cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3380461.v1
title: Robust treatment comparison based on utilities of semi-competing risks in non-small-cell lung cancer

description: A design is presented for a randomized clinical trial comparing two second-line treatments, chemotherapy versus chemotherapy plus reirradiation, for treatment of recurrent non-small-cell lung cancer. The central research question is whether the potential efficacy benefit that adding reirradiation to chemotherapy may provide justifies its potential for increasing the risk of toxicity. The design uses two co-primary outcomes: time to disease progression or death, and time to severe toxicity. Because patients may be given an active third-line treatment at disease progression that confounds second-line treatment effects on toxicity and survival following disease progression, for the purpose of this comparative study follow-up ends at disease progression or death. In contrast, follow-up for disease progression or death continues after severe toxicity, so these are semi-competing risks. A conditionally conjugate Bayesian model that is robust to misspecification is formulated using piecewise exponential distributions. A numerical utility function is elicited from the physicians that characterizes desirabilities of the possible co-primary outcome realizations. A comparative test based on posterior mean utilities is proposed. A simulation study is presented to evaluate test performance for a variety of treatment differences, and a sensitivity assessment to the elicited utility function is performed. General guidelines are given for constructing a design in similar settings, and a computer program for simulation and trial conduct is provided.
DOI: 10.6084/m9.figshare.3380458
title: NanoWiki (release 3)

description: Third release of the NanoWiki dataset. This release extends the Linked Data feature, introducing owl:sameAs and skos:closeMatch. The first is used in the new ChEMBL bundle with a few derived fullerenes. A GEO bundle has also been added. Most nanomaterials are now linked directly to articles (with DOIs). The data now describes 420 nanomaterials with 900 measurements (physchem and bioassay data) from 43 research articles.
DOI: 10.6084/m9.figshare.3380404
title: Yeast two-hybrid interactions between <i>Arabidopsis lyrata S</i> Receptor Kinase and the ARC1 E3 ligase

description: Here we describe protein-protein interactions between signaling components in the conserved self-incompatibility pathway from <i>Brassica spp</i>. and <i>Arabidopsis lyrata</i>. Previously, we had demonstrated that ARC1 is necessary in <i>A. lyrata</i> for the rejection of self-pollen by the self-incompatibility pathway. The results described here demonstrate that <i>A. lyrata</i> ARC1 interacts with <i>A. lyrata S</i> Receptor Kinase (SRK<sub>1</sub>) in the yeast 2-hybrid system. <i>A. lyrata</i> ARC1 also interacted with <i>B. napus</i> SRK<sub>910</sub> illustrating that interactions in this pathway are conserved across species. Finally, we discuss how the more widely occurring interactions between SRK and ARC1-related family members may be modulated <i>in vivo</i> by expression and subcellular localization patterns resulting in a particular response.
DOI: 10.6084/m9.figshare.3380404.v1
title: Yeast two-hybrid interactions between <i>Arabidopsis lyrata S</i> Receptor Kinase and the ARC1 E3 ligase

description: Here we describe protein-protein interactions between signaling components in the conserved self-incompatibility pathway from <i>Brassica spp</i>. and <i>Arabidopsis lyrata</i>. Previously, we had demonstrated that ARC1 is necessary in <i>A. lyrata</i> for the rejection of self-pollen by the self-incompatibility pathway. The results described here demonstrate that <i>A. lyrata</i> ARC1 interacts with <i>A. lyrata S</i> Receptor Kinase (SRK<sub>1</sub>) in the yeast 2-hybrid system. <i>A. lyrata</i> ARC1 also interacted with <i>B. napus</i> SRK<sub>910</sub> illustrating that interactions in this pathway are conserved across species. Finally, we discuss how the more widely occurring interactions between SRK and ARC1-related family members may be modulated <i>in vivo</i> by expression and subcellular localization patterns resulting in a particular response.
DOI: 10.6084/m9.figshare.3380398
title: Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner

description: Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous <i>eNOS</i> knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the <i>eNOS</i> gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
DOI: 10.6084/m9.figshare.3380398.v1
title: Maternal eNOS Deficiency Determines a Fatty Liver Phenotype of the Offspring in a Sex Dependent Manner

description: Maternal environmental factors can impact the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous <i>eNOS</i> knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the <i>eNOS</i> gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
DOI: 10.6084/m9.figshare.3380398.v3
title: Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner

description: Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous <i>eNOS</i> knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the <i>eNOS</i> gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
DOI: 10.6084/m9.figshare.3380398.v2
title: Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner

description: Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous <i>eNOS</i> knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the <i>eNOS</i> gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
DOI: 10.6084/m9.figshare.3380395
title: An unbiased nuclear proteomics approach reveals novel nuclear protein components that participates in MAMP-triggered immunity

description: (MAMP)-triggered immunity (MTI) is the first layer of molecular defense encountered by pathogens. Genetic screens have contributed to our knowledge of MTI, but are limited to phenotype-causing mutations. Here we attempt to identify novel factors involved in the early event leading to plant MTI by comparing the nuclear proteomes of two Arabidopsis genotypes treated with chitosan. Our approach revealed that following chitosan treatment, <i>cerk1</i> plants had many nuclear accumulating proteins in common, but also some unique ones, when compared with Col-0 plants. Analysis of the identified proteins revealed a nuclear accumulation of DNA-modifying enzymes, RNA-binding proteins and ribosomal proteins. Our results demonstrate that nuclear proteomic is a valid, phenotype-independent approach to uncover factor involved in cellular processes.
DOI: 10.6084/m9.figshare.3380395.v1
title: An unbiased nuclear proteomics approach reveals novel nuclear protein components that participates in MAMP-triggered immunity

description: (MAMP)-triggered immunity (MTI) is the first layer of molecular defense encountered by pathogens. Genetic screens have contributed to our knowledge of MTI, but are limited to phenotype-causing mutations. Here we attempt to identify novel factors involved in the early event leading to plant MTI by comparing the nuclear proteomes of two Arabidopsis genotypes treated with chitosan. Our approach revealed that following chitosan treatment, <i>cerk1</i> plants had many nuclear accumulating proteins in common, but also some unique ones, when compared with Col-0 plants. Analysis of the identified proteins revealed a nuclear accumulation of DNA-modifying enzymes, RNA-binding proteins and ribosomal proteins. Our results demonstrate that nuclear proteomic is a valid, phenotype-independent approach to uncover factor involved in cellular processes.
DOI: 10.6084/m9.figshare.3380377
title: BoxB - Courtship Control

description: Videos measuring courtship behaviours of 2 day old male <i>Drosophila melanogaster </i>with immature (&gt;20 hours old) virgin females with no predation threat from zebra jumping spiders (controls). Trials from April 11-16th 2016
DOI: 10.6084/m9.figshare.3380377.v2
title: BoxB - Courtship Control

description: Videos measuring courtship behaviours of 2 day old male <i>Drosophila melanogaster </i>with immature (&gt;20 hours old) virgin females with no predation threat from zebra jumping spiders (controls). Trials from April 11-16th 2016
DOI: 10.6084/m9.figshare.3380377.v1
title: BoxB - Immature Control

description: Videos measuring courtship behaviours of 2 day old male <i>Drosophila melanogaster </i>with immature (&gt;20 hours old) virgin females with no predation threat from zebra jumping spiders (controls). Trials from April 11-16th 2016
DOI: 10.6084/m9.figshare.3380299
title: State of knowledge on global extinction risk of plants

description: Presentation covering the state of knowledge on global extinction risk of plants. Presented at the State of the World's Plants Symposium 11th May: http://science.kew.org/state-worlds-plants-symposium<br><br><br>
DOI: 10.6084/m9.figshare.3380299.v2
title: State of knowledge on global extinction risk of plants

description: Presentation covering the state of knowledge on global extinction risk of plants. Presented at the State of the World's Plants Symposium 11th May: http://science.kew.org/state-worlds-plants-symposium<br><br><br>
DOI: 10.6084/m9.figshare.3380269
title: pint, a tool for renaming observer photographs at sea and checking meta data

description: This excel tables enables observer to rename pictures at sea. Additionnally observers and technical coordinators can easily plot metadata from pictures: iso/speed/aperture combination for photo-identification<br>
DOI: 10.6084/m9.figshare.3380269.v1
title: pint, a tool for renaming observer photographs at sea and checking meta data

description: This excel tables enables observer to rename pictures at sea. Additionnally observers and technical coordinators can easily plot metadata from pictures: iso/speed/aperture combination for photo-identification<br>
DOI: 10.6084/m9.figshare.3380269.v2
title: pint, a tool for renaming observer photographs at sea and checking meta data

description: This excel tables enables observer to rename pictures at sea. Additionnally observers and technical coordinators can easily plot metadata from pictures: iso/speed/aperture combination for photo-identification<br>
DOI: 10.6084/m9.figshare.3380269.v4
title: pint, a tool for renaming observer photographs at sea and checking meta data

description: This excel tables enables observer to rename pictures at sea. Additionnally observers and technical coordinators can easily plot metadata from pictures: iso/speed/aperture combination for photo-identification<br>
DOI: 10.6084/m9.figshare.3380269.v3
title: pint, a tool for renaming observer photographs at sea and checking meta data

description: This excel tables enables observer to rename pictures at sea. Additionnally observers and technical coordinators can easily plot metadata from pictures: iso/speed/aperture combination for photo-identification<br>
DOI: 10.6084/m9.figshare.3380185
title: Conserved features in the structure, mechanism and biogenesis of the inverse autotransporter protein family

description: Conserved features in the structure, mechanism and biogenesis of the inverse autotransporter protein family - tree files and alignments published in Genome Biology and Evolution (Heinz et al. 2016)
DOI: 10.6084/m9.figshare.3380185.v1
title: Conserved features in the structure, mechanism and biogenesis of the inverse autotransporter protein family

description: Conserved features in the structure, mechanism and biogenesis of the inverse autotransporter protein family - tree files and alignments published in Genome Biology and Evolution (Heinz et al. 2016)
DOI: 10.6084/m9.figshare.3380152
title: Defecation into clothing without forewarning and mean radiation dose to bowel and anal-sphincter among gynecological cancer survivors

description: <b>Background:</b> To analyze the relationship between mean radiation dose to the bowels and the anal-sphincter and occurrence of ‘defecation into clothing without forewarning’, a specific and serious fecal incontinence symptom after gynecological radiotherapy. Additional potential risk factors associated with the symptom are explored. <b>Material and methods:</b> Data were collected for 519 eligible gynecological cancer survivors, treated with pelvic radiotherapy, with a median follow-up of 5.8 years, using a study-specific questionnaire and medical records. Correlations between defecation into clothing without forewarning and mean dose to organs at risk; the anal-sphincter region, the rectum, the sigmoid and the small intestines were investigated, also taking other risk factors into account. <b>Results:</b> Twelve percent reported having had the symptom at least once in the preceding six months. Mean doses &gt;50 Gy to the anal-sphincter region, the rectum, the sigmoid and the small intestines were related to the occurrence of the symptom. Significantly associated risk factors were deliveries with high birth weight, heart failure and lactose and/or gluten intolerance. After adjusting for these factors, mean doses &gt;50 Gy to the anal-sphincter region, the sigmoid and the small intestines remained related to the occurrence of the symptom. <b>Conclusion:</b> Mean doses to the bowels and anal-sphincter region are related to the risk of defecation into clothing without forewarning in long-term gynecological cancer survivors treated with pelvic radiotherapy. Further radiobiological modeling may distinguish which organ(s) contribute most to development of the symptom.
DOI: 10.6084/m9.figshare.3380152.v1
title: Defecation into clothing without forewarning and mean radiation dose to bowel and anal-sphincter among gynecological cancer survivors

description: <b>Background:</b> To analyze the relationship between mean radiation dose to the bowels and the anal-sphincter and occurrence of ‘defecation into clothing without forewarning’, a specific and serious fecal incontinence symptom after gynecological radiotherapy. Additional potential risk factors associated with the symptom are explored. <b>Material and methods:</b> Data were collected for 519 eligible gynecological cancer survivors, treated with pelvic radiotherapy, with a median follow-up of 5.8 years, using a study-specific questionnaire and medical records. Correlations between defecation into clothing without forewarning and mean dose to organs at risk; the anal-sphincter region, the rectum, the sigmoid and the small intestines were investigated, also taking other risk factors into account. <b>Results:</b> Twelve percent reported having had the symptom at least once in the preceding six months. Mean doses &gt;50 Gy to the anal-sphincter region, the rectum, the sigmoid and the small intestines were related to the occurrence of the symptom. Significantly associated risk factors were deliveries with high birth weight, heart failure and lactose and/or gluten intolerance. After adjusting for these factors, mean doses &gt;50 Gy to the anal-sphincter region, the sigmoid and the small intestines remained related to the occurrence of the symptom. <b>Conclusion:</b> Mean doses to the bowels and anal-sphincter region are related to the risk of defecation into clothing without forewarning in long-term gynecological cancer survivors treated with pelvic radiotherapy. Further radiobiological modeling may distinguish which organ(s) contribute most to development of the symptom.
DOI: 10.6084/m9.figshare.3380128
title: An investigation into the hexagonal phases formed in high-concentration dispersions of well-defined cylindrical block copolymer micelles

description: This paper presents a detailed analysis of the structure of the hexagonal phase of poly(ferrocenylsilane) (PFS)-based cylindrical micelles found at concentrations above ca. 5 wt. % in non-polar solvents such as decane. Small-angle X-ray scattering indicated that the hexagonal order is not long-range. In all samples, deviations in the lower order peak positions were observed with respect to those expected for a perfect hexagonal lattice, with the degree of deviation correlating with micelle length. Furthermore, analysis of the peak shapes and peak widths suggests that the phase possesses intermediate translational order similar. to the hexatic phase. The observed features can be reproduced by amending Hosemann’s paracrystal theory to include a distribution of lattice parameters to model well and poorly condensed regions. It is proposed that this distribution arises due to the bending and intertwining of individual micelles in a hexagonal lattice, resulting in a kinetically trapped phase that is initially neither perfectly hexagonal nor canonically hexatic but which anneals over time towards a perfect hexagonal lattice.
DOI: 10.6084/m9.figshare.3380128.v1
title: An investigation into the hexagonal phases formed in high-concentration dispersions of well-defined cylindrical block copolymer micelles

description: This paper presents a detailed analysis of the structure of the hexagonal phase of poly(ferrocenylsilane) (PFS)-based cylindrical micelles found at concentrations above ca. 5 wt. % in non-polar solvents such as decane. Small-angle X-ray scattering indicated that the hexagonal order is not long-range. In all samples, deviations in the lower order peak positions were observed with respect to those expected for a perfect hexagonal lattice, with the degree of deviation correlating with micelle length. Furthermore, analysis of the peak shapes and peak widths suggests that the phase possesses intermediate translational order similar. to the hexatic phase. The observed features can be reproduced by amending Hosemann’s paracrystal theory to include a distribution of lattice parameters to model well and poorly condensed regions. It is proposed that this distribution arises due to the bending and intertwining of individual micelles in a hexagonal lattice, resulting in a kinetically trapped phase that is initially neither perfectly hexagonal nor canonically hexatic but which anneals over time towards a perfect hexagonal lattice.