cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4765111
title: ShearSplink sequencing data (WapCre;Cdh1F/F;SB mice)

description: Pooled ShearSplink sequencing data accompanying the manuscript "Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma" by Kas, S.M., de Ruiter, J.R. and Schipper, K et al. in Nature Genetics, 2017.<br>Sequencing data was obtained from Sleeping Beauty-induced tumors in WapCre;Cdh1F/F;SB (WapCre;Cdh1F/F;T2/Onc;Rosa26Lox66SBLox71/+) mice. As a result of the ShearSplink protocol, the sequence reads contain part of the SB transposon sequence, the T7 linker (which is used to recognise the unique end of individual sequences) and the barcode of the corresponding sample<br>
DOI: 10.6084/m9.figshare.4765102
title: Supplementary data

description: UC Serologic markers<br>
DOI: 10.6084/m9.figshare.4765111.v1
title: ShearSplink sequencing data (WapCre;Cdh1F/F;SB mice)

description: Pooled ShearSplink sequencing data accompanying the manuscript "Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma" by Kas, S.M., de Ruiter, J.R. and Schipper, K et al. in Nature Genetics, 2017.<br>Sequencing data was obtained from Sleeping Beauty-induced tumors in WapCre;Cdh1F/F;SB (WapCre;Cdh1F/F;T2/Onc;Rosa26Lox66SBLox71/+) mice. As a result of the ShearSplink protocol, the sequence reads contain part of the SB transposon sequence, the T7 linker (which is used to recognise the unique end of individual sequences) and the barcode of the corresponding sample<br>
DOI: 10.6084/m9.figshare.4765102.v1
title: Supplementary data

description: UC Serologic markers<br>
DOI: 10.6084/m9.figshare.4765087
title: data_Christianen et al._2017_Ecology_figshare.xlsx

description: Wadden Sea Carbon isotope dataset.Christianen et al. Ecology in press.
DOI: 10.6084/m9.figshare.4765093
title: Incorporating in situ habitat patchiness in site selection models reveals that site fidelity is not always a consequence of animal choice

description: Using a tractable study system, starfish movements were simulated among rock pools based on empirical data. Data included number of individuals that showed fidelity to a rock pool, distance displaced from rock pools at high tide and low tide, maximum distance moved after 5 days, number of animals that left a rock pool during high tide and direction of departures. 3D maps of test rock pools were created from field images. Random movements of starfish were simulated within those 3d images using the empirical data of starfish movement. The authors showed that site fidelity could be a response of animal site selection or the lack of available habitats within the landscape.
DOI: 10.6084/m9.figshare.4765072
title: Neuropsychological correlates of schizotypy: a systematic review and meta-analysis of cross-sectional studies

description: <b>Introduction:</b> Cognitive deficits can precede the onset of psychotic episodes and predict the onset of the illness in individuals with schizotypy traits. In some studies, high levels of schizotypy were associated with impairments in memory, attention, executive functions, and verbal fluency. This review provides a more comprehensive understanding of cognitive impairments related to schizoytpy. <b>Methods:</b> A systematic review of “schizotypy and neuropsychological measures” was conducted, and it retrieved 67 studies. All papers with case-control design showing means and standard deviations from neuropsychological measures were included in a meta-analysis (n = 40). A comparison between our finding and another metaanalysis with patients with schizophrenia-spectrum disorders [Fatouros-Bergman, H., Cervenka, S., Flyckt, L., Edman, G., & Farde, L. (2014). Meta-analysis of cognitive performance in drugnaive patients with schizophrenia. Schizophrenia Research. doi:10.1016/j.schres.2014.06.034] was performed to study the similarities on the MATRICS domains between the two disorders. <b>Results:</b> We found evidence of worse functioning of verbal and visual-spatial working memory, and of language in people with schizotypy or with schizotypal traits. Working memory deficit is present in both schizotypy and schizophrenia with larger effect sizes compared to other domains. <b>Conclusions:</b> Working memory deficit might be a cognitive marker of the risk of psychosis. Interventions targeting cognitive deficits early may be crucial to the prevention of psychosis.
DOI: 10.6084/m9.figshare.4765093.v1
title: Incorporating in situ habitat patchiness in site selection models reveals that site fidelity is not always a consequence of animal choice

description: Using a tractable study system, starfish movements were simulated among rock pools based on empirical data. Data included number of individuals that showed fidelity to a rock pool, distance displaced from rock pools at high tide and low tide, maximum distance moved after 5 days, number of animals that left a rock pool during high tide and direction of departures. 3D maps of test rock pools were created from field images. Random movements of starfish were simulated within those 3d images using the empirical data of starfish movement. The authors showed that site fidelity could be a response of animal site selection or the lack of available habitats within the landscape.
DOI: 10.6084/m9.figshare.4765072.v1
title: Neuropsychological correlates of schizotypy: a systematic review and meta-analysis of cross-sectional studies

description: <b>Introduction:</b> Cognitive deficits can precede the onset of psychotic episodes and predict the onset of the illness in individuals with schizotypy traits. In some studies, high levels of schizotypy were associated with impairments in memory, attention, executive functions, and verbal fluency. This review provides a more comprehensive understanding of cognitive impairments related to schizoytpy. <b>Methods:</b> A systematic review of “schizotypy and neuropsychological measures” was conducted, and it retrieved 67 studies. All papers with case-control design showing means and standard deviations from neuropsychological measures were included in a meta-analysis (n = 40). A comparison between our finding and another metaanalysis with patients with schizophrenia-spectrum disorders [Fatouros-Bergman, H., Cervenka, S., Flyckt, L., Edman, G., & Farde, L. (2014). Meta-analysis of cognitive performance in drugnaive patients with schizophrenia. Schizophrenia Research. doi:10.1016/j.schres.2014.06.034] was performed to study the similarities on the MATRICS domains between the two disorders. <b>Results:</b> We found evidence of worse functioning of verbal and visual-spatial working memory, and of language in people with schizotypy or with schizotypal traits. Working memory deficit is present in both schizotypy and schizophrenia with larger effect sizes compared to other domains. <b>Conclusions:</b> Working memory deficit might be a cognitive marker of the risk of psychosis. Interventions targeting cognitive deficits early may be crucial to the prevention of psychosis.
DOI: 10.6084/m9.figshare.4765081
title: Catalyst-coated cement beads for the degradation and mineralization of fungicide carbendazim using laboratory and pilot-scale reactor: catalyst stability analysis

description: The fixed-bed photocatalytic degradation of fungicide carbendazim using catalyst-coated spherical cement beads has been investigated. Thirty beads with optimum size 13 mm along with 0.3 gL<sup>−1</sup> H<sub>2</sub>O<sub>2</sub> with an initial concentration of carbendazim of 10 mgL<sup>−1</sup> were the optimized conditions for better degradation. The reduction in COD and total organic carbon along with the generation of nitrite and nitrate ions under the optimized conditions confirms the complete mineralization of compound. The suggested degradation pathway for carbendazim has also been proposed as intermediates formed during photodegradation were analyzed through gas chromatography–mass spectrometry. The coated cement beads were found to be durable even after 30 cycles as confirmed by scanning electron microscopy and energy dispersive spectroscopy analysis. Scale-up trails have also been carried out in a solar-baffled fixed-bed reactor for the degradation of pollutant to seek the commercial viability of the technique.
DOI: 10.6084/m9.figshare.4765081.v1
title: Catalyst-coated cement beads for the degradation and mineralization of fungicide carbendazim using laboratory and pilot-scale reactor: catalyst stability analysis

description: The fixed-bed photocatalytic degradation of fungicide carbendazim using catalyst-coated spherical cement beads has been investigated. Thirty beads with optimum size 13 mm along with 0.3 gL<sup>−1</sup> H<sub>2</sub>O<sub>2</sub> with an initial concentration of carbendazim of 10 mgL<sup>−1</sup> were the optimized conditions for better degradation. The reduction in COD and total organic carbon along with the generation of nitrite and nitrate ions under the optimized conditions confirms the complete mineralization of compound. The suggested degradation pathway for carbendazim has also been proposed as intermediates formed during photodegradation were analyzed through gas chromatography–mass spectrometry. The coated cement beads were found to be durable even after 30 cycles as confirmed by scanning electron microscopy and energy dispersive spectroscopy analysis. Scale-up trails have also been carried out in a solar-baffled fixed-bed reactor for the degradation of pollutant to seek the commercial viability of the technique.
DOI: 10.6084/m9.figshare.4765087.v1
title: data_Christianen et al._2017_Ecology_figshare.xlsx

description: Wadden Sea Carbon isotope dataset.Christianen et al. Ecology in press.
DOI: 10.6084/m9.figshare.4765024
title: Bedrock Ground Stone Features on Chacuaco Creek, Southeastern Colorado

description: In southeastern Colorado, bedrock ground stone (BGS) features, also called bedrock metates or mortars, are a well-recognized part of the archaeological record. Although sometimes documented or recorded, they are rarely studied. However, elsewhere BGS are considered an important aspect of subsistence strategies, landscape adaptation, and symbolic ideology. A critical examination of any aspect of material culture begins with an unbiased description, and subsequent development of methods to scientifically examine the phenomena. This paper offers a methodology for recording BGS features to encourage reporting in the region. Results underscore the importance of developing accurate feature planviews, but also illustrate that minimal metric data (length, width, and depth) offer insight into how the landscape was inhabited by ancient peoples.
DOI: 10.6084/m9.figshare.4765015
title: Perl programs from Lucas et al. 2017

description: extract_3utr.plPerl program to extract 3'UTR sequences from RefSeq transcriptome databases.extract_B-ID.plShort perl script used to parse Repeat Masker output to get only indicdences of B and ID elements in mouse 3'UTRs (not MIRs)
DOI: 10.6084/m9.figshare.4765024.v1
title: Bedrock Ground Stone Features on Chacuaco Creek, Southeastern Colorado

description: In southeastern Colorado, bedrock ground stone (BGS) features, also called bedrock metates or mortars, are a well-recognized part of the archaeological record. Although sometimes documented or recorded, they are rarely studied. However, elsewhere BGS are considered an important aspect of subsistence strategies, landscape adaptation, and symbolic ideology. A critical examination of any aspect of material culture begins with an unbiased description, and subsequent development of methods to scientifically examine the phenomena. This paper offers a methodology for recording BGS features to encourage reporting in the region. Results underscore the importance of developing accurate feature planviews, but also illustrate that minimal metric data (length, width, and depth) offer insight into how the landscape was inhabited by ancient peoples.
DOI: 10.6084/m9.figshare.4765015.v1
title: Perl programs from Lucas et al. 2017

description: extract_3utr.plPerl program to extract 3'UTR sequences from RefSeq transcriptome databases.extract_B-ID.plShort perl script used to parse Repeat Masker output to get only indicdences of B and ID elements in mouse 3'UTRs (not MIRs)
DOI: 10.6084/m9.figshare.4764976
title: A potential functional association between mutant BMPR2 and primary ovarian insufficiency

description: Primary ovarian insufficiency (POI) affects ~1% of women in the general population. Despite numerous attempts at identifying POI genetic aetiology, coding mutations in only a few genes have been functionally related to POI pathogenesis. It has been suggested that mutant BMPR2 might contribute towards the phenotype. Several BMP15 (a BMPR2 ligand) coding mutations in human species have been related to POI pathogenesis. The BMPR2 p.Ser987Phe mutation, previously identified in a woman with POI, might therefore lead to cellular dysfunction contributing to the phenotype. To explore such an assumption, the present study assessed potential pathogenic subcellular localization/aggregation patterns associated with the p.Ser987Phe mutant form of BMPR2 in a relevant model for studying ovarian function. A significant increase in protein-like aggregation patterns was identified at the endoplasmic reticulum (ER) which permitted us to establish, for the first time, a potential functional association between mutant BMPR2 and POI aetiology. Since BMPR2 mutant forms were previously related to idiopathic pulmonary arterial hypertension, BMPR2 mutations may be related to an as-yet-to-be described syndromic form of POI involving pulmonary dysfunction. Additional assays are necessary to confirm that BMPR2 abnormal subcellular patterns are composed by aggregates. <b>Abbreviations</b>: POI: primary ovarian insufficiency; ER: endoplasmic reticulum; NGS: next generation sequencing
DOI: 10.6084/m9.figshare.4764976.v1
title: A potential functional association between mutant BMPR2 and primary ovarian insufficiency

description: Primary ovarian insufficiency (POI) affects ~1% of women in the general population. Despite numerous attempts at identifying POI genetic aetiology, coding mutations in only a few genes have been functionally related to POI pathogenesis. It has been suggested that mutant BMPR2 might contribute towards the phenotype. Several BMP15 (a BMPR2 ligand) coding mutations in human species have been related to POI pathogenesis. The BMPR2 p.Ser987Phe mutation, previously identified in a woman with POI, might therefore lead to cellular dysfunction contributing to the phenotype. To explore such an assumption, the present study assessed potential pathogenic subcellular localization/aggregation patterns associated with the p.Ser987Phe mutant form of BMPR2 in a relevant model for studying ovarian function. A significant increase in protein-like aggregation patterns was identified at the endoplasmic reticulum (ER) which permitted us to establish, for the first time, a potential functional association between mutant BMPR2 and POI aetiology. Since BMPR2 mutant forms were previously related to idiopathic pulmonary arterial hypertension, BMPR2 mutations may be related to an as-yet-to-be described syndromic form of POI involving pulmonary dysfunction. Additional assays are necessary to confirm that BMPR2 abnormal subcellular patterns are composed by aggregates. <b>Abbreviations</b>: POI: primary ovarian insufficiency; ER: endoplasmic reticulum; NGS: next generation sequencing
DOI: 10.6084/m9.figshare.4764853
title: Brain MRI Dataset MINC files (.mnc)

description: Brain MR images along with the ground truths of WM, GM and CSF regions.<br>For each case, brain masks for six 2D slices (150, 175, 200, 210, 225, 250) are also given.
DOI: 10.6084/m9.figshare.4763812
title: Bayesian Modal Estimation of the Four-Parameter Item Response Model in Real, Realistic, and Idealized Data Sets

description: In this study, we explored item and person parameter recovery of the four-parameter model (4PM) in over 24,000 real, realistic, and idealized data sets. In the first analyses, we fit the 4PM and three alternative models to data from three Minnesota Multiphasic Personality Inventory-Adolescent form factor scales using Bayesian modal estimation (BME). Our results indicated that the 4PM fits these scales better than simpler item Response Theory (IRT) models. Next, using the parameter estimates from these real data analyses, we estimated 4PM item parameters in 6,000 realistic data sets to establish minimum sample size requirements for accurate item and person parameter recovery. Using a factorial design that crossed discrete levels of item parameters, sample size, and test length, we also fit the 4PM to an additional 18,000 idealized data sets to extend our parameter recovery findings. Our combined results demonstrated that 4PM item parameters and parameter functions (e.g., item response functions) can be accurately estimated using BME in moderate to large samples (<i>N</i> ⩾ 5, 000) and person parameters can be accurately estimated in smaller samples (<i>N</i> ⩾ 1, 000). In the supplemental files, we report annotated code that shows how to estimate 4PM item and person parameters in (Chalmers, 2012).
DOI: 10.6084/m9.figshare.4763812.v1
title: Bayesian Modal Estimation of the Four-Parameter Item Response Model in Real, Realistic, and Idealized Data Sets

description: In this study, we explored item and person parameter recovery of the four-parameter model (4PM) in over 24,000 real, realistic, and idealized data sets. In the first analyses, we fit the 4PM and three alternative models to data from three Minnesota Multiphasic Personality Inventory-Adolescent form factor scales using Bayesian modal estimation (BME). Our results indicated that the 4PM fits these scales better than simpler item Response Theory (IRT) models. Next, using the parameter estimates from these real data analyses, we estimated 4PM item parameters in 6,000 realistic data sets to establish minimum sample size requirements for accurate item and person parameter recovery. Using a factorial design that crossed discrete levels of item parameters, sample size, and test length, we also fit the 4PM to an additional 18,000 idealized data sets to extend our parameter recovery findings. Our combined results demonstrated that 4PM item parameters and parameter functions (e.g., item response functions) can be accurately estimated using BME in moderate to large samples (<i>N</i> ⩾ 5, 000) and person parameters can be accurately estimated in smaller samples (<i>N</i> ⩾ 1, 000). In the supplemental files, we report annotated code that shows how to estimate 4PM item and person parameters in (Chalmers, 2012).
DOI: 10.6084/m9.figshare.4763821.v2
title: The pre-mRNA retention and splicing complex controls expression of the Mediator subunit Med20

description: The heterotrimeric pre-mRNA retention and splicing (RES) complex, consisting of Bud13p, Snu17p and Pml1p, promotes splicing and nuclear retention of a subset of intron-containing pre-mRNAs. Yeast cells deleted for individual RES genes show growth defects that are exacerbated at elevated temperatures. Although the growth phenotypes correlate to the splicing defects in the individual mutants, the underlying mechanism is unknown. Here, we show that the temperature sensitive (Ts) growth phenotype of <i>bud13Δ</i> and <i>snu17Δ</i> cells is a consequence of inefficient splicing of <i>MED20</i> pre-mRNA, which codes for a subunit of the Mediator complex; a co-regulator of RNA polymerase II transcription. The <i>MED20</i> pre-mRNA splicing defect is less pronounced in <i>pml1Δ</i> cells, explaining why they grow better than the other two RES mutants at elevated temperatures. Inactivation of the cytoplasmic nonsense-mediated mRNA decay (NMD) pathway in the RES mutants leads to accumulation of <i>MED20</i> pre-mRNA, indicating that inefficient nuclear retention contributes to the growth defect. Further, the Ts phenotype of <i>bud13Δ</i> and <i>snu17Δ</i> cells is partially suppressed by the inactivation of NMD, showing that the growth defects are augmented by the presence of a functional NMD pathway. Collectively, our results demonstrate an important role of the RES complex in maintaining the Med20p levels.
DOI: 10.6084/m9.figshare.4763821.v1
title: The pre-mRNA retention and splicing complex controls expression of the Mediator subunit Med20

description: The heterotrimeric pre-mRNA retention and splicing (RES) complex, consisting of Bud13p, Snu17p and Pml1p, promotes splicing and nuclear retention of a subset of intron-containing pre-mRNAs. Yeast cells deleted for individual RES genes show growth defects that are exacerbated at elevated temperatures. Although the growth phenotypes correlate to the splicing defects in the individual mutants, the underlying mechanism is unknown. Here, we show that the temperature sensitive (Ts) growth phenotype of <i>bud13Δ</i> and <i>snu17Δ</i> cells is a consequence of inefficient splicing of <i>MED20</i> pre-mRNA, which codes for a subunit of the Mediator complex; a co-regulator of RNA polymerase II transcription. The <i>MED20</i> pre-mRNA splicing defect is less pronounced in <i>pml1Δ</i> cells, explaining why they grow better than the other 2 RES mutants at elevated temperatures. Inactivation of the cytoplasmic nonsense-mediated mRNA decay (NMD) pathway in the RES mutants leads to accumulation of <i>MED20</i> pre-mRNA, indicating that inefficient nuclear retention contributes to the growth defect. Further, the Ts phenotype of <i>bud13Δ</i> and <i>snu17Δ</i> cells is partially suppressed by the inactivation of NMD, showing that the growth defects are augmented by the presence of a functional NMD pathway. Collectively, our results demonstrate an important role of the RES complex in maintaining the Med20p levels.
DOI: 10.6084/m9.figshare.4763692
title: Modulation of transcription factor binding and epigenetic regulation of the <i>MLH1</i> CpG island and shore by polymorphism rs1800734 in colorectal cancer

description: The <i>MLH1</i> promoter polymorphism rs1800734 is associated with <i>MLH1</i> CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with <i>MLH1</i> shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, <i>MLH1</i> CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated <i>MLH1</i> shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the <i>MLH1</i> promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the <i>MLH1</i> shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the <i>MLH1</i> CpG island in which it is located.