cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4772134
title: Supplementary Material for: Inactivation of Macrophage Rab7 by Burkholderia cenocepacia

description: Strains of the <i>Burkholderia cepacia </i>complex can survive within macrophages by arresting the maturation of phagocytic vacuoles. The bacteria preclude fusion of the phagosome with lysosomes by a process that is poorly understood. Using murine macrophages, we investigated the stage at which maturation is arrested and analyzed the underlying mechanism. Vacuoles containing <i>B. cenocepacia </i>strain J2315, an isolate of the transmissible ET12 clone, recruited Rab5 and synthesized phosphatidylinositol-3-phosphate, indicating progression to the early phagosomal stage. Despite the fact that the <i>B. cenocepacia</i>-containing vacuoles rarely fused with lysosomes, they could nevertheless acquire the late phagosomal markers CD63 and Rab7. Fluorescence recovery after photobleaching and use of a probe that detects Rab7-guanosine triphosphate indicated that activation of Rab7 was impaired by <i>B. cenocepacia, </i>accounting at least in part for the inability of the vacuole to merge with lysosomes. The Rab7 defect was not due to excessive cholesterol accumulation and was confined to the infected vacuoles. Jointly, these experiments indicate that <i>B. cenocepacia </i>express virulence factors capable of interfering with Rab7 function and thereby with membrane traffic.
DOI: 10.6084/m9.figshare.4772164.v1
title: Internet data sources for disease surveillance: Assessment of suitability

description: This assessment evaluates 34 internet activity data sources for use in disease surveillance. Our goals are to (a) understand the available data on internet usage and activity well enough to (b) identify real-world internet data sources that can be used both for evaluating our theories of disease surveillance and building<br>operational internet data-based disease surveillance systems.<br><br>The assessment (pdf) and raw data (excel spreadsheet) are attached.<br>
DOI: 10.6084/m9.figshare.4772158.v1
title: Supplementary Material for: Early Diagnosis of Intra-Abdominal Inflammation and Sepsis by Neutrophil CD64 Expression in Newborns

description: <i>Background:</i> Newborn infants with intra-abdominal inflammation/sepsis often present with nonspecific signs in the early stages of the disease, but can rapidly develop life-threatening complications. A reliable ‘early’ biomarker would be invaluable. <i>Objective:</i> To evaluate the effectiveness of neutrophil CD64 as an ‘early’ biomarker of intra-abdominal inflammation/sepsis. <i>Methods:</i> Blood was collected from newborns with suspected intra-abdominal pathology for neutrophil CD64 and C-reactive protein (CRP) determination at the onset of clinical presentation and 24 h later. They were classified into three groups: intra-abdominal inflammation/sepsis (group 1), extra-abdominal sepsis (group 2) and nonsepsis (group 3). Between-group comparisons were made by Kruskal-Wallis and χ<sup>2</sup> tests. Receiver-operating characteristic curves and diagnostic utilities for single and combination of tests were determined. <i>Results:</i> 310 infants were recruited (102, 34 and 174 in groups 1, 2 and 3, respectively). CD64 (conventional cutoff = 6,010 antibody-PE molecules bound/cell) had substantially better sensitivity (0.81 vs. 0.56) and negative predictive value (0.90 vs. 0.79) for diagnosing intra-abdominal sepsis than CRP, at presentation. Pairing CD64 with routine abdominal radiograph (AXR) substantially increased the sensitivity and negative predictive value for group 1 to 0.99 and 0.99, respectively. By adjusting the CD64 cutoff to 12,500 units, a substantial improvement in specificity could be achieved (0.62 to 0.80) without significantly compromising sensitivity (0.99 to 0.97). <i>Conclusions:</i> CD64 is a sensitive and ‘early’ biomarker for diagnosing intra-abdominal inflammation/sepsis. Intra-abdominal catastrophes, including necrotizing enterocolitis, intestinal necrosis, perforation and peritonitis can confidently be excluded using CD64 and AXR early in the course of the disease.
DOI: 10.6084/m9.figshare.4771579
title: Supplementary Material for: Ccm1 Regulates Microvascular Morphogenesis during Angiogenesis

description: Cerebral cavernous malformations (CCMs) are characterized by abnormally dilated intracranial capillaries that have a propensity to bleed. The development of some CCMs in humans has been attributed to mutations in CCM1 and CCM2 genes. In animal models, major cardiovascular defects caused by both gene mutations have been observed. However, the effects of the loss of Ccm function on the microvasculature in animal models are less defined. Using high-resolution imaging in vivo, we demonstrated that the loss of Ccm1 in zebrafish embryos leads to failed microvascular lumenization during angiogenesis due to impaired intraendothelial vacuole formation and fusion. No developmental changes during vasculogenesis and the initial stage of angiogenesis were observed, being in contrast to prior reports. In vivo zebrafish studies were further substantiated by in vitro findings in human endothelial cells that elucidated the biochemical pathways of CCM1 deficiency. We found that CCM1 regulates angiogenic microvascular lumen formation through Rac1 small GTPase. In summary, Ccm1 has been identified as a key angiogenic modulator in microvascular tubulogenesis. Additionally, the microvascular pathology observed in developing Ccm1 mutant zebrafish embryos mirrors that seen in human CCM lesions, suggesting that zebrafish might provide a superior animal model to study the pathogenesis of human CCM.
DOI: 10.6084/m9.figshare.4772131.v1
title: Equine cartilage secretome 5 days IL-1 treatment in vitro;'Neopeptide Analyser' output files

description: Neopeptide Analyser output files.<br>Experiment n=8 equine metacarpophalangeal cartilage explants from grossly normal joints treated in vitro with 10ng/ml IL-1 for 5 days. Secretome samples collected and pooled for 5 days. Media samples tryspin digested and run on an Orbitrap-Velos mass spectrometer. Raw files input into Progenesis QIP and label-free quantification undertaken with Mascot used to search for semi-tryptic peptides. Peptide measurements output file from ProgenesisQIP is then used as the input file into the 'Neopeptide Analyser' for neopeptide identification. The files here are the output files from the 'Neopeptide Analyser'. They are suffixed _filter and _processed.
DOI: 10.6084/m9.figshare.4771195
title: Supplementary Material for: Basophil CD203c Levels Are Increased at Baseline and Can Be Used to Monitor Omalizumab Treatment in Subjects with Nut Allergy

description: <i>Rationale:</i> Basophils contribute to anaphylaxis and allergies. We examined the utility of assessing basophil-associated surface antigens (CD11b/CD63/CD123/CD203c/CD294) in characterizing and monitoring subjects with nut allergy. <i>Methods:</i> We used flow cytometry to analyze basophils at baseline (without any activation) and after ex vivo stimulation of whole blood by addition of nut or other allergens for 2, 10, and 30 min. We also evaluated whether basophil expression of CD11b/CD63/CD123/CD203c/CD294 was altered in subjects treated with anti-IgE monoclonal antibody (omalizumab) to reduce plasma levels of IgE. <i>Results:</i> We demonstrate that basophil CD203c levels are increased at baseline in subjects with nut allergy compared to healthy controls (13 subjects in each group, p &lt; 0.0001). Furthermore, we confirm that significantly increased expression of CD203c occurs on subject basophils when stimulated with the allergen to which the subject is sensitive and can be detected rapidly (10 min of stimulation, n = 11, p &lt; 0.0008). In 5 subjects with severe peanut allergy, basophil CD203c expression following stimulation with peanut allergen was significantly decreased (p &lt; 0.05) after 4 and 8 weeks of omalizumab treatment but returned toward pretreatment levels after treatment cessation. <i>Conclusions:</i> Subjects with nut allergy show an increase of basophil CD203c levels at baseline and following rapid ex vivo stimulation with nut allergen. Both can be reduced by omalizumab therapy. These results highlight the potential of using basophil CD203c levels for baseline diagnosis and therapeutic monitoring in subjects with nut allergy.
DOI: 10.6084/m9.figshare.4772134.v1
title: Supplementary Material for: Inactivation of Macrophage Rab7 by Burkholderia cenocepacia

description: Strains of the <i>Burkholderia cepacia </i>complex can survive within macrophages by arresting the maturation of phagocytic vacuoles. The bacteria preclude fusion of the phagosome with lysosomes by a process that is poorly understood. Using murine macrophages, we investigated the stage at which maturation is arrested and analyzed the underlying mechanism. Vacuoles containing <i>B. cenocepacia </i>strain J2315, an isolate of the transmissible ET12 clone, recruited Rab5 and synthesized phosphatidylinositol-3-phosphate, indicating progression to the early phagosomal stage. Despite the fact that the <i>B. cenocepacia</i>-containing vacuoles rarely fused with lysosomes, they could nevertheless acquire the late phagosomal markers CD63 and Rab7. Fluorescence recovery after photobleaching and use of a probe that detects Rab7-guanosine triphosphate indicated that activation of Rab7 was impaired by <i>B. cenocepacia, </i>accounting at least in part for the inability of the vacuole to merge with lysosomes. The Rab7 defect was not due to excessive cholesterol accumulation and was confined to the infected vacuoles. Jointly, these experiments indicate that <i>B. cenocepacia </i>express virulence factors capable of interfering with Rab7 function and thereby with membrane traffic.
DOI: 10.6084/m9.figshare.4771195.v1
title: Supplementary Material for: Basophil CD203c Levels Are Increased at Baseline and Can Be Used to Monitor Omalizumab Treatment in Subjects with Nut Allergy

description: <i>Rationale:</i> Basophils contribute to anaphylaxis and allergies. We examined the utility of assessing basophil-associated surface antigens (CD11b/CD63/CD123/CD203c/CD294) in characterizing and monitoring subjects with nut allergy. <i>Methods:</i> We used flow cytometry to analyze basophils at baseline (without any activation) and after ex vivo stimulation of whole blood by addition of nut or other allergens for 2, 10, and 30 min. We also evaluated whether basophil expression of CD11b/CD63/CD123/CD203c/CD294 was altered in subjects treated with anti-IgE monoclonal antibody (omalizumab) to reduce plasma levels of IgE. <i>Results:</i> We demonstrate that basophil CD203c levels are increased at baseline in subjects with nut allergy compared to healthy controls (13 subjects in each group, p &lt; 0.0001). Furthermore, we confirm that significantly increased expression of CD203c occurs on subject basophils when stimulated with the allergen to which the subject is sensitive and can be detected rapidly (10 min of stimulation, n = 11, p &lt; 0.0008). In 5 subjects with severe peanut allergy, basophil CD203c expression following stimulation with peanut allergen was significantly decreased (p &lt; 0.05) after 4 and 8 weeks of omalizumab treatment but returned toward pretreatment levels after treatment cessation. <i>Conclusions:</i> Subjects with nut allergy show an increase of basophil CD203c levels at baseline and following rapid ex vivo stimulation with nut allergen. Both can be reduced by omalizumab therapy. These results highlight the potential of using basophil CD203c levels for baseline diagnosis and therapeutic monitoring in subjects with nut allergy.
DOI: 10.6073/pasta/473f3e62307895ad29fbe6a04e65dd66
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 1 meteorological station: Daily summary data: 2013 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-1 met station. Air temperature, relative humidity, wind speed and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.4771579.v1
title: Supplementary Material for: Ccm1 Regulates Microvascular Morphogenesis during Angiogenesis

description: Cerebral cavernous malformations (CCMs) are characterized by abnormally dilated intracranial capillaries that have a propensity to bleed. The development of some CCMs in humans has been attributed to mutations in CCM1 and CCM2 genes. In animal models, major cardiovascular defects caused by both gene mutations have been observed. However, the effects of the loss of Ccm function on the microvasculature in animal models are less defined. Using high-resolution imaging in vivo, we demonstrated that the loss of Ccm1 in zebrafish embryos leads to failed microvascular lumenization during angiogenesis due to impaired intraendothelial vacuole formation and fusion. No developmental changes during vasculogenesis and the initial stage of angiogenesis were observed, being in contrast to prior reports. In vivo zebrafish studies were further substantiated by in vitro findings in human endothelial cells that elucidated the biochemical pathways of CCM1 deficiency. We found that CCM1 regulates angiogenic microvascular lumen formation through Rac1 small GTPase. In summary, Ccm1 has been identified as a key angiogenic modulator in microvascular tubulogenesis. Additionally, the microvascular pathology observed in developing Ccm1 mutant zebrafish embryos mirrors that seen in human CCM lesions, suggesting that zebrafish might provide a superior animal model to study the pathogenesis of human CCM.
DOI: 10.6084/m9.figshare.4770412
title: Supplementary Material for: Linkage Analysis of Autopsy-Confirmed Familial Alzheimer Disease Supports an Alzheimer Disease Locus in 8q24

description: <i>Background/Aims:</i> We have previously reported the results of an extended genome-wide scan of Swedish Alzheimer disease (AD)-affected families; in this paper, we analyzed a subset of these families with autopsy-confirmed AD. <i>Methods:</i> We report the fine-mapping, using both microsatellite markers and single-nucleotide polymorphisms (SNPs), in the observed maximum logarithm of the odds (LOD)-2 unit (LOD<sub>max</sub>-2) region under the identified linkage peak, linkage analysis of the fine-mapping data with additionally analyzed pedigrees, and association analysis of SNPs selected from candidate genes in the linked interval. The subset was made on the criterion of at least one autopsy-confirmed AD case per family, resulting in 24 families. <i>Results:</i> Linkage analysis of a family subset having at least one autopsy-confirmed AD case showed a significant nonparametric single-point LOD score of 4.4 in 8q24. Fine-mapping under the linkage peak with 10 microsatellite markers yielded an increase in the multipoint (mpt) LOD score from 2.1 to 3.0. SNP genotyping was performed on 21 selected candidate transcripts of the LOD<sub>max</sub>-2 region. Both family-based association and linkage analysis were performed on extended material from 30 families, resulting in a suggestive linkage at peak marker rs6577853 (mpt LOD score = 2.4). <i>Conclusion:</i> The 8q24 region has been implicated to be involved in AD etiology.
DOI: 10.6084/m9.figshare.4772086.v2
title: Water depletion and curves around roots and soil

description: To the left of the root, water is depleted from films around soil particles where pore space water is first pulled from large pore spaces and water in thin films is strong adsorbed to the soil particles and scarcely available to the plant. Mucilage helps stabilize the water gradient as it has been observed water content can increase near the root surface when mucilage is available. Water curves on right side show the water content in soil near the root surface without (top) and with (bottom) mucilage.
DOI: 10.6084/m9.figshare.4769848
title: PowerPoint Slides for: Fistula and Survival Outcomes after Fistula Creation among Predialysis Chronic Kidney Disease Stage 5 Patients

description: <b><i>Background:</i></b> Most guidelines recommend the creation of arteriovenous fistula (AVF) in patients with chronic kidney disease (CKD) stage 4. However, an increasing number of studies suggest that early AVF creation leads to high rates of AVF failure and death before dialysis commencement. Only the Japanese guideline recommends AVF creation at CKD stage 5; however, no data are available regarding access-related outcomes at this stage. <b><i>Method:</i></b> This was a multicenter cohort study involving Japanese CKD stage 5 patients who underwent preemptive AVF creation from 2009 to 2013. The primary outcome was unnecessary AVF creation, defined as death before requiring dialysis or AVF failure before dialysis commencement. The secondary outcome was dialysis commencement. The associations with candidate predictors and the outcomes were examined. <b><i>Results:</i></b> A total of 303 patients were registered. Four cases of death before dialysis and 13 cases of AVF failure before dialysis commencement were observed. A total of 283 patients who advanced to dialysis were found to have functional AVFs. The cumulative incidences of unnecessary AVF creation and dialysis commencement at 1 year were 4.8 and 89.3%, respectively. Competing risk regression analyses showed that age ≥75 years (subhazard ratio [SHR] 3.12, 95% CI 1.20-8.09) and female gender (SHR 3.31, 95% CI 1.20-9.09) were associated with unnecessary AVF creation. <b><i>Conclusions:</i></b> A low incidence of unnecessary AVF creation was revealed among Japanese patients who received AVF at CKD stage 5. These results may help clarify the natural history of unnecessary AVF creation for other countries reformatting their guidelines regarding late vascular access creation.
DOI: 10.6084/m9.figshare.4772086.v3
title: Water depletion and curves around roots and soil

description: To the left of the root, water is depleted from films around soil particles where pore space water is first pulled from large pore spaces and water in thin films is strong adsorbed to the soil particles and scarcely available to the plant. Mucilage helps stabilize the water gradient as it has been observed water content can increase near the root surface when mucilage is available. Water curves on right side show the water content in soil near the root surface without (top) and with (bottom) mucilage.
DOI: 10.6084/m9.figshare.4769815
title: Number of users at Academia.edu and ResearchGate

description: Chart showing the number of registered users over time for the academic social networking sites Academia.edu (pink) and ResearchGate (blue). Also accompanied by a spreadsheet which includes the data and links to the sources for each data point. Data collected March 2017.
DOI: 10.6084/m9.figshare.4769815.v1
title: Number of users at Academia.edu and ResearchGate

description: Chart showing the number of registered users over time for the academic social networking sites Academia.edu (pink) and ResearchGate (blue). Also accompanied by a spreadsheet which includes the data and links to the sources for each data point. Data collected March 2017.
DOI: 10.6084/m9.figshare.4769752
title: Conflict and Cooperation in Paranoia: A Large-Scale Behavioural Experiment

description: Data and R code to reproduce analyses. <br>
DOI: 10.6084/m9.figshare.4769791
title: numpy-stl

description: Simple library to make working with STL files (and 3D objects in general) fast and easy.
DOI: 10.6084/m9.figshare.4769752.v1
title: Conflict and Cooperation in Paranoia: A Large-Scale Behavioural Experiment

description: Data and R code to reproduce analyses. <br>
DOI: 10.6084/m9.figshare.4769746
title: Equine cartilage secretome 5 days IL-1 treatment in vitro; Progenesis semi tryptic peptides measurements file for input into the Neopeptide Analyser

description: Progenesis semitryptic peptide file for use as input into Neopeptide Analyser.<br>Experiment n=8 equine metacarpophalangeal cartilage explants from grossly normal joints treated in vitro with 10ng/ml IL-1 for 5 days. Secretome samples collected and pooled for 5 days. Media samples trypsin digested and run on an Orbitrap-Velos mass spectrometer. Raw files input into Progenesis QIP and label-free quantification undertaken with Mascot used to search for semi-tryptic peptides. Peptide measurements output file from ProgenesisQIP is then used as the input file into the 'Neopeptide Analyser' for neopeptide identification. Progenesis QIP peptide measurements file is for input into Neopeptide App for neopeptide identification.
DOI: 10.6084/m9.figshare.4769662
title: Measured heave natural period of the bottom cylinder from Wave energy absorption by a submerged air bag connected to a rigid float

description: Measured heave natural period of the bottom cylinder
DOI: 10.6084/m9.figshare.4769656
title: Measured device responses in regular incident waves from Wave energy absorption by a submerged air bag connected to a rigid float

description: Measured device responses in regular incident waves
DOI: 10.6084/m9.figshare.4769662.v1
title: Measured heave natural period of the bottom cylinder from Wave energy absorption by a submerged air bag connected to a rigid float

description: Measured heave natural period of the bottom cylinder
DOI: 10.6084/m9.figshare.4769656.v1
title: Measured device responses in regular incident waves from Wave energy absorption by a submerged air bag connected to a rigid float

description: Measured device responses in regular incident waves
DOI: 10.6084/m9.figshare.4769638
title: Hydraulic conductivity of bedding-parallel cracks in shale as a function of shear and normal stress

description: A CSV file containing all experimental conditions and tabulations of results