cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4785670
title: Supplementary Material for: Moderate-Grade Germinal Matrix Haemorrhage Activates Cell Division in the Neonatal Mouse Subventricular Zone

description: Precise temporal and spatial control of the neural stem/progenitor cells within the subventricular zone (SVZ) germinal matrix of the brain is important for normal development in the third trimester and the early postnatal period. The high metabolic demands of proliferating germinal matrix precursors, coupled with the flimsy structure of the germinal matrix cerebral vasculature, are thought to account for the high rates of haemorrhage in extremely- and very-low-birth-weight preterm infants. Germinal matrix haemorrhage can commonly extend to intraventricular haemorrhage (IVH). Because neural stem/progenitor cells are sensitive to microenvironmental cues from the ventricular, intermediate, and basal domains within the germinal matrix, haemorrhage has been postulated to impact neurological outcomes through aberration of normal neural stem/progenitor cell behaviour. We developed an animal model of neonatal germinal matrix haemorrhage using stereotactic injection of autologous blood into the mouse neonatal germinal matrix. Pathological analysis at 4 days postinjury showed high rates of intraventricular extension and ventricular dilatation but low rates of parenchymal disruption outside the germinal zone, recapitulating key features of human “Papile grade III” IVH. At 4 days postinjury we observed proliferation in the wall of the lateral ventricle with significantly increased numbers of transient amplifying cells within the SVZ and the corpus callosum. Analysis at 21 days postinjury revealed that cortical development was also affected, with increased neuronal and concomitant reduced oligodendroglial differentiation. At the molecular level, we showed downregulation of the expression of the transmembrane receptor Notch2 in CD133<sup>+ve</sup> cells of the SVZ, raising the possibility that the burst of precocious proliferation seen in our experimental mouse model and the skewed differentiation could be mediated by downregulation of the Notch pathway within the proximal/ventricular domain. These findings raise the possibility that Notch regulation plays a critical role in mediating the response of the neonatal SVZ to ischaemic and haemorrhagic insults.
DOI: 10.6084/m9.figshare.4785670.v1
title: Supplementary Material for: Moderate-Grade Germinal Matrix Haemorrhage Activates Cell Division in the Neonatal Mouse Subventricular Zone

description: Precise temporal and spatial control of the neural stem/progenitor cells within the subventricular zone (SVZ) germinal matrix of the brain is important for normal development in the third trimester and the early postnatal period. The high metabolic demands of proliferating germinal matrix precursors, coupled with the flimsy structure of the germinal matrix cerebral vasculature, are thought to account for the high rates of haemorrhage in extremely- and very-low-birth-weight preterm infants. Germinal matrix haemorrhage can commonly extend to intraventricular haemorrhage (IVH). Because neural stem/progenitor cells are sensitive to microenvironmental cues from the ventricular, intermediate, and basal domains within the germinal matrix, haemorrhage has been postulated to impact neurological outcomes through aberration of normal neural stem/progenitor cell behaviour. We developed an animal model of neonatal germinal matrix haemorrhage using stereotactic injection of autologous blood into the mouse neonatal germinal matrix. Pathological analysis at 4 days postinjury showed high rates of intraventricular extension and ventricular dilatation but low rates of parenchymal disruption outside the germinal zone, recapitulating key features of human “Papile grade III” IVH. At 4 days postinjury we observed proliferation in the wall of the lateral ventricle with significantly increased numbers of transient amplifying cells within the SVZ and the corpus callosum. Analysis at 21 days postinjury revealed that cortical development was also affected, with increased neuronal and concomitant reduced oligodendroglial differentiation. At the molecular level, we showed downregulation of the expression of the transmembrane receptor Notch2 in CD133<sup>+ve</sup> cells of the SVZ, raising the possibility that the burst of precocious proliferation seen in our experimental mouse model and the skewed differentiation could be mediated by downregulation of the Notch pathway within the proximal/ventricular domain. These findings raise the possibility that Notch regulation plays a critical role in mediating the response of the neonatal SVZ to ischaemic and haemorrhagic insults.
DOI: 10.6084/m9.figshare.4785664
title: Supplementary Material for: Clinical Trial of Vadadustat in Patients with Anemia Secondary to Stage 3 or 4 Chronic Kidney Disease

description: <b><i>Background:</i></b> Therapeutic options for the treatment of anemia secondary to chronic kidney disease (CKD) remain limited. Vadadustat (AKB-6548) is an oral hypoxia-inducible factor prolyl-hydroxylase domain (HIF-PHD) inhibitor that is being investigated for the treatment of anemia secondary to CKD. <b><i>Methods:</i></b> A phase 2a, multicenter, randomized, double-blind, placebo-controlled, dose-ranging trial (NCT01381094) was undertaken in adults with anemia secondary to CKD stage 3 or 4. Eligible subjects were evenly randomized to 5 groups: 240, 370, 500, or 630 mg of once-daily oral vadadustat or placebo for 6 weeks. All subjects received low-dose supplemental oral iron (50 mg daily). The primary endpoint was the mean absolute change in hemoglobin (Hb) from baseline to the end of treatment. Secondary endpoints included iron indices, safety, and tolerability. <b><i>Results:</i></b> Ninety-three subjects were randomized. Compared with placebo, vadadustat significantly increased Hb after 6 weeks in a dose-dependent manner (analysis of variance; <i>p </i>&lt; 0.0001). Vadadustat increased the total iron-binding capacity and decreased concentrations of ferritin and hepcidin. The proportion of subjects with at least 1 treatment-emergent adverse event was similar between vadadustat- and placebo-treated groups. No significant changes in blood pressure, vascular endothelial growth factor, C-reactive protein, or total cholesterol were observed. Limitations of this study included its small sample size and short treatment duration. <b><i>Conclusions:</i></b> Vadadustat increased Hb levels and improved biomarkers of iron mobilization and utilization in patients with anemia secondary to stage 3 or 4 CKD. Global multicenter, randomized phase 3 trials are ongoing in non-dialysis-dependent and dialysis-dependent patients.
DOI: 10.6084/m9.figshare.4785667
title: Supplementary Material for: Analyzing Change: A Primer on Multilevel Models with Applications to Nephrology

description: The analysis of change is central to the study of kidney research. In the past 25 years, newer and more sophisticated methods for the analysis of change have been developed; however, as of yet these newer methods are underutilized in the field of kidney research. Repeated measures ANOVA is the traditional model that is easy to understand and simpler to interpret, but it may not be valid in complex real-world situations. Problems with the assumption of sphericity, unit of analysis, lack of consideration for different types of change, and missing data, in the repeated measures ANOVA context are often encountered. Multilevel modeling, a newer and more sophisticated method for the analysis of change, overcomes these limitations and provides a better framework for understanding the true nature of change. The present article provides a primer on the use of multilevel modeling to study change. An example from a clinical study is detailed and the method for implementation in SAS is provided.
DOI: 10.6084/m9.figshare.4785661
title: Supplementary Material for: Human copy number polymorphic genes

description: Recent large-scale genomic studies within human populations have identified numerous genomic regions as copy number variant (CNV). As these CNV regions often overlap coding regions of the genome, large lists of potentially copy number polymorphic genes have been produced that are candidates for disease association. Most of the current data regarding normal genic variation, however, has been generated using BAC or SNP microarrays, which lack precision especially with respect to exons. To address this, we assessed 2,790 candidate CNV genes defined from available studies in nine well-characterized HapMap individuals by designing a customized oligonucleotide microarray targeted specifically to exons. Using exon array comparative genomic hybridization (aCGH), we detected 255 (9%) of the candidates as true CNVs including 134 with evidence of variation over the entire gene. Individuals differed in copy number from the control by an average of 100 gene loci. Both partial- and whole-gene CNVs were strongly associated with segmental duplications (55 and 71%, respectively) as well as regions of positive selection. We confirmed 37% of the whole-gene CNVs using the fosmid end sequence pair (ESP) structural variation map for these same individuals. If we modify the end sequence pair mapping strategy to include low-sequence identity ESPs (98–99.5%) and ESPs with an everted orientation, we can capture 82% of the missed genes leading to more complete ascertainment of structural variation within duplicated genes. Our results indicate that segmental duplications are the source of the majority of full-length copy number polymorphic genes, most of the variant genes are organized as tandem duplications, and a significant fraction of these genes will represent paralogs with levels of sequence diversity beyond thresholds of allelic variation. In addition, these data provide a targeted set of CNV genes enriched for regions likely to be associated with human phenotypic differences due to copy number changes and present a source of copy number responsive oligonucleotide probes for future association studies.
DOI: 10.6084/m9.figshare.4785658
title: Supplementary Material for: Sildenafil Enhances Quantity of Immature Neurons and Promotes Functional Recovery in the Developing Ischemic Mouse Brain

description: <b><i>Background:</i></b> Hypoxic-ischemic (HI) injury to the developing brain occurs in 1 out of 1,000 live births and remains a major cause of significant morbidity and mortality. A large number of survivors suffer from long-term sequelae including seizures and neurological deficits. However, the pathophysiological mechanisms of recovery after HI insult are not clearly understood, and preventive measures or clinical treatments are nonexistent or not sufficiently effective in the clinical setting. Sildenafil as a specific phosphodiesterase 5 inhibitor leads to increased levels of the second messenger cyclic guanosine monophosphate (cGMP) and promotes functional recovery and neurogenesis after ischemic injury to the adult brain. <b><i>Objective:</i></b> Here, we investigated the effect of sildenafil treatment on activation of intracellular signaling pathways, histological and neurogenic response including functional recovery after an ischemic insult to the developing brain. <b><i>Design/Methods:</i></b> Nine-day-old C57BL/6 mice were subjected either to sham operation or underwent ligation of the right common carotid artery followed by hypoxia (8%) for 60 min. Animals were either administered sildenafil (10 mg/kg, i.p.) or vehicle 2 h after hypoxia. A subgroup of animals received multiple injections of 10 mg/kg daily on 5 consecutive days. Pups were either perfusion fixed at postnatal days 14 or 47 for immunohistochemical analysis, or brains were dissected 2, 6, 12, and 24 h after the end of hypoxia and analyzed for cGMP, pAkt, pGSK-3β, and β-catenin by means of ELISA or immunoblotting. In addition, behavioral studies using the wire hang test and elevated plus maze were conducted 21 and 38 days after HI injury. <b><i>Results:</i></b> Based on cresyl violet staining, single or multiple sildenafil injections did not reveal any differences in injury scoring compared to sham animals. However, cerebral levels of cGMP were altered after sildenafil therapy. Treatment significantly increased numbers of immature neurons, as indicated by doublecortin immunoreactivity in the ipsilateral subventricular zone and striatum. In addition, animals treated with sildenafil after HI insult demonstrated improved functional recovery. pAkt, pGSK-3β, and β-catenin levels vary after HI injury but additional sildenafil treatment had no impact on protein expression compared to the level of sham controls. <b><i>Conclusions:</i></b> Here, we report that treatment with sildenafil after HI insult did not improve histological brain injury scores. Nevertheless, our results suggest involvement of the cGMP and PI3K/Akt/GSK-3β signaling pathway with promotion of a neurogenic response and reduction of neurological deficits. In summary, sildenafil may have a role in promoting recovery from HI injury in the developing brain.
DOI: 10.6084/m9.figshare.4785643
title: Experiments.zip

description: Thermodynamic Framework to Assess Low Abundance DNA Mutation Detection by Hybridization<br><br>Raw Agilent data files used in the experiments
DOI: 10.6084/m9.figshare.4785661.v1
title: Supplementary Material for: Human copy number polymorphic genes

description: Recent large-scale genomic studies within human populations have identified numerous genomic regions as copy number variant (CNV). As these CNV regions often overlap coding regions of the genome, large lists of potentially copy number polymorphic genes have been produced that are candidates for disease association. Most of the current data regarding normal genic variation, however, has been generated using BAC or SNP microarrays, which lack precision especially with respect to exons. To address this, we assessed 2,790 candidate CNV genes defined from available studies in nine well-characterized HapMap individuals by designing a customized oligonucleotide microarray targeted specifically to exons. Using exon array comparative genomic hybridization (aCGH), we detected 255 (9%) of the candidates as true CNVs including 134 with evidence of variation over the entire gene. Individuals differed in copy number from the control by an average of 100 gene loci. Both partial- and whole-gene CNVs were strongly associated with segmental duplications (55 and 71%, respectively) as well as regions of positive selection. We confirmed 37% of the whole-gene CNVs using the fosmid end sequence pair (ESP) structural variation map for these same individuals. If we modify the end sequence pair mapping strategy to include low-sequence identity ESPs (98–99.5%) and ESPs with an everted orientation, we can capture 82% of the missed genes leading to more complete ascertainment of structural variation within duplicated genes. Our results indicate that segmental duplications are the source of the majority of full-length copy number polymorphic genes, most of the variant genes are organized as tandem duplications, and a significant fraction of these genes will represent paralogs with levels of sequence diversity beyond thresholds of allelic variation. In addition, these data provide a targeted set of CNV genes enriched for regions likely to be associated with human phenotypic differences due to copy number changes and present a source of copy number responsive oligonucleotide probes for future association studies.
DOI: 10.6084/m9.figshare.4785652
title: Supplementary Material for: Biomechanics of the Bat Limb Skeleton: Scaling, Material Properties and Mechanics

description: <em>Background/Aims:</em> Wing skeletons of bats are uniquely specialized for flight, reflecting both evolutionary history and the need to maintain structural integrity while generating aerodynamic forces. <i>Methods:</i> We analyzed the anatomical structure of bat wing skeletons in the context of scaling patterns relative to other mammals, material properties and the mechanical function of the wing bones during flight. <i>Results:</i> Compared with nonvolant mammals, the bones of the bat forelimb are elongated, even after correcting for shared phylogenetic history. Bats have consistently larger-diameter bones in the forelimb than do nonvolant mammals but significantly narrower hindlimb bones. Mineralization in the cortical bone of wings is lower than in the long bones of other adult mammals, with a proximodistal gradient of decreasing mineralization. The distal phalanges have only a small amount of mineralized tissue underlying the articular cartilage. Loads required to elicit a 10% length deflection in the wing bones of <i>Glossophaga soricina</i> varied approximately 50-fold along the wing and flexural stiffness nearly 200-fold. Commensurate with low mineralization and flexural stiffness, bat bones experience extraordinarily high bending strains during flight. <i>Conclusion:</i> Bat limb skeletons share features with other mammals and possess specialized characteristics, mostly related to the mechanical demands of flight.
DOI: 10.6084/m9.figshare.4785553
title: PONE-D-16-45371_Data_S3Fig

description: Quantification of mitosis duration as observed in the live-cell imaging in control and Kif15-, KBP-, or Kif15/KBP-silenced cells. The duration of mitosis was defined as the time needed for cells to progress from NEBD till start of telophase (determined as the time of contraction of the cleavage furrow). Time is represented in minutes.
DOI: 10.6084/m9.figshare.4785553.v1
title: PONE-D-16-45371_Data_S3Fig

description: Quantification of mitosis duration as observed in the live-cell imaging in control and Kif15-, KBP-, or Kif15/KBP-silenced cells. The duration of mitosis was defined as the time needed for cells to progress from NEBD till start of telophase (determined as the time of contraction of the cleavage furrow). Time is represented in minutes.
DOI: 10.6084/m9.figshare.4785643.v1
title: Experiments.zip

description: Raw Agilent data files used in the experiments
DOI: 10.6084/m9.figshare.4785541
title: PONE-D-16-45371_Data_S2DFig

description: Quantification of chromosome alignment in control and KBP-silenced cells either transiently expressing empty vector or siRNA-resistant flag-tagged KBP. Cells with bipolar spindles were categorized based upon the degree of chromosome alignment, i.e. fully aligned chromosomes (metaphase cells), misaligned chromosomes (most chromosomes have congressed to the metaphase plate, few chromosomes are not aligned yet). Values represent the number of cells observed in each category.
DOI: 10.6084/m9.figshare.4785538
title: PONE-D-16-45371_Data_S2CFig

description: Quantification of the number of monopolar versus bipolar spindles in HeLa and HeLa EICs cells silenced for control, Eg5, KBP or Kif15 siRNA. Values represent the number of cells in each category.
DOI: 10.6084/m9.figshare.4785541.v1
title: PONE-D-16-45371_Data_S2DFig

description: Quantification of chromosome alignment in control and KBP-silenced cells either transiently expressing empty vector or siRNA-resistant flag-tagged KBP. Cells with bipolar spindles were categorized based upon the degree of chromosome alignment, i.e. fully aligned chromosomes (metaphase cells), misaligned chromosomes (most chromosomes have congressed to the metaphase plate, few chromosomes are not aligned yet). Values represent the number of cells observed in each category.
DOI: 10.6084/m9.figshare.4785535
title: PONE-D-16-45371_Data_S2BFig

description: Quantification of the spindle length in control and KBP-silenced cells. Lengths are measured in micrometer.
DOI: 10.6084/m9.figshare.4785538.v1
title: PONE-D-16-45371_Data_S2CFig

description: Quantification of the number of monopolar versus bipolar spindles in HeLa and HeLa EICs cells silenced for control, Eg5, KBP or Kif15 siRNA. Values represent the number of cells in each category.
DOI: 10.6084/m9.figshare.4785535.v1
title: PONE-D-16-45371_Data_S2BFig

description: Quantification of the spindle length in control and KBP-silenced cells. Lengths are measured in micrometer.
DOI: 10.6084/m9.figshare.4785523
title: Genome-wide analysis of LPS-induced inflammatory response in the rat ventral hippocampus: Modulatory activity of the antidepressant agomelatine

description: <b>Objectives:</b> Several studies reported that antidepressant drugs have immune-regulatory effects by acting on specific inflammatory mediators. However, considering the highly complex nature of the inflammatory response, we have adopted an unbiased genome-wide strategy to investigate the immune-regulatory activity of the antidepressant agomelatine in modulating the response to an acute inflammatory challenge. <b>Methods:</b> Microarray analysis was used to identify genes modulated in the ventral hippocampus of adult rats chronically treated with agomelatine (40 mg/kg, os) before being challenged with a single injection of lipopolysaccharide (LPS; 250 μg/kg, i.p.). <b>Results:</b> The administration of LPS induced the transcription of 284 genes mainly associated with pathways related to the immune/inflammatory system. Agomelatine modulated pathways not only connected to its antidepressant activity, but was also able to prevent the activation of genes induced by LPS. Further comparisons between gene lists of the diverse experimental groups led to the identification of a few transcripts modulated by LPS on which agomelatine has the larger effect of normalisation. Among them, we found the pro-inflammatory cytokine <i>Il-1β</i> and, interestingly, the metabotropic glutamatergic transporter <i>Grm2</i>. <b>Conclusions:</b> These results are useful to better characterise the association between depression and inflammation, revealing new potential targets for pharmacological intervention for depression associated to inflammation.
DOI: 10.6084/m9.figshare.4785517
title: Effect of gross morphology on modern planktonic foraminiferal test strength under compression

description: Raw data for all crushing experiments, wall thickness measurements, and results for all pair-wise Kolmogorov-Smirnov Tests
DOI: 10.6084/m9.figshare.4785523.v1
title: Genome-wide analysis of LPS-induced inflammatory response in the rat ventral hippocampus: Modulatory activity of the antidepressant agomelatine

description: <b>Objectives:</b> Several studies reported that antidepressant drugs have immune-regulatory effects by acting on specific inflammatory mediators. However, considering the highly complex nature of the inflammatory response, we have adopted an unbiased genome-wide strategy to investigate the immune-regulatory activity of the antidepressant agomelatine in modulating the response to an acute inflammatory challenge. <b>Methods:</b> Microarray analysis was used to identify genes modulated in the ventral hippocampus of adult rats chronically treated with agomelatine (40 mg/kg, os) before being challenged with a single injection of lipopolysaccharide (LPS; 250 μg/kg, i.p.). <b>Results:</b> The administration of LPS induced the transcription of 284 genes mainly associated with pathways related to the immune/inflammatory system. Agomelatine modulated pathways not only connected to its antidepressant activity, but was also able to prevent the activation of genes induced by LPS. Further comparisons between gene lists of the diverse experimental groups led to the identification of a few transcripts modulated by LPS on which agomelatine has the larger effect of normalisation. Among them, we found the pro-inflammatory cytokine <i>Il-1β</i> and, interestingly, the metabotropic glutamatergic transporter <i>Grm2</i>. <b>Conclusions:</b> These results are useful to better characterise the association between depression and inflammation, revealing new potential targets for pharmacological intervention for depression associated to inflammation.
DOI: 10.6084/m9.figshare.4785505
title: Arabidopsis plants

description: Illustrations of Arabidopsis thaliana plants at different developmental stages<br>