the open ocean. Sailfish approached sardine schools about equally often from the front and rear, but prior to attack there was a chasing period in which sardines attempted to swim away from the predator. Consequently, all sailfish attacks were directed at the rear and peripheral positions of the school, resulting in higher predation risk for individuals at these positions. During attacks, sailfish slash at sardines with their bill causing prey injury including scale removal and tissue damage. Sardines injured in previous attacks were more often found in the rear half of the school than in the front half. Moreover, injured fish had lower tail-beat frequencies and lagged behind uninjured fish. Injuries inflicted by sailfish bills may, therefore, hinder prey swimming speed and drive spatial sorting in prey schools through passive self-assortment. We found only partial support for the theoretical predictions from current predator–prey models, highlighting the importance of incorporating more realistic predator–prey dynamics into these models.This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
DOI: 10.6084/m9.figshare.5103856
title: Supplementary Material for: Prediction of Time to Castration-Resistant Prostate Cancer Using Bone Scan Index in Men with Metastatic Hormone-Sensitive Prostate Cancer

description: <b><i>Introduction:</i></b> We evaluated bone scan index (BSI) as a predictive biomarker for time to castration-resistant prostate cancer (CRPC) in patients with metastatic hormone-sensitive prostate cancer (mHSPC). <b><i>Materials and Methods:</i></b> We identified 85 consecutive mHSPC patients treated with first-line androgen deprivation therapy. We analyzed the correlations between time to CRPC and clinicopathological characteristics, including age, prostate-specific antigen (PSA) level, Gleason score, clinical TNM stage, hemoglobin, lactate dehydrogenase, C-reactive protein, and BSI. <b><i>Results:</i></b> The median BSI was 2.7%. Progression to CRPC occurred in 55 (64.7%) patients and the median time to CRPC was 12.9 months. In multivariate analysis, 3 significant risk factors for time to CRPC were identified: age (&gt;73 vs. ≤73 years; hazard ratio [HR] 0.53), <i>p</i> = 0.038, PSA level (&gt;270 vs. ≤270 ng/mL; HR 0.53, <i>p</i> = 0.038), and BSI (&gt;2.7 vs. ≤2.7%; HR 2.97, <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> Age, PSA level, and BSI were found to be significant predictive factors for time to CRPC in patients with mHSPC.
DOI: 10.6084/m9.figshare.5103859.v1
title: Data supplement from Injury-mediated decrease in locomotor performance increases predation risk in schooling fish

description: The costs and benefits of group living often depend on the spatial position of individuals within groups and the ability of individuals to occupy preferred positions. For example, models of predation events for moving prey groups predict higher mortality risk for individuals at the periphery and front of groups. We investigated these predictions in sardine (<i>Sardinella aurita</i>) schools under attack from group hunting sailfish (<i>Istiophorus platypterus</i>) in the open ocean. Sailfish approached sardine schools about equally often from the front and rear, but prior to attack there was a chasing period in which sardines attempted to swim away from the predator. Consequently, all sailfish attacks were directed at the rear and peripheral positions of the school, resulting in higher predation risk for individuals at these positions. During attacks, sailfish slash at sardines with their bill causing prey injury including scale removal and tissue damage. Sardines injured in previous attacks were more often found in the rear half of the school than in the front half. Moreover, injured fish had lower tail-beat frequencies and lagged behind uninjured fish. Injuries inflicted by sailfish bills may, therefore, hinder prey swimming speed and drive spatial sorting in prey schools through passive self-assortment. We found only partial support for the theoretical predictions from current predator–prey models, highlighting the importance of incorporating more realistic predator–prey dynamics into these models.This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.