cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120377.v1
title: Supplementary Material for: Linkage of Pluripotent Stem Cell- Associated Transcripts to Regulatory Gene Networks

description: Knowledge of the transcriptional circuitry responsible for pluripotentiality and self-renewal in embryonic stem cells is tantamount to understanding early mammalian development and a prerequisite to determining their therapeutic potential. Various techniques have employed genomics to identify transcripts that were abundant in stem cells, in an attempt to define the molecular basis of ‘stemness’. In this study, we have extended traditional genomic analyses to identify <i>cis</i>-elements that might be implicated in the control of embryonic stem cell-restricted gene promoters. The strategy relied on the generation of a problem-specific list from serial analysis of gene expression profiles and subsequent promoter analyses to identify frameworks of multiple <i>cis</i>-elements conserved in space and orientation among genes from the problem-specific list. Subsequent experimental data suggest that 2 novel transcription factors, B-Myb and Maz, predicted from these models, are implicated either in the maintenance of the undifferentiated stem cell state or in early steps of differentiation.
DOI: 10.6084/m9.figshare.5120389.v1
title: Supplementary Material for: FGF2 Signaling in Mouse Embryonic Fibroblasts Is Crucial for Self-Renewal of Embryonic Stem Cells

description: Human embryonic stem cells (hESCs) can be maintained undifferentiated (pluripotent) or differentiated to basically all functional cell types, depending on the culture conditions used. Culture of hESCs in the presence of medium conditioned by mouse embryonic fibroblasts (MEFs) can be used to keep hESCs undifferentiated. This observation suggests that MEFs produce factors required for the pluripotency of hESCs. The data presented here show that fibroblast growth factor 2 (FGF2) treatment of MEFs is crucial for the production of these factors. To identify the potential factors that are expressed in the presence of FGF2 in MEFs, a global expression profile analysis using microarrays was performed. This analysis indicated that 17 secreted factors are downregulated in the absence of FGF2. These factors include several ligands for known signaling receptors, extracellular proteases and components of the extracellular matrix, that may all be involved in signaling events. Surprisingly, we found that selective blocking of extracellular signal-regulated kinase (ERK) signaling by the MAPK/ERK kinase (MEK) inhibitor U0126 affected the expression of only some of the FGF2-regulated genes, suggesting FGF2-induced pathways that are independent of ERK signaling. It has been shown recently that activation of Activin/Nodal signaling and inhibition of bone morphogenetic protein signaling are required for the maintenance of pluripotency. Accordingly, among the 17 FGF2-regulated genes we found inhibin βB that can lead to the assembly of Activin B and gremlin 1 that codes for an antagonist of bone morphogenetic proteins. This study identifies potentially important factors involved in the maintenance of pluripotency in hESCs and may allow the development of defined culture conditions without contaminating material from animal cells.
DOI: 10.6084/m9.figshare.5120365
title: Supplementary Material for: Clinical, cytogenetic and molecular evaluation in a dog with bilateral cryptorchidism and hypospadias

description: The aim of this study was to estimate prognostic factors in a Dalmatian dog with bilateral cryptorchidism and hypospadias. Cytogenetic and molecular analyses revealed a normal karyotype (2n = 78,XY) and the presence of <i>SRY, INSL3</i> and <i>RXFP2 </i>genes with a normal DNA sequence for <i>SRY</i> and <i>RXFP2</i>, while the <i>INSL3</i> sequence differed slightly from the normal one due to a heterozygous nucleotide change involving amino acid 22 of the INSL3 dog precursor protein. Levels of plasmatic testosterone were only 0.01 ng/ml, while FSH and LH serum levels were not detectable. After the human chorionic gonadotropin (hCG) test, the serum testosterone level was 0.01 ng/ml. Therefore, the phenotypic aetiology of this subject can not be well-defined because cryptorchidism and hypospadias were frequent clinical features with high genetic heterogeneity.
DOI: 10.6084/m9.figshare.5120368.v1
title: Supplementary Material for: Complete mitochondrial genomes of <i>Bos taurus</i> and <i>Bos indicus</i> provide new insights into intra-species variation, taxonomy and domestication

description: The taurine and zebuine cattle breeds comprise the majority of the world cattle population but their taxonomic status is still controversial. The two forms of cattle are currently classified as <i>Bos taurus </i>and <i>Bos indicus </i>species and are differentiated primarily by the presence or absence of a hump. However, these two species hybridize readily, producing fully fertile offspring. We have determined and analyzed complete <i>B. taurus </i>and <i>B. indicus </i>mitochondrial genome sequences to investigate the extent of sequence divergences and to study their taxonomic status by molecular dating. The sequences encompassed 16,338 and 16,339 nucleotides, respectively, and differed at 237 positions. Estimated divergence times indicated that the two cattle lineages separated 1.7–2.0 million years ago. Combined phylogenetic analyses of 18 new and 130 previously reported extant <i>B. taurus </i>and <i>B. indicus </i>control region sequences with data from 32 archaeological specimens of the extinct wild aurochs (<i>Bos primigenius</i>) identified four major maternal lineages. <i>B. primigenius </i>haplotypes were present in all but the <i>B. indicus </i>lineage, and one <i>B. taurus </i>sequence clustered with <i>B. primigenius </i>P haplotypes that were not previously linked with domestic cattle. The <i>B. indicus </i>cluster and a recently reported new <i>B. primigenius </i>haplotype that represents a new lineage were approximately equidistant from the <i>B. taurus </i>cluster. These data suggest domestications from several differentiated populations of <i>B. primigenius </i>and a subspecies status for taurine (<i>B. primigenius taurus</i>) and zebuine (<i>B. primigenius indicus</i>) cattle.
DOI: 10.6084/m9.figshare.5120371.v1
title: Supplementary Material for: A BAC contig map over the proximal ∼3.3 Mb region of horse chromosome 21

description: A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. The clones form two contigs – each corresponding to the respective human chromosomes – that are estimated to be separated by a gap of ∼200 kb. Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. The BACs provide a 4–5× coverage of the region and span an estimated length of ∼3.3 Mb. The region presently contains one mapped marker per 22 kb on average, which represents a major improvement over the previous resolution of one marker per 380 kb obtained through the generation of a dense RH map for this segment. Dual color fluorescence in situ hybridization on metaphase and interphase chromosomes verified the relative order of some of the BACs and helped to orient them accurately in the contigs. Despite having similar gene order and content, the equine region covered by the contigs appears to be distinctly smaller than the corresponding region in human (3.3 Mb vs. 5.5–6 Mb) because the latter harbors a host of repetitive elements and gene families unique to humans/primates. Considering limited representation of the region in the latest version of the horse whole genome sequence EquCab2, the dense map developed in this study will prove useful for the assembly and annotation of the sequence data on ECA21 and will be instrumental in rapid search and isolation of candidate genes for traits mapped to this region.
DOI: 10.6084/m9.figshare.5120374.v1
title: Supplementary Material for: Stem Cell Research within the Priority Program 1109 of the German Research Foundation, 2001–2007

description: Medicine
DOI: 10.6084/m9.figshare.5120353
title: Supplementary Material for: Reversal of Cellular Roles in Angiogenesis: Implications for Anti-Angiogenic Therapy

description: Medicine
DOI: 10.6084/m9.figshare.5120356
title: Supplementary Material for: Human Eosinophils Show Chemotaxis to Lymphoid Chemokines and Exhibit Antigen-Presenting-Cell-Like Properties upon Stimulation with IFN-γ, IL-3 and GM-CSF

description: <i>Background:</i> Eosinophils are multifunctional leukocytes. Under physiological conditions, they circulate in the blood and through the tissues to serve their functions. In certain inflammatory states, they enter the T-cell areas of lymph nodes (LNs) that drain the inflamed tissue and communicate with T cells in LNs, but the underlying mechanism that regulates their trafficking to LNs is not yet fully explored. Here, we report that a human eosinophilic leukemia cell line, EoL-1, and human peripheral blood (PB) eosinophils become reactive to the lymphoid chemokines CCL21 and CCL25 upon stimulation. <i>Methods:</i> EoL-1 cells were differentiated with dibutyryl cyclic AMP (dEoL-1) and subsequently pulsed with IFN-γ, IL-3 and GM-CSF. The eosinophil fraction was purified from normal human adult PB and incubated for 1 day with the same cytokine combination. <i>Results:</i> Upon cytokine stimulation, dEoL-1 cells expressed chemokine receptors CCR7, CCR9 and CCR3 and developed chemotactic responsiveness to CCL21, CCL25 and CCL11, which bind to the respective receptors. Human PB eosinophils also showed chemotactic responsiveness to CCL21 and CCL25 upon stimulation with IFN-γ, IL-3 and GM-CSF. In addition, the cytokine-stimulated dEoL-1 cells expressed costimulatory molecules, including CD40, CD80, CD86 and HLA-DR, and also expressed a tolerogenic and Th2-polarizing enzyme, indoleamine 2,3-dioxygenase. <i>Conclusions:</i> These in vitro observations raise the possibility that eosinophils may utilize lymphoid chemokines to enter LNs and serve antigen-presenting functions in the LN under certain inflammatory conditions.
DOI: 10.6084/m9.figshare.5120359
title: Supplementary Material for: Der Therapieerleben-Fragebogen (TeF) für Patienten und Angehörige

description: The Therapy Experience Questionnaire for Patients and Relatives <i>Background: </i>Building a working alliance in psychotherapy requires that the patient and his relatives have a good understanding of what is going on in therapy. A questionnaire is presented that allows assessing in a multidimensional parallel approach the experiences that patients and close relatives or significant others have with psychotherapy. <i>Methods: </i>118 items were collected and tested in 54 patients and 51 relatives. Subsequently, the number of items was reduced, subscales were constructed on the basis of factor analyses, parallel forms of the questionnaire were built for patients and relatives, and reliability was tested. <i>Results: </i>The final questionnaire consists of 40 items that reliably represent 6 dimensions: (1) fears of negative consequences of therapy, (2) feeling informed about the therapy, (3) positive impact of the therapy on the social network and everyday life, (4) positive consequences of the therapy on personal competencies, (5) personal commitment to the therapy, (6) suspiciousness of the therapy and feelings of helplessness towards it. <i>Conclusions: </i>The ‘Therapy Experience Questionnaire for Patients and Relatives’ is suitable to be completed by patients and close relatives and allows assessing how they perceive the experience of psychotherapy.
DOI: 10.6084/m9.figshare.5120353.v1
title: Supplementary Material for: Reversal of Cellular Roles in Angiogenesis: Implications for Anti-Angiogenic Therapy

description: Medicine
DOI: 10.6084/m9.figshare.5120362
title: Supplementary Material for: Genetics of Sex Determination in Tilapiine Species

description: We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In <i>Oreochromis karongae</i> and <i>Tilapia mariae</i> the sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In <i>O. niloticus</i> and <i>T. zillii</i> the sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). A more complex pattern was observed in <i>O. aureus</i> and <i>O. mossambicus</i>, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. Sex-specific recombination suppression was found in the female heterogametic sex. Sequence analysis showed the accumulation of repetitive elements in this region. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in this clade. This variation in sex determination mechanisms among closely related species makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates.
DOI: 10.6084/m9.figshare.5120359.v1
title: Supplementary Material for: Der Therapieerleben-Fragebogen (TeF) für Patienten und Angehörige

description: The Therapy Experience Questionnaire for Patients and Relatives <i>Background: </i>Building a working alliance in psychotherapy requires that the patient and his relatives have a good understanding of what is going on in therapy. A questionnaire is presented that allows assessing in a multidimensional parallel approach the experiences that patients and close relatives or significant others have with psychotherapy. <i>Methods: </i>118 items were collected and tested in 54 patients and 51 relatives. Subsequently, the number of items was reduced, subscales were constructed on the basis of factor analyses, parallel forms of the questionnaire were built for patients and relatives, and reliability was tested. <i>Results: </i>The final questionnaire consists of 40 items that reliably represent 6 dimensions: (1) fears of negative consequences of therapy, (2) feeling informed about the therapy, (3) positive impact of the therapy on the social network and everyday life, (4) positive consequences of the therapy on personal competencies, (5) personal commitment to the therapy, (6) suspiciousness of the therapy and feelings of helplessness towards it. <i>Conclusions: </i>The ‘Therapy Experience Questionnaire for Patients and Relatives’ is suitable to be completed by patients and close relatives and allows assessing how they perceive the experience of psychotherapy.
DOI: 10.6084/m9.figshare.5120362.v1
title: Supplementary Material for: Genetics of Sex Determination in Tilapiine Species

description: We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In <i>Oreochromis karongae</i> and <i>Tilapia mariae</i> the sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In <i>O. niloticus</i> and <i>T. zillii</i> the sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). A more complex pattern was observed in <i>O. aureus</i> and <i>O. mossambicus</i>, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. Sex-specific recombination suppression was found in the female heterogametic sex. Sequence analysis showed the accumulation of repetitive elements in this region. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in this clade. This variation in sex determination mechanisms among closely related species makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates.
DOI: 10.6084/m9.figshare.5120365.v1
title: Supplementary Material for: Clinical, cytogenetic and molecular evaluation in a dog with bilateral cryptorchidism and hypospadias

description: The aim of this study was to estimate prognostic factors in a Dalmatian dog with bilateral cryptorchidism and hypospadias. Cytogenetic and molecular analyses revealed a normal karyotype (2n = 78,XY) and the presence of <i>SRY, INSL3</i> and <i>RXFP2 </i>genes with a normal DNA sequence for <i>SRY</i> and <i>RXFP2</i>, while the <i>INSL3</i> sequence differed slightly from the normal one due to a heterozygous nucleotide change involving amino acid 22 of the INSL3 dog precursor protein. Levels of plasmatic testosterone were only 0.01 ng/ml, while FSH and LH serum levels were not detectable. After the human chorionic gonadotropin (hCG) test, the serum testosterone level was 0.01 ng/ml. Therefore, the phenotypic aetiology of this subject can not be well-defined because cryptorchidism and hypospadias were frequent clinical features with high genetic heterogeneity.
DOI: 10.6084/m9.figshare.5120350
title: Supplementary Material for: Writer’s Cramp as a Manifestation of Cervical Demyelinating Lesions

description: Medicine
DOI: 10.6084/m9.figshare.5120341
title: Supplementary Material for: Co-Occurrence of Seizure and Chorea in a Patient with Nonketotic Hyperglycemia

description: Medicine
DOI: 10.6084/m9.figshare.5120332
title: poster-delft_fig-1

description: Figure 1 for Poster at Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5120335
title: Supplementary Material for: Genes and proteins involved in the control of meiosis

description: Medicine
DOI: 10.6084/m9.figshare.5120338
title: Supplementary Material for: History - Geschichte

description: Medicine
DOI: 10.6084/m9.figshare.5120335.v1
title: Supplementary Material for: Genes and proteins involved in the control of meiosis

description: Medicine
DOI: 10.6084/m9.figshare.5120338.v1
title: Supplementary Material for: History - Geschichte

description: Medicine
DOI: 10.6084/m9.figshare.5120341.v1
title: Supplementary Material for: Co-Occurrence of Seizure and Chorea in a Patient with Nonketotic Hyperglycemia

description: Medicine
DOI: 10.6084/m9.figshare.5120332.v1
title: poster-delft_fig-1

description: Figure 1 for Poster at Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5120275
title: Data on socio-hydrology study

description: modelling results<br>
DOI: 10.6084/m9.figshare.5120275.v1
title: Data on socio-hydrology study

description: modelling results<br>
DOI: 10.6084/m9.figshare.5120074
title: Data and analysis for Experiment 3

description: Data and analysis script for Experiment 3 from "Persistent biases in binocular rivalry dynamics within the visual field."<br>
DOI: 10.6084/m9.figshare.5120074.v1
title: Data and analysis for Experiment 3

description: Data and analysis script for Experiment 3 from "Persistent biases in binocular rivalry dynamics within the visual field."<br>
DOI: 10.6084/m9.figshare.5120062
title: A multi-trait systems approach reveals a response cascade to bleaching in corals - supplementary material and experimental data for stress-response traits

description: <b>A multi-trait systems approach reveals a response cascade to bleaching in corals - supplementary material and experimental data file</b>
DOI: 10.6084/m9.figshare.5120056
title: Placer gold and associated supergene mineralogy at Macraes Flat, East Otago, New Zealand

description: Macraes Flat occupies a shallow upland tectonic basin that contains only Late Pleistocene sediments. The gold-bearing Hyde–Macraes Shear Zone is hosted by schist basement that underlies the basin. Supergene alteration of the mineralised shear zone has been occurring periodically since the Eocene, with both oxidised and unoxidised alteration of gold-bearing sulphides and associated silicates. This alteration led to liberation of gold from encapsulation in sulphides and enhancement of gold particle size into millimetre-scale irregular particles by supergene processes. Erosion of the supergene zone during faulting and tilting of basin margins in the Pleistocene has transferred gold particles into proximal placers on the basin floor. Nanoparticulate and microparticulate authigenic gold has formed on the surface of the supergene gold particles, intergrown with secondary minerals that include arsenolite, Fe sulphates and Fe oxyhydroxide. Chemical gold mobilisation and reprecipitation was facilitated by fluctuating redox conditions and pH variations near to the sulphide–sulphate redox boundary over the last 40 Ma.
DOI: 10.6084/m9.figshare.5120062.v1
title: A multi-trait systems approach reveals a response cascade to bleaching in corals - supplementary material and experimental data for stress-response traits

description: <b>A multi-trait systems approach reveals a response cascade to bleaching in corals - supplementary material and experimental data file</b>
DOI: 10.6084/m9.figshare.5120020
title: Comparative genomic survey of Bacillus cereus isolates in the Brazilian dairy production chain

description: Assembled genomes of 69 <i>Bacillus cereus</i> isolates from various points and locations of the dairy production process in Brazil. <br>Contig files labelled by BIGs IDs, which are included with isolate info spreadsheet.
DOI: 10.6084/m9.figshare.5120005
title: Plant diversity changes associated to <i>Gunnera tinctoria</i> invasion in Irish grasslands

description: In this study we have assessed and quantify the impacts of the invasive species <i>Gunnera tinctoria</i> on vegetation biodiversity at three different habitats, namely grasslands, riparian and coastal cliffs. Habitat selection was based on the extent and dominance of <i>G. tinctoria</i> invasion, e.g. grasslands and riparian habitats. Coastal cliffs were chosen as they are one of the few habitats which have little to no human influences. We hypothesized that alpha and beta vegetation diversity will be significantly reduced at all habitat types, irrespective if the habitats are highly disturbed, human influenced or semi-natural. Additionally, we hypothesized that changes in plant assemblage structure and composition will be associated to the invasion of <i>G. tinctoria</i>.Plant assemblages were sampled in July 2009 at twelve sites in three different habitats (grassland, coastal cliff and waterways), differing in the invasion status by the <i>Gunnera tinctoria</i>, in Achill Island, Co. Mayo, West Ireland. Within each habitat two locations were selected and within each location one invaded and one non-invaded site were sampled. The two locations in the grassland habitat were Dooega (53° 57.2’ N, 9°57.9’ W) and Sraheens (53° 57.2’ N, 9°57.9’ W), the two locations in the coastal cliff habitat were Dooega and Keel, and in the waterways the two sampled locations were Ashleam and Dooega River. In each habitat, invaded and non-invaded sites were chosen so that they were geographically interspersed. When possible, sites were chosen randomly from a larger pool of candidate sites and based on monitoring programme in the area. At each site, an area of 100 x 100 m was randomly selected were 4 replicated 1 m<sup>2</sup> quadrats were sampled. Percentage cover was estimated using the point-intercept method with a quadrat of 1 m<sup>2</sup> and 144 intersection points. Most conspicuous taxa were identified to species level, while others were grouped into functional-form groups. The intersection data was then transformed into percentage cover. Plants present in the quadrat not recorded by this method were given a cover of 1%. In the case of multi-strata growth, total percentage cover exceeded 100%.