cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6840173
title: Supplementary Material for: Presentation, Evaluation, Management, and Outcomes of Acute Stroke in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis

description: <b><i>Aims:</i></b> We performed a systematic review to evaluate stroke presentation, evaluation, management, and outcomes among studies conducted in low- and middle-income countries (LMIC). <b><i>Methods:</i></b> We searched MEDLINE (Ovid), Embase (Elsevier), and the Global Health (EBSCOhost) databases between January 2005 and June 2017 for studies conducted in LMICs defined by the World Bank. We pooled prevalence estimates using an inverse-variance weighting method and stratified by the country income group. <b><i>Results:</i></b> The search identified 36 hospital-based studies (64,256 participants) in LMICs. Mean (SD) age ranged from 51 (14) to 72 (12) years, and 29–56% of patients were women. Hypertension was the most commonly reported risk factor (64% [95% CI 59–69]). In settings where MRI was not used, head CT scans were reported among 90% patients (95% CI 79–97). Overall, 3% (95% CI 2–4) of patients were treated with tissue plasminogen activator, and 78% (95% CI 66–88) were treated with antiplatelet therapy. Overall, the rate of in-hospital mortality was 14% (95% CI 10–19), and the rate of in-hospital pneumonia was 17% (95% CI 14–20). <b><i>Conclusions:</i></b> Our review<b><i></i></b> revealed the low use of evidence-based practices for acute stroke care in LMIC. The true use in hospitals that do not conduct this research is probably even lower. Strategies to evaluate and improve health system performance for acute stroke care, including implantation of stroke units and making thrombolysis more available and affordable are needed in LMIC. Registration in Prospero: CRD42017069325.
DOI: 10.6084/m9.figshare.6840173.v1
title: Supplementary Material for: Presentation, Evaluation, Management, and Outcomes of Acute Stroke in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis

description: <b><i>Aims:</i></b> We performed a systematic review to evaluate stroke presentation, evaluation, management, and outcomes among studies conducted in low- and middle-income countries (LMIC). <b><i>Methods:</i></b> We searched MEDLINE (Ovid), Embase (Elsevier), and the Global Health (EBSCOhost) databases between January 2005 and June 2017 for studies conducted in LMICs defined by the World Bank. We pooled prevalence estimates using an inverse-variance weighting method and stratified by the country income group. <b><i>Results:</i></b> The search identified 36 hospital-based studies (64,256 participants) in LMICs. Mean (SD) age ranged from 51 (14) to 72 (12) years, and 29–56% of patients were women. Hypertension was the most commonly reported risk factor (64% [95% CI 59–69]). In settings where MRI was not used, head CT scans were reported among 90% patients (95% CI 79–97). Overall, 3% (95% CI 2–4) of patients were treated with tissue plasminogen activator, and 78% (95% CI 66–88) were treated with antiplatelet therapy. Overall, the rate of in-hospital mortality was 14% (95% CI 10–19), and the rate of in-hospital pneumonia was 17% (95% CI 14–20). <b><i>Conclusions:</i></b> Our review<b><i></i></b> revealed the low use of evidence-based practices for acute stroke care in LMIC. The true use in hospitals that do not conduct this research is probably even lower. Strategies to evaluate and improve health system performance for acute stroke care, including implantation of stroke units and making thrombolysis more available and affordable are needed in LMIC. Registration in Prospero: CRD42017069325.
DOI: 10.6084/m9.figshare.6840134
title: Supplementary Material for: Altered White Matter Diffusivity of the Cingulum Angular Bundle in Posttraumatic Stress Disorder

description: <b><i>Purpose of the Study:</i></b> Prior studies showed posttraumatic stress disorder (PTSD)-related alterations in white matter integrity, but most of these studies have used region-based approaches. We address this limitation by investigating the relationship between PTSD severity and fractional anisotropy (FA) using a tract-based approach. <b><i>Procedures:</i></b> Structural and diffusion magnetic resonance imaging were acquired from 67 combat-exposed US Veterans and processed using FSL/FreeSurfer TRActs Constrained by UnderLying Anatomy. Partial correlations were conducted between PTSD severity and FA of the cingulum and uncinate fasciculi covarying for age, sex, and head motion. <b><i>Results:</i></b> Only FA of the left cingulum angular bundle (CAB) was positively correlated with PTSD symptom severity (<i>r</i> = 0.433, <i>p</i> = 0.001, <i>df</i> = 57) and remained significant after Bonferroni correction. <b><i>Conclusions:</i></b> This finding may imply greater organization of the CAB with increasing PTSD severity. The CAB connects directly to the cingulate cortex and the hippocampal subiculum, critical nodes of the default mode network, as well as being implicated in neurodegeneration pathology, decision-making, and executive functions, which may help explain previously shown alterations in this network in PTSD. <b><i>Message of the Paper:</i></b> Further study of white matter tract integrity in PTSD is warranted, particularly to investigate whether the CAB connections with both higher-order cognitive functioning and emotion processing regions contribute to the pathophysiology and comorbidity of PTSD.
DOI: 10.6084/m9.figshare.6840134.v1
title: Supplementary Material for: Altered White Matter Diffusivity of the Cingulum Angular Bundle in Posttraumatic Stress Disorder

description: <b><i>Purpose of the Study:</i></b> Prior studies showed posttraumatic stress disorder (PTSD)-related alterations in white matter integrity, but most of these studies have used region-based approaches. We address this limitation by investigating the relationship between PTSD severity and fractional anisotropy (FA) using a tract-based approach. <b><i>Procedures:</i></b> Structural and diffusion magnetic resonance imaging were acquired from 67 combat-exposed US Veterans and processed using FSL/FreeSurfer TRActs Constrained by UnderLying Anatomy. Partial correlations were conducted between PTSD severity and FA of the cingulum and uncinate fasciculi covarying for age, sex, and head motion. <b><i>Results:</i></b> Only FA of the left cingulum angular bundle (CAB) was positively correlated with PTSD symptom severity (<i>r</i> = 0.433, <i>p</i> = 0.001, <i>df</i> = 57) and remained significant after Bonferroni correction. <b><i>Conclusions:</i></b> This finding may imply greater organization of the CAB with increasing PTSD severity. The CAB connects directly to the cingulate cortex and the hippocampal subiculum, critical nodes of the default mode network, as well as being implicated in neurodegeneration pathology, decision-making, and executive functions, which may help explain previously shown alterations in this network in PTSD. <b><i>Message of the Paper:</i></b> Further study of white matter tract integrity in PTSD is warranted, particularly to investigate whether the CAB connections with both higher-order cognitive functioning and emotion processing regions contribute to the pathophysiology and comorbidity of PTSD.
DOI: 10.6084/m9.figshare.6840113
title: Supplementary Material for: Biomarker Discovery by Mass Spectrometry in Cerebrospinal Fluid and Plasma after Global Hypoxia-Ischemia in Newborn Piglets

description: <b><i>Background:</i></b> Biomarkers may qualify diagnosis, treatment allocation, and prognostication in neonatal encephalopathy. Biomarker development is challenged by competing etiologies, inter-individual genetic variability, and a lack of specific neonatal markers. To address these challenges, we used a standardized neonatal hypoxic-ischemic (HI) encephalopathy model with pre- and post-HI sampling of cerebrospinal fluid (CSF) and plasma. <b><i>Objectives:</i></b> The study aimed to identify novel candidate protein biomarkers of HI encephalopathy in a newborn piglet model in CSF and plasma. <b><i>Methods:</i></b> F<sub>i</sub>O<sub>2</sub> was lowered to 4% in 6 newborn piglets, then adjusted over a 45-min period keeping the amplitude integrated-EEG &lt; 7 µV to induce HI encephalopathy. CSF and plasma was sampled pre-HI and 2 h after HI, protein levels were then analyzed by mass spectrometry. <b><i>Results:</i></b> Protein levels after HI changed significantly for 18 CSF proteins and 37 plasma proteins. CSF and plasma data showed distinct information, although peptidyl-prolyl cis-trans isomerase A had elevated levels in both fluids. HI regulation involved functional groups such as the antioxidant system, cell proliferation, cell structure, and apoptosis. S100-A8, which increased the most in CSF (9.5 fold), is known to be involved in inflammatory and immune response and to be highly regulated during injury. In plasma, increased proteins included FABP1 (31.8 fold) and proteins with antioxidant (SOD1, GPX3) and lectin function (REG3A, LGALS3). <b><i>Conclusions:</i></b> In this exploratory study, we have identified candidate biomarkers for HI in CSF and plasma, many not previously associated with HI. Identified proteins are promising candidates for further validation in time series experiments and clinical studies.
DOI: 10.6084/m9.figshare.6840113.v1
title: Supplementary Material for: Biomarker Discovery by Mass Spectrometry in Cerebrospinal Fluid and Plasma after Global Hypoxia-Ischemia in Newborn Piglets

description: <b><i>Background:</i></b> Biomarkers may qualify diagnosis, treatment allocation, and prognostication in neonatal encephalopathy. Biomarker development is challenged by competing etiologies, inter-individual genetic variability, and a lack of specific neonatal markers. To address these challenges, we used a standardized neonatal hypoxic-ischemic (HI) encephalopathy model with pre- and post-HI sampling of cerebrospinal fluid (CSF) and plasma. <b><i>Objectives:</i></b> The study aimed to identify novel candidate protein biomarkers of HI encephalopathy in a newborn piglet model in CSF and plasma. <b><i>Methods:</i></b> F<sub>i</sub>O<sub>2</sub> was lowered to 4% in 6 newborn piglets, then adjusted over a 45-min period keeping the amplitude integrated-EEG &lt; 7 µV to induce HI encephalopathy. CSF and plasma was sampled pre-HI and 2 h after HI, protein levels were then analyzed by mass spectrometry. <b><i>Results:</i></b> Protein levels after HI changed significantly for 18 CSF proteins and 37 plasma proteins. CSF and plasma data showed distinct information, although peptidyl-prolyl cis-trans isomerase A had elevated levels in both fluids. HI regulation involved functional groups such as the antioxidant system, cell proliferation, cell structure, and apoptosis. S100-A8, which increased the most in CSF (9.5 fold), is known to be involved in inflammatory and immune response and to be highly regulated during injury. In plasma, increased proteins included FABP1 (31.8 fold) and proteins with antioxidant (SOD1, GPX3) and lectin function (REG3A, LGALS3). <b><i>Conclusions:</i></b> In this exploratory study, we have identified candidate biomarkers for HI in CSF and plasma, many not previously associated with HI. Identified proteins are promising candidates for further validation in time series experiments and clinical studies.
DOI: 10.6084/m9.figshare.6840077
title: Study 2

description: refer to manuscript and supplement "Individual Differences in Object Recognition", Richler et al., revision submitted to Psychological Review on July 19, 2018
DOI: 10.6084/m9.figshare.6840077.v1
title: Study 2

description: refer to manuscript and supplement "Individual Differences in Object Recognition", Richler et al., revision submitted to Psychological Review on July 19, 2018
DOI: 10.6084/m9.figshare.6840041
title: Uncorrelated healing response of tendon and ear injuries in MRL highlight a role for the local tendon environment in driving scarless healing

description: <b><i>Purpose</i></b>: Tendon tears are common injuries that heal with scar formation. Interestingly, MRL/MpJ mice heal without scar in several tissues, including tendon. Most hypotheses regarding scarless healing implicate the systemic environment. However, the tissue-specificity of this regenerative response and our previous findings showing regeneration of sub-rupture tendon injuries, which lack an overt systemic response, motivate a tissue-driven hypothesis. Our objective is to investigate the potential of the local tendon environment in driving scarless healing (1) by comparing the systemic response and the healing capacity associated with ear and tendon injuries in MRL/MpJ mice, and (2) by comparing intrinsic healing properties between MRL/MpJ and normal healer C57Bl/6 tendons. <b><i>Methods</i></b>: We examined the systemic inflammatory and local structural environments of ear and tendon punch injuries in MRL/MpJ and C57Bl/6 mice. Systemic differences were analyzed to assess effects of different injuries on the inflammatory response. Correlations were assessed between MRL/MpJ ear and tendon injuries to compare the extent of healing between regenerative tissues. <b><i>Results</i></b>: Analysis showed similarities between the systemic environment in MRL/MpJ post ear or tendon injuries. However, comparable inflammatory responses did not translate into analogous healing between tissues, suggesting that the systemic environment is not the driver of regeneration. Supporting the regenerative role of the local environment, healing MRL/MpJ tendons exhibited improved matrix and cell alignment and a distinct composition of growth factors and Hyaluronan from C57Bl/6. <b><i>Conclusion</i></b>: These findings support the tissue-driven hypothesis for MRL/MpJ tendon regeneration and motivate further investigation regarding specific roles of extracellular factors in scarless healing.
DOI: 10.6084/m9.figshare.6840032
title: Study 1

description: refer to the manuscript and supplement "Individual Differences in Object Recognition" (latest revision submitted July 19 2018 to Psychological Review)
DOI: 10.6084/m9.figshare.6840041.v1
title: Uncorrelated healing response of tendon and ear injuries in MRL highlight a role for the local tendon environment in driving scarless healing

description: <b><i>Purpose</i></b>: Tendon tears are common injuries that heal with scar formation. Interestingly, MRL/MpJ mice heal without scar in several tissues, including tendon. Most hypotheses regarding scarless healing implicate the systemic environment. However, the tissue-specificity of this regenerative response and our previous findings showing regeneration of sub-rupture tendon injuries, which lack an overt systemic response, motivate a tissue-driven hypothesis. Our objective is to investigate the potential of the local tendon environment in driving scarless healing (1) by comparing the systemic response and the healing capacity associated with ear and tendon injuries in MRL/MpJ mice, and (2) by comparing intrinsic healing properties between MRL/MpJ and normal healer C57Bl/6 tendons. <b><i>Methods</i></b>: We examined the systemic inflammatory and local structural environments of ear and tendon punch injuries in MRL/MpJ and C57Bl/6 mice. Systemic differences were analyzed to assess effects of different injuries on the inflammatory response. Correlations were assessed between MRL/MpJ ear and tendon injuries to compare the extent of healing between regenerative tissues. <b><i>Results</i></b>: Analysis showed similarities between the systemic environment in MRL/MpJ post ear or tendon injuries. However, comparable inflammatory responses did not translate into analogous healing between tissues, suggesting that the systemic environment is not the driver of regeneration. Supporting the regenerative role of the local environment, healing MRL/MpJ tendons exhibited improved matrix and cell alignment and a distinct composition of growth factors and Hyaluronan from C57Bl/6. <b><i>Conclusion</i></b>: These findings support the tissue-driven hypothesis for MRL/MpJ tendon regeneration and motivate further investigation regarding specific roles of extracellular factors in scarless healing.
DOI: 10.6084/m9.figshare.6839981
title: Aerobactin/salmochelin representative virulence plasmids

description: These 12 representative plasmids carry distinct lineages of the virulence-associated aerobactin and/or salmochelin biosynthesis loci in <i>K. pneumoniae</i>.Included in this folder are the individual annotated gbk files for each representative plasmid and the Mauve alignment files for the 12 plasmids. For more information and accession numbers for these genomes, please see bioRxiv preprint.
DOI: 10.6084/m9.figshare.6839993
title: Reproductive success of Anacyclus clavatus and A. valentinus

description: Data set describing floral visitors and reproductive success of the rayed daisy <i>Anacyclus clavatus </i>and the rayless <i>A. valentinus</i> in three sites: i) sympatric, ii) rayed, and iii) rayless site. It also includes a pollen limitation and a ray removal experiment.<br>
DOI: 10.6084/m9.figshare.6839906
title: Supplementary Material for: Metformin Does Not Affect Clinically Relevant Outcomes in Patients with Idiopathic Pulmonary Fibrosis

description: <b><i>Background:</i></b> Diabetes mellitus is a possible risk factor for the development of idiopathic pulmonary fibrosis (IPF), yet the effect of antidiabetic therapy on the course of IPF is unknown. <b><i>Objectives:</i></b> This post hoc analysis assessed the effect of metformin on clinically relevant outcomes in patients with IPF. <b><i>Methods:</i></b> For the primary analysis, patients randomized to placebo (<i>n</i> = 624) in 3 phase 3, double-blind, controlled trials of pirfenidone (CAPACITY [NCT00287716 and NCT00287729]; ASCEND [NCT01366209]) were categorized by baseline metformin use. The primary outcome was disease progression (forced vital capacity [FVC] decline ≥10%, 6-min walking distance [6MWD] decline ≥50 m, or death). Other outcomes included mortality, hospitalization, FVC decline (≥10 and ≥5%), and 6MWD decline. Outcomes were also assessed in patients with diabetes and/or hyperglycemia (impaired glucose tolerance [IGT] and diabetes population [IGT-diabetes population]) and all patients included in the 3 studies (intention-to-treat [ITT] population). <b><i>Results:</i></b> Overall, 71 (11.4%) patients were metformin users and 553 (88.6%) were nonmetformin users. Baseline data were similar between groups, except for a higher percentage of males (84.5 vs. 73.2%) and a history of diabetes (98.6 vs. 11.6%) in metformin users versus nonmetformin users. The unadjusted 1-year analyses demonstrated no significant differences in disease progression or other outcomes. A higher proportion of metformin users compared with nonmetformin users had a relative FVC decline of ≥5% (63.4 vs. 50.6%, <i>p</i> = 0.043). Results were similar for the IGT-diabetes population and for the ITT population. Multivariable analyses yielded similar results. <b><i>Conclusions:</i></b> Metformin has no effect on clinically relevant outcomes in patients with IPF.
DOI: 10.6084/m9.figshare.6839918
title: Code and data to reproduce "When can competition and dispersal lead to checkerboard distributions?"

description: Code and data to reproduce:<br>&gt; Dallas,TA, B Melbourne, and A Hastings 2018. "When can competition and dispersal lead to checkerboard distributions?" Journal of Animal Ecology <br><br>
DOI: 10.6084/m9.figshare.6839918.v1
title: Code and data to reproduce "When can competition and dispersal lead to checkerboard distributions?"

description: Code and data to reproduce:<br>&gt; Dallas and Hastings 2018. "When can competition and dispersal lead to checkerboard distributions?" Journal of Animal Ecology<br><br>
DOI: 10.6084/m9.figshare.6839885
title: Hybridisation and detection of a hybrid zone between mesic and desert ragworts (<i>Senecio</i>) across an aridity gradient in the eastern Mediterranean

description: <b>Background</b>: Hybrid zones provide excellent opportunities for studying plant adaptation and speciation. <b>Aims</b>: We tested whether two herbaceous species of <i>Senecio, S. vernalis</i> and <i>S. glaucus</i>, hybridise in the eastern Mediterranean region and form a hybrid zone across an aridity gradient in the Jordan Rift Valley. <b>Methods</b>: Allozyme variation surveyed across both species was analysed by the programme STRUCTURE to assign individuals to genetic groups and determine levels of admixture. Populations in the Jordan Rift Valley were subsequently subjected to a cline analysis. <b>Results</b>: STRUCTURE showed that interspecific hybrids were produced at low frequency along the Israeli coastal plain where <i>S. glaucus</i> is represented by ssp. <i>glaucus</i>. In contrast, hybrids were more commonly produced in central populations of the Jordan Rift Valley. Here, the two species form a hybrid zone with <i>S. vernalis</i> occurring in mesic sites to the north and <i>S. glaucus</i> (ssp. <i>coronopifolius</i>) in arid sites to the south. Cline analysis showed that the hybrid zone is centred towards the northern end of the Dead Sea, but the analysis failed to distinguish how it is maintained. <b>Conclusions</b>: Future detailed genetic and ecological analysis of the <i>Senecio</i> hybrid zone should improve our understanding of plant adaptation and speciation across aridity gradients.
DOI: 10.6084/m9.figshare.6839885.v1
title: Hybridisation and detection of a hybrid zone between mesic and desert ragworts (<i>Senecio</i>) across an aridity gradient in the eastern Mediterranean

description: <b>Background</b>: Hybrid zones provide excellent opportunities for studying plant adaptation and speciation. <b>Aims</b>: We tested whether two herbaceous species of <i>Senecio, S. vernalis</i> and <i>S. glaucus</i>, hybridise in the eastern Mediterranean region and form a hybrid zone across an aridity gradient in the Jordan Rift Valley. <b>Methods</b>: Allozyme variation surveyed across both species was analysed by the programme STRUCTURE to assign individuals to genetic groups and determine levels of admixture. Populations in the Jordan Rift Valley were subsequently subjected to a cline analysis. <b>Results</b>: STRUCTURE showed that interspecific hybrids were produced at low frequency along the Israeli coastal plain where <i>S. glaucus</i> is represented by ssp. <i>glaucus</i>. In contrast, hybrids were more commonly produced in central populations of the Jordan Rift Valley. Here, the two species form a hybrid zone with <i>S. vernalis</i> occurring in mesic sites to the north and <i>S. glaucus</i> (ssp. <i>coronopifolius</i>) in arid sites to the south. Cline analysis showed that the hybrid zone is centred towards the northern end of the Dead Sea, but the analysis failed to distinguish how it is maintained. <b>Conclusions</b>: Future detailed genetic and ecological analysis of the <i>Senecio</i> hybrid zone should improve our understanding of plant adaptation and speciation across aridity gradients.