cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4750966.v1
title: Supplementary Material for: Embryonic Stem Cells Facilitate the Isolation of Persistent Clonal Cardiovascular Progenitor Cell Lines and Leukemia Inhibitor Factor Maintains Their Self-Renewal and Myocardial Differentiation Potential in vitro

description: Compelling evidence for the existence of somatic stem cells in the heart of different mammalian species has been provided by numerous groups; however, so far it has not been possible to maintain these cells as self-renewing and phenotypically stable clonal cell lines in vitro. Thus, we sought to identify a surrogate stem cell niche for the isolation and persistent maintenance of stable clonal cardiovascular progenitor cell lines, enabling us to study the mechanism of self-renewal and differentiation in these cells. Using postnatal murine hearts with a selectable marker as the stem cell source and embryonic stem cells and leukemia inhibitory factor (LIF)-secreting fibroblasts as a surrogate niche, we succeeded in the isolation of stable clonal cardiovascular progenitor cell lines. These cell lines self-renew in an LIF-dependent manner. They express both stemness transcription factors Oct4, Sox2, and Nanog and early myocardial transcription factors Nkx2.5, GATA4, and Isl-1 at the same time. Upon LIF deprivation, they exclusively differentiate to functional cardiomyocytes and endothelial and smooth muscle cells, suggesting that these cells are mesodermal intermediates already committed to the cardiogenic lineage. Cardiovascular progenitor cell lines can be maintained for at least 149 passages over 7 years without phenotypic changes, in the presence of LIF-secreting fibroblasts. Isolation of wild-type cardiovascular progenitor cell lines from adolescent and old mice has finally demonstrated the general feasibility of this strategy for the isolation of phenotypically stable somatic stem cell lines.
DOI: 10.7910/dvn/pkjufn/b13mqs
title: FCC2002.248.ran

description: :unav
DOI: 10.6084/m9.figshare.4750900
title: Supplementary Material for: Apathy Secondary to Stroke: A Systematic Review and Meta-Analysis

description: <strong><em>Background:</em></strong> Apathy is a disturbance of motivation, frequent in survivors of stroke. Several studies have evaluated the rate of apathy secondary to stroke and risk factors. Different conclusions and contradictory findings have been published. We aimed to perform a systematic review and meta-analysis of all studies evaluating apathy secondary to stroke to better estimate its rate and risk factors, and explore associations with poorer outcomes. <b><i>Methods:</i></b> We searched PubMed, Cochrane Library, PsychINFO and PsycBITE databases and screened references of included studies and review articles for additional citations. Search results and data extraction was performed independently. We systematically reviewed available publications reporting investigations on ischemic and intracerebral hemorrhagic stroke and apathy. Quality assessment of the studies was performed independently. Subgroup analyses were performed according to stroke phase (acute and post-acute), stroke past history (first-ever and any-stroke) and patient age (younger and older patients). Pooled odds ratios (OR) and standardized mean difference, and 95% confidence intervals (CI), were derived by random-effects meta-analysis. Heterogeneity was assessed with I<sup>2</sup> test. <b><i>Results:</i></b> From the initial 1,399 publications, we included 19 studies (2,221 patients). The pooled rate of apathy was 36.3% (95% CI 30.3–42.8; I<sup>2</sup> = 46.8), which was similar for acute [39.5% (95% CI 28.9–51.1)] and post-acute phase [34.3% (95% CI 27.8–41.4)], and about three times higher than the rate of depression [12.1% (95% CI 8.2–17.3)]. Apathetic patients were on average 2.74 years older (95% CI 1.25–4.23; I<sup>2</sup> = 0%). No gender differences were found. Depression (OR 2.29; 95% CI 1.41–3.72; I<sup>2</sup> = 44%) and cognitive impairment (OR 2.90; 95% CI 1.09–7.72; I<sup>2</sup> = 14%) were more frequent and severe in apathetic patients. Apathy rate was similar for ischemic and hemorrhagic stroke type and for left- and right-sided hemispheric lesions. Clinical global outcome was similar between apathetic and nonapathetic patients. <b><i>Conclusion:</i></b> Apathy secondary to stroke is a more frequent neuropsychiatric disturbance than depression. Apathetic patients are more frequently and severely depressed and cognitively impaired. A negative impact of apathy secondary to stroke on clinical global outcome cannot be ascribed. Future research should properly address its predictor factors and evaluate the impact of apathy treatment options in stroke patients.
DOI: 10.6084/m9.figshare.4750933
title: Supplementary Material for: Identification of Infection- and Defense-Related Genes via a Dynamic Host-Pathogen Interaction Network Using a Candida Albicans-Zebrafish Infection Model

description: <em>Candida albicans</em> infections and candidiasis are difficult to treat and create very serious therapeutic challenges. In this study, based on interactive time profile microarray data of <i>C. albicans </i>and zebrafish during infection, the infection-related protein-protein interaction (PPI) networks of the two species and the intercellular PPI network between host and pathogen were simultaneously constructed by a dynamic interaction model, modeled as an integrated network consisting of intercellular invasion and cellular defense processes during infection. The signal transduction pathways in regulating morphogenesis and hyphal growth of <i>C. albicans</i> were further investigated based on significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins from which we can gain more insight into the pathogenic role of hyphal development in the <i>C. albicans</i> infection process. Important defense-related proteins in zebrafish were predicted using the same approach. The hyphal growth PPI network, zebrafish PPI network and host-pathogen intercellular PPI network were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of <i>C. albicans</i> and the immune response of the host, and may help improve medical therapies and facilitate the development of new antifungal drugs.
DOI: 10.6084/m9.figshare.4750936.v1
title: Supplementary Material for: Homomorphic Sex Chromosomes and the Intriguing Y Chromosome of Ctenomys Rodent Species (Rodentia, Ctenomyidae)

description: Unlike the X chromosome, the mammalian Y chromosome undergoes evolutionary decay resulting in small size. This sex chromosomal heteromorphism, observed in most species of the fossorial rodent <i>Ctenomys</i>, contrasts with the medium-sized, homomorphic acrocentric sex chromosomes of closely related <i>C. maulinus </i>and <i>C. </i>sp. To characterize the sequence composition of these chromosomes, fluorescent banding, self-genomic in situ hybridization, and fluorescent in situ hybridization with an X painting probe were performed on mitotic and meiotic plates. High molecular homology between the sex chromosomes was detected on mitotic material as well as on meiotic plates immunodetected with anti-SYCP3 and anti-γH2AX. The Y chromosome is euchromatic, poor in repetitive sequences and differs from the X by the loss of a block of pericentromeric chromatin. Inferred from the G-banding pattern, an inversion and the concomitant prevention of recombination in a large asynaptic region seems to be crucial for meiotic X chromosome inactivation. These peculiar findings together with the homomorphism of <i>Ctenomys</i> sex chromosomes are discussed in the light of the regular purge that counteracts Muller's ratchet and the probable mechanisms accounting for their origin and molecular homology.
DOI: 10.7910/dvn/pkjufn/zuwjfy
title: FCC2001.140.ran

description: :unav
DOI: 10.6084/m9.figshare.4750900.v1
title: Supplementary Material for: Apathy Secondary to Stroke: A Systematic Review and Meta-Analysis

description: <strong><em>Background:</em></strong> Apathy is a disturbance of motivation, frequent in survivors of stroke. Several studies have evaluated the rate of apathy secondary to stroke and risk factors. Different conclusions and contradictory findings have been published. We aimed to perform a systematic review and meta-analysis of all studies evaluating apathy secondary to stroke to better estimate its rate and risk factors, and explore associations with poorer outcomes. <b><i>Methods:</i></b> We searched PubMed, Cochrane Library, PsychINFO and PsycBITE databases and screened references of included studies and review articles for additional citations. Search results and data extraction was performed independently. We systematically reviewed available publications reporting investigations on ischemic and intracerebral hemorrhagic stroke and apathy. Quality assessment of the studies was performed independently. Subgroup analyses were performed according to stroke phase (acute and post-acute), stroke past history (first-ever and any-stroke) and patient age (younger and older patients). Pooled odds ratios (OR) and standardized mean difference, and 95% confidence intervals (CI), were derived by random-effects meta-analysis. Heterogeneity was assessed with I<sup>2</sup> test. <b><i>Results:</i></b> From the initial 1,399 publications, we included 19 studies (2,221 patients). The pooled rate of apathy was 36.3% (95% CI 30.3–42.8; I<sup>2</sup> = 46.8), which was similar for acute [39.5% (95% CI 28.9–51.1)] and post-acute phase [34.3% (95% CI 27.8–41.4)], and about three times higher than the rate of depression [12.1% (95% CI 8.2–17.3)]. Apathetic patients were on average 2.74 years older (95% CI 1.25–4.23; I<sup>2</sup> = 0%). No gender differences were found. Depression (OR 2.29; 95% CI 1.41–3.72; I<sup>2</sup> = 44%) and cognitive impairment (OR 2.90; 95% CI 1.09–7.72; I<sup>2</sup> = 14%) were more frequent and severe in apathetic patients. Apathy rate was similar for ischemic and hemorrhagic stroke type and for left- and right-sided hemispheric lesions. Clinical global outcome was similar between apathetic and nonapathetic patients. <b><i>Conclusion:</i></b> Apathy secondary to stroke is a more frequent neuropsychiatric disturbance than depression. Apathetic patients are more frequently and severely depressed and cognitively impaired. A negative impact of apathy secondary to stroke on clinical global outcome cannot be ascribed. Future research should properly address its predictor factors and evaluate the impact of apathy treatment options in stroke patients.
DOI: 10.7910/dvn/pkjufn/1hm8fk
title: FCC2003.063.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/qjzbm8
title: FCC2001.266.ran

description: :unav
DOI: 10.6084/m9.figshare.4750837
title: Supplementary Material for: Molecular Characteristics of Pancreatic Ductal Adenocarcinomas with High-Grade Pancreatic Intraepithelial Neoplasia (PanIN) Are Different from Those without High-Grade PanIN

description: <b><i>Aims:</i></b> We reported that pancreatic ductal adenocarcinomas (PDACs) without high-grade pancreatic intraepithelial neoplasia (PanIN) in the vicinity had worse prognoses than PDACs with high-grade PanIN. However, the molecular characteristics of PDACs with and without high-grade PanIN have not been compared. The aim of this study is to clarify the molecular characteristics of PDACs with and without high-grade PanIN. <b><i>Method and Results:</i></b> We reviewed all of a consecutive series of 100 patients with PDACs and divided them into 2 groups: the PDACs with PanIN-2 or PanIN-3 in the background (the PanIN-high group, <i>n</i> = 60) and the PDACs without PanIN-2 or PanIN-3 in the background (the PanIN-low group, <i>n</i> = 40). We evaluated the p53, p16, and SMAD4 expressions in the invasive ductal carcinoma (IDC) components by immunohistochemical staining. <i>KRAS</i> mutation was also analyzed in 80 tumors. The PanIN-low group showed significantly more frequent “high p53 expression” and “loss of SMAD4 expression” than the PanIN-high group (<i>p</i> = 0.048 and <i>p</i> = 0.019, respectively). Loss of p16 expression was not significantly different between the groups. The rate of <i>KRAS</i> wild type was significantly higher in the PanIN-low group than the PanIN-high group (<i>p</i> = 0.024). <b><i>Conclusions:</i></b> Our results demonstrated that the molecular characteristics in the PDACs with high-grade PanIN were different from those in the PDACs without high-grade PanIN. PDACs without high-grade PanIN may develop via a pathway other than the PanIN-carcinoma sequence.
DOI: 10.6084/m9.figshare.4750861
title: PowerPoint Slides for: Oxidative Balance Score and the Risk of End-Stage Renal Disease and Cardiovascular Disease

description: <b><i>Background:</i></b> Oxidative balance score (OBS) is a composite measure of oxidative stress-related exposures. The aim of this study was to investigate the association between OBS, end-stage renal disease (ESRD), and cardiovascular disease (CVD). <b><i>Methods:</i></b> Using data from the Chronic Renal Insufficiency Cohort, we calculated the main exposure OBS by summing up 12 apriori-defined pro- and antioxidant factors obtained from the diet history questionnaire and lifestyle assessment. We divided OBS into quartiles (Q1-Q4), with Q1 (predominance of pro-oxidants) as the reference. We analyzed OBS quartiles as an ordinal variable. Crude and adjusted hazards ratios (HRs) and 95% CIs were estimated using Cox proportional hazards models for time to ESRD and CVD. <b><i>Results:</i></b> Compared to Q1, Q4 (high antioxidant) was associated with ESRD in the crude model (HR 1.35, 95% CI 1.08-1.69) and adjusting for age, sex, and race (HR 1.36, 95% CI 1.09-1.71) but not in the fully adjusted model (HR 1.12, 95% CI 0.84-1.51). HR of ESRD increased as the OBS quartiles increased in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05) but not in the fully adjusted model (<i>p</i><sub>trend</sub> = 0.30). Compared to Q1, Q4 was associated with CVD in the crude (HR 1.33, 95% CI 1.06-1.68) but not adjusted models. The HR of CVD increased with an increase in OBS quartiles in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05). <b><i>Conclusion:</i></b> The reverse association between OBS and progression to ESRD suggests that perhaps the effect of oxidative balance-related exposure is different in the setting of established chronic kidney disease.
DOI: 10.7910/dvn/pkjufn/hgr3se
title: FCC2001.172.ran

description: :unav
DOI: 10.6084/m9.figshare.4750831
title: Automatic stimulus evaluation depends on goal-relevance

description: Raw data as described by <br>Spruyt, Tibboel, De Schryver, & De Houwer (submitted). Automatic stimulus evaluation depends on goal-relevance. Paper submitted for publication.
DOI: 10.6084/m9.figshare.4750837.v1
title: Supplementary Material for: Molecular Characteristics of Pancreatic Ductal Adenocarcinomas with High-Grade Pancreatic Intraepithelial Neoplasia (PanIN) Are Different from Those without High-Grade PanIN

description: <b><i>Aims:</i></b> We reported that pancreatic ductal adenocarcinomas (PDACs) without high-grade pancreatic intraepithelial neoplasia (PanIN) in the vicinity had worse prognoses than PDACs with high-grade PanIN. However, the molecular characteristics of PDACs with and without high-grade PanIN have not been compared. The aim of this study is to clarify the molecular characteristics of PDACs with and without high-grade PanIN. <b><i>Method and Results:</i></b> We reviewed all of a consecutive series of 100 patients with PDACs and divided them into 2 groups: the PDACs with PanIN-2 or PanIN-3 in the background (the PanIN-high group, <i>n</i> = 60) and the PDACs without PanIN-2 or PanIN-3 in the background (the PanIN-low group, <i>n</i> = 40). We evaluated the p53, p16, and SMAD4 expressions in the invasive ductal carcinoma (IDC) components by immunohistochemical staining. <i>KRAS</i> mutation was also analyzed in 80 tumors. The PanIN-low group showed significantly more frequent “high p53 expression” and “loss of SMAD4 expression” than the PanIN-high group (<i>p</i> = 0.048 and <i>p</i> = 0.019, respectively). Loss of p16 expression was not significantly different between the groups. The rate of <i>KRAS</i> wild type was significantly higher in the PanIN-low group than the PanIN-high group (<i>p</i> = 0.024). <b><i>Conclusions:</i></b> Our results demonstrated that the molecular characteristics in the PDACs with high-grade PanIN were different from those in the PDACs without high-grade PanIN. PDACs without high-grade PanIN may develop via a pathway other than the PanIN-carcinoma sequence.
DOI: 10.6084/m9.figshare.4750861.v1
title: PowerPoint Slides for: Oxidative Balance Score and the Risk of End-Stage Renal Disease and Cardiovascular Disease

description: <b><i>Background:</i></b> Oxidative balance score (OBS) is a composite measure of oxidative stress-related exposures. The aim of this study was to investigate the association between OBS, end-stage renal disease (ESRD), and cardiovascular disease (CVD). <b><i>Methods:</i></b> Using data from the Chronic Renal Insufficiency Cohort, we calculated the main exposure OBS by summing up 12 apriori-defined pro- and antioxidant factors obtained from the diet history questionnaire and lifestyle assessment. We divided OBS into quartiles (Q1-Q4), with Q1 (predominance of pro-oxidants) as the reference. We analyzed OBS quartiles as an ordinal variable. Crude and adjusted hazards ratios (HRs) and 95% CIs were estimated using Cox proportional hazards models for time to ESRD and CVD. <b><i>Results:</i></b> Compared to Q1, Q4 (high antioxidant) was associated with ESRD in the crude model (HR 1.35, 95% CI 1.08-1.69) and adjusting for age, sex, and race (HR 1.36, 95% CI 1.09-1.71) but not in the fully adjusted model (HR 1.12, 95% CI 0.84-1.51). HR of ESRD increased as the OBS quartiles increased in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05) but not in the fully adjusted model (<i>p</i><sub>trend</sub> = 0.30). Compared to Q1, Q4 was associated with CVD in the crude (HR 1.33, 95% CI 1.06-1.68) but not adjusted models. The HR of CVD increased with an increase in OBS quartiles in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05). <b><i>Conclusion:</i></b> The reverse association between OBS and progression to ESRD suggests that perhaps the effect of oxidative balance-related exposure is different in the setting of established chronic kidney disease.
DOI: 10.7910/dvn/pkjufn/ut0rbn
title: FCC2001.154.ran

description: :unav
DOI: 10.6084/m9.figshare.4750831.v1
title: Automatic stimulus evaluation depends on goal-relevance

description: Raw data as described by <br>Spruyt, Tibboel, De Schryver, & De Houwer (submitted). Automatic stimulus evaluation depends on goal-relevance. Paper submitted for publication.
DOI: 10.6084/m9.figshare.4750807
title: Small carnivore ecosystem services data

description: This file set contains the data analysed in Williams, S.T., Maree, N., Taylor, P., Belmain, S.R., Keith, M. and Swanepoel, L.H. (2017) Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service? Ecosystem Services. doi: 10.1016/j.ecoser.2017.12.006<br><br>There are two types of data included:1. data from a camera trap survey of small carnivores in a rural agro-ecosystem South Africa. 2. data from a questionnaire survey of perceptions of small carnivores and the potential ecosystems services they could provide. <br>Both raw and processed data are included, along with an R script is also included, showing how we analysed the camera trap data. Please see the article for further details. Please contact Sam Williams (samual.t.williams@gmail.com) or Lourens Swanepoel (lourens.swanepoel.univen@gmail.com) if you have any questions. <br>The files provided in this file set are as follows:<br>## Camera trap data <br>- Raw Camtrap data.csvThe raw data from the camera traps.<br>- CameraTraps.xlsContains attributes of camera trap sites used for the camera trap survey.<br>- The following processed dat were used in the occupancy analysis - SpData.txt - box1.txt - species names.csv - LUTdetailed.shp (land use shapefile used for plotting maps) <br>- analysis code.RR code used to analyse camera trap data<br><br>## Questionnaire data<br>- questionRaw.csvAll questionnaire data in a raw form<br>A graphical abstract is also included.
DOI: 10.6084/m9.figshare.4750801
title: Supplementary Material for: Prospective Evaluation of a Prenatal Sonographic Clubfoot Classification System

description: <strong><em>Background:</em></strong> The purpose of this study was to prospectively evaluate our recently described fetal sonographic classification system for prenatal diagnosis of clubfoot. <b><i>Methods:</i></b> Over 18 months, we prospectively enrolled consecutive pregnant patients evaluated for a prenatally diagnosed clubfoot. Prenatal sonographic scores assigned by a radiologist were compared to final clinical diagnosis and severity given by a pediatric orthopedic surgeon. Pearson's χ<sup>2</sup> test and logistic regression were used in statistical analyses on the subject level. Generalized estimating equations were used in analyses on the foot level to account for intrasubject correlation. <b><i>Results:</i></b> There were 50 subjects, with 26 unilateral and 24 bilateral clubfeet, according to the prenatal ultrasound (US). A total of 51 (69%) of 74 feet and 36 (72%) of 50 subjects had a postnatal diagnosis of clubfoot. The accuracy of diagnosis in cases of a severe, moderate, and mild US score was 94, 70, and 25%, respectively (p = 0.003 comparing moderate-severe vs. mild). US severity correlated with the Dimeglio classification scoring system (Spearman's correlation 0.30). <b><i>Conclusion:</i></b> The fetal sonographic scoring system is predictive of clinical severity after birth, and improves the ability to counsel families with a prenatal diagnosis of clubfoot.
DOI: 10.7910/dvn/pkjufn/e4mhwd
title: FCC2001.176.ran

description: :unav
DOI: 10.6084/m9.figshare.4750798
title: Supplementary Material for: Increased Survival in the Red Flour Beetle after Oral Priming with Bacteria-Conditioned Media

description: Immune priming is defined as enhanced protection upon secondary exposure to a pathogen. Such enhanced resistance after prior exposure has been demonstrated for a number of insect species including the red flour beetle, <i>Tribolium castaneum</i>. In testing this phenomenon, the majority of studies have focused on introducing the pathogen into the insect's hemocoel via septic wounding through the cuticle. Although such septic injury can occur in nature, many pathogens enter their hosts via the oral route, i.e. by ingestion. <i>Bacillus thuringiensis</i> bacteria are well-known insect pathogens that infect their host orally. We found that <i>T. castaneum</i> larvae showed increased survival after oral exposure to <i>B. thuringiensis</i>, when they had been orally primed with filter-sterilized media in which spores of <i>B. thuringiensis</i> had been raised. Such priming was achieved only with a naturally pathogenic strain of <i>B. thuringiensis</i> and a strain that was made pathogenic by transfer of plasmids. Moreover, primed larvae were smaller in size 24 h after priming and had a longer developmental time, indicating that investment in such a response comes at a cost. However, the increased survival in primed larvae was not caused by larval size differences upon challenge.
DOI: 10.7910/dvn/pkjufn/uwq9kx
title: FCC2001.110.ran

description: :unav