cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9699071.v1
title: Supplementary Material for: Changes in Cytokines, Haemodynamics and Microcirculation in Patients with Sepsis/Septic Shock Undergoing Continuous Renal Replacement Therapy and Blood Purification with CytoSorb

description: <b><i>Background:</i></b> Extracorporeal blood purification therapies have been proposed as a strategy to remove inflammatory mediators during sepsis, thus improving outcome. <b><i>Objectives:</i></b> We aimed to evaluate changes in cytokines, haemodynamics and microcirculation during blood purification with Cytosorb adsorber in septic patients. <b><i>Methods:</i></b> Prospective observational study on critically ill adult patients with sepsis/septic shock underwent renal replacement therapy (RRT) for acute renal failure and haemoadsorption with Cytosorb as adjunctive therapy for 24 h. Measurements were taken at baseline, after 6 and 24 h: haemodynamic parameters, arterial and central venous blood gases, plasma levels of tumour necrosis factor alpha, interleukin (IL) 1-beta, IL-6, IL-8 and IL-10. The sublingual microcirculation was assessed with sidestream dark field videomicroscopy to evaluate the perfused vessel density (PVD) and microvascular flow quality. Tissue oxygenation and microvascular reactivity were assessed with thenar near infrared spectroscopy (NIRS) with a vascular occlusion test. <b><i>Results:</i></b> Nine patients; plasma levels of IL-8 decreased at 24 h (<i>p</i> &lt; 0.05 versus 6 h); no significant variation was found for other cytokines. Haemodynamic remained stable throughout the observation. Microvascular perfusion improved over time, with an increase in PVDs at 6 and 24 h (from 13.9 [13.3–16.4] to 15.7 [15–17.3] and 17 [14.8–18.6] mm/mm<sup>2</sup> respectively, <i>p</i> = 0.003) and total vessel densities at 24 h (14.9 [13.9–16.9] vs. 17.9 [15.3–20], <i>p</i> = 0.0015). No significant variation was detected in NIRS-derived parameters. The Sequential Organ Failure Assessment score decreased from 12 ± 3 to 10 ± 1 at 24 h (<i>p</i> = 0.039). <b><i>Conclusions:</i></b> In septic patients undergoing RRT, haemoadsorption with Cytosorb seems to determine a decreasing in plasma levels of IL-8, although levels of other cytokines did not vary significantly, and an improvement of microcirculation despite no significant variation in macro-haemodynamics.
DOI: 10.6084/m9.figshare.13125026.v1
title: Frist 64 complete and high quality SARS-CoV-2 sequences reported from Bangladesh

description: Initial 64 SARS-CoV-2 sequences submitted from Bangladesh
DOI: 10.6084/m9.figshare.7764023.v2
title: fluorescence data

description: there are two zip files. fluorescence source data.zipStored the source images and PSFs in the experiments<br>Evaluation_and_image_sequence.zip Stored the reconstructed images submitted for the inspection by biologists. Zoomed-in images by our boost-decon and the comparative methods (Huygens,TBV-PB,RLTV, WPL,PURELET) were sent to biologists with info about their processing methods removed for visual inspection. The excel tables are the recorded acceptance rate and quality score for each image by the biologists. Each excel file is from one biologist only.<br>
DOI: 10.6084/m9.figshare.9876467.v3
title: Facial segment assignments

description: The facial segment mat file contains the level and cluster assignment for each of the facial segments ('info') as well as the level and cluster assignment for each of the 7,160 vertices, which can be used to visualize the facial segments ('label'). <br>
DOI: 10.6084/m9.figshare.26928172.v1
title: Eddy detection and Tracking techniques

description: Eddy detection and tracking for surface and subsurface eddies, modified for the Peru-Chile EBUS from Nagai et.al. 2015
DOI: 10.6084/m9.figshare.28204511.v1
title: Food Biophysics sensory excel.xlsx

description: Data are raw values obtained from assessment of the effects of varying quantities and sizes of bird-eye pepper on nutrient composition, sensory profile and shelf stability of meat of broiler chickens
DOI: 10.6084/m9.figshare.27242604.v2
title: Significant NO2 Formation in Truck Exhaust Plumes and Its Association with Ambient O3: Evidence from Extensive Plume-chasing Measurements

description: This dataset includes two main sections: Quality Control and Supplemental Data. It includes five types of data: sampling time, pollutant concentrations, emission factors, meteorological conditions, and characteristics of test vehicles.
DOI: 10.6084/m9.figshare.26866831.v1
title: Temperature-dependence of regional heterothermy in a diminutive ectotherm

description: Dataset describing variation in temperature between the head and the cloaca for ringnecked snakes (Diadophis punctatus) in the laboratory and in the field. SnakeID= unique ID assigned to each snake. CollectionDate= the date that snakes were collected and when field body temperatures were measured. Gravid=whether eggs were palpated in the abdomen of snakes, where 1=gravid and 0= not gravid. Ecdysis=whether snakes were close to the time when they would shed, assessed by the presence of opaque eye scales and shedding skin, where 1=ecdydic and 0=non-edcydic. Life stage= whether snakes were juveniles or adults, where A=adult and J=juvenile. SVL_mm=snout-vent length in mm. Mass_g=body mass in g. Scars=the presence of any visually detectable scars on the body, where 1= presence of scars and 0= no scars. Handling_time= the duration between capture and measurement of body temperature. Field_mouth= the temperature of the mouth as measured immediately after capture in the field. Field_cloaca=the temperature of the cloaca as measured immediately after capture in the field. 15_head= the temperature of the head measured after 1 h in an incubator at 15 degrees Celsius. 15_cloaca=the temperature of the cloaca after 1 h in an incubator at 15 degrees Celsius. 20_head= the temperature of the head measured after 1 h in an incubator at 20 degrees Celsius. 20_cloaca=the temperature of the cloaca after 1 h in an incubator at 20 degrees Celsius. 25_head= the temperature of the head measured after 1 h in an incubator at 25 degrees Celsius. 25_cloaca=the temperature of the cloaca after 1 h in an incubator at 25 degrees Celsius. 30_head= the temperature of the head measured after 1 h in an incubator at 30 degrees Celsius. 30_cloaca=the temperature of the cloaca after 1 h in an incubator at 30 degrees Celsius. 32_head= the temperature of the head measured after 1 h in an incubator at 32 degrees Celsius. 32_cloaca=the temperature of the cloaca after 1 h in an incubator at 32 degrees Celsius.
DOI: 10.6084/m9.figshare.7831964.v1
title: Supplementary Material for: Genetic Variant Screening of DNA Repair Genes in Myelodysplastic Syndrome Identifies a Novel Mutation in the <b><i>XRCC2</i></b> Gene

description: <b><i>Background:</i></b> We aimed to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with myelodysplastic syndrome (MDS). <b><i>Methods:</i></b> Targeted enrichment resequencing of 84 DNA repair genes was initially performed on a screening cohort of MDS patients. Real-time polymerase chain reaction was used for genotyping selected SNPs in the validation cohort of patients. <b><i>Results:</i></b> A heterozygous frameshift mutation in the <i>XRCC2</i> gene was identified. It leads to the formation of a truncated non-functional protein and decreased <i>XRCC2</i> expression level. Decreased expression levels of all DNA repair genes functionally connected with mutated <i>XRCC2</i> were also present. Moreover, a synonymous substitution in the <i>PRKDC</i> gene<i></i> and 2 missense mutations in the <i>SMUG1</i> and <i>XRCC1</i> genes were also found. In the screening cohort, 6 candidate SNPs were associated with the tendency to develop MDS: rs4135113 (TDG, p = 0.03), rs12917 (MGMT, p = 0.003), rs2230641 (CCNH, p = 0.01), rs2228529 and rs2228526 (ERCC6, p = 0.04 and p = 0.03), and rs1799977 (MLH1, p = 0.04). In the validation cohort, only a polymorphism in <i>MLH1</i> was significantly associated with development of MDS in patients with poor cytogenetics (p = 0.0004). <b><i>Conclusion:</i></b> Our study demonstrates that genetic variants are present in DNA repair genes of MDS patients and may be associated with susceptibility to MDS.
DOI: 10.6084/m9.figshare.24901452.v1
title: 参考文献 1.rar

description: 参考“<b>钨电子束粉末床熔融中粉末床与熔化区域之间的分层孔隙缺陷和累积效应</b>”。
DOI: 10.6084/m9.figshare.14054057.v1
title: Supplementary Material for: Metformin Inhibits Abdominal Aortic Aneurysm Formation through the Activation of the AMPK/mTOR Signaling Pathway

description: <b><i>Background and Objective:</i></b> Epidemiological evidence suggests that the antidiabetic drug metformin (MET) can also inhibit abdominal aortic aneurysm (AAA) formation. However, the underlying protective mechanism remains unknown. It has been reported that phosphorylated AMP-activated protein kinase (AMPK) levels are significantly lower in AAA tissues than control aortic tissues. AMPK activation can inhibit the downstream signaling molecule called mechanistic target of rapamycin (mTOR), which has also been reported be upregulated in thoracic aneurysms. Thus, blocking mTOR signaling could attenuate AAA progression. MET is a known agonist of AMPK. Therefore, in this study, we investigated if MET could inhibit formation of AAA by activating the AMPK/mTOR signaling pathway. <b><i>Materials and Methods:</i></b> The AAA animal model was induced by intraluminal porcine pancreatic elastase (PPE) perfusion in male Sprague Dawley rats. The rats were treated with MET or compound C (C.C), which is an AMPK inhibitor. AAA formation was monitored by serial ultrasound. Aortas were collected 4 weeks after surgery and subjected to immunohistochemistry, Western blot, and transmission electron microscopy analyses. <b><i>Results:</i></b> MET treatment dramatically inhibited the formation of AAA 4 weeks after PPE perfusion. MET reduced the aortic diameter, downregulated both macrophage infiltration and matrix metalloproteinase expression, decreased neovascularization, and preserved the contractile phenotype of the aortic vascular smooth muscle cells. Furthermore, we detected an increase in autophagy after MET treatment. All of these effects were reversed by the AMPK inhibitor C.C. <b><i>Conclusion:</i></b> This study demonstrated that MET activates AMPK and suppresses AAA formation. Our study provides a novel mechanism for MET and suggests that MET could be potentially used as a therapeutic candidate for preventing AAA.
DOI: 10.6084/m9.figshare.22735106.v2
title: Rehearsal_012022.csv

description: Data set in CSV file of the Rehearsal from 01/20/22
DOI: 10.6084/m9.figshare.5816433.v1
title: A Brazilian-Portuguese version of the Kinesthetic and Visual Motor Imagery Questionnaire

description: ABSTRACT Motor imagery has emerged as a potential rehabilitation tool in stroke. The goals of this study were: 1) to develop a translated and culturally-adapted Brazilian-Portugese version of the Kinesthetic and Visual Motor Imagery Questionnaire (KVIQ20-P); 2) to evaluate the psychometric characteristics of the scale in a group of patients with stroke and in an age-matched control group; 3) to compare the KVIQ20 performance between the two groups. Methods Test-retest, inter-rater reliabilities, and internal consistencies were evaluated in 40 patients with stroke and 31 healthy participants. Results In the stroke group, ICC confidence intervals showed excellent test-retest and inter-rater reliabilities. Cronbach’s alpha also indicated excellent internal consistency. Results for controls were comparable to those obtained in persons with stroke. Conclusions The excellent psychometric properties of the KVIQ20-P should be considered during the design of studies of motor imagery interventions for stroke rehabilitation.
DOI: 10.6084/m9.figshare.12993479.v1
title: Supplementary Material for: Characterization of Clinical Cases of Malignant PEComa via Comprehensive Genomic Profiling of DNA and RNA

description: <b><i>Purpose:</i></b> Perivascular epithelioid cell tumor (PEComa) is a rare mesenchymal soft tissue neoplasm often linked to mTOR pathway activation via TSC2 mutation. We analyzed a series of 31 consecutive metastatic PEComa (mPEComa) cases using a combined DNA/RNA hybrid capture-based comprehensive genomic profiling (CGP) assay to assess the genomic landscape of mPEComa. <b><i>Patients and Methods:</i></b> Formalin-fixed, paraffin-embedded (FFPE) blocks or slides were obtained from tumors from 31 unique patients with mPEC­oma. DNA and RNA were extracted and CGP was performed on 405 genes using a targeted next-generation sequencing (NGS) assay in a CLIA-certified lab. <b><i>Results:</i></b> All cases had locally advanced or metastatic disease, and 58% of patients were female with a median age of 50 years (range 8–76), and 17 and 14 specimens were from primary and metastatic sites, respectively. One hundred genomic alterations were identified in the cohort, with an average of 3.2 genomic alterations/case including alterations in <i>TSC2</i> 32.3% of cases (10), <i>TSC1</i> 9.6% (3), <i>TFE3</i> 16.1% (5, all fusions), and folliculin (<i>FLCN</i>) 6.4% (2), with all occurring in mutually exclusive fashion. Of <i>TSC2</i> mutant cases, 70% had biallelic inactivation of this locus, as were 100% of <i>TSC1</i> mutant cases. Two <i>TSC1/2</i> wildtype cases harbored truncating mutations in <i>FLCN</i>, both of which were under LOH. Five <i>TFE3</i> fusion cases were identified including the novel 5′ fusion partner <i>ZC3H4</i>. <b><i>Conclusions:</i></b> We describe for the first time mPEComa cases with <i>FLCN</i> mutations under LOH, further characterizing dysregulation of the mTOR pathway as a unifying theme in mPEC­oma. Cumulatively, we demonstrate the feasibility and potential utility of segregating mPEComa by <i>TSC</i>, <i>TFE3</i>, and <i>FLCN</i> status via CGP in clinical care.
DOI: 10.6084/m9.figshare.20010485.v1
title: Convergence in phosphorus constraints to photosynthesis dataset

description: Data on photosynthesis and photosynthetic parameters of native trees at natural sites measured in the field. Photosynthesis data are from the Farquhar photosynthesis model (e.g., Vcmax, Jmax) using controlled photosynthetic responses to [CO2] for a set of 52 pan-tropical and subtropical sites across South America, Africa, Asia and Australia. Associated with each measurement is leaf N concentration and leaf P concentration as well as leaf mass per unit area. Farquhar photosynthesis model parameters Vcmax and Jmax were fit using the plantecophys package. Inlcuded in this dataset are data measured at tree-top from trees at 6 canopy crane sites. Further details about the measurements and data are in Ellsworth et al. (2022) Nature Communications.
DOI: 10.6084/m9.figshare.5127322.v1
title: Supplementary Material for: Unique Roles of TLR9- and MyD88-Dependent and -Independent Pathways in Adaptive Immune Responses to AAV-Mediated Gene Transfer

description: The immune system represents a significant barrier to successful gene therapy with adeno-associated viral (AAV) vectors. In particular, adaptive immune responses to the viral capsid or the transgene product are of concern. The sensing of AAV by toll-like receptors (TLRs) TLR2 and TLR9 has been suggested to play a role in innate immunity to the virus and may also shape subsequent adaptive immune responses. Here, we investigated the functions of TLR2, TLR9 and the downstream signaling adaptor MyD88 in antibody and CD8+ T-cell responses. Antibody formation against the transgene product occurred largely independently of TLR signaling following gene transfer with AAV1 or AAV2 vectors, whereas loss of signaling through the TLR9-MyD88 pathway substantially reduced CD8+ T-cell responses. In contrast, MyD88 (but neither of the TLRs) regulated antibody responses to capsid. B cell-intrinsic MyD88 was required for the formation of anti-capsid IgG2c independently of vector serotype or route of administration. However, MyD88<sup>-/-</sup> mice instead produced anti-capsid IgG1 that emerged with delayed kinetics but nonetheless completely prevented in vivo readministration. We conclude that there are distinct roles for TLR9 and MyD88 in promoting adaptive immune responses to AAV-mediated gene transfer and that there are redundant MyD88-dependent and MyD88-independent mechanisms that stimulate neutralizing antibody formation against AAV.
DOI: 10.60893/figshare.jcp.27207936.v1
title: Supplemetary material

description: Force field parameters, bending frequencies, continuous and intermittent lifetime correlation functions
DOI: 10.17632/y7w5j472ww
title: Characterization of multidrug-resistant hypervirulent ST367-KL1 Klebsiella quasipneumoniae subsp. similipneumoniae strain harbouring blaCTX-M-14 plasmid

description: Relevant data for the article: including plasmid homology comparisons, phenotyping data, and genome sequences for phylogenetic tree construction
DOI: 10.17632/y7w5j472ww.1
title: Characterization of multidrug-resistant hypervirulent ST367-KL1 Klebsiella quasipneumoniae subsp. similipneumoniae strain harbouring blaCTX-M-14 plasmid

description: Relevant data for the article: including plasmid homology comparisons, phenotyping data, and genome sequences for phylogenetic tree construction
DOI: 10.6084/m9.figshare.6634136.v1
title: Supplementary Material for: Development of a PD-L1-Expressing Orthotopic Liver Cancer Model: Implications for Immunotherapy for Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Anti-programmed cell death-1(anti-PD1) treatment has shown promising antitumor efficacy in patients with advanced hepatocellular carcinoma (HCC). This study sought to explore the functional significance of programmed death ligand-1 (PD-L1) expression in tumor cells in the tumor microenvironment. <b><i>Methods:</i></b> The mouse liver cancer cell line BNL-MEA was transfected with PD-L1 plasmids and stable clones expressing PD-L1 were selected. An orthotopic HCC model was generated by implanting the cells into the subcapsular space of BALB/c mice. Cell growth features were measured by proliferation assay, colony formation, flow cytometry (in vitro), ultrasonography, and animal survival (in vivo). The changes in T-cell function were examined by cytokine assay, expression of T-cell related genes, and flow cytometry. The efficacy of anti-PD1 therapy was compared between the parental and PD-L1-expressing tumors. <b><i>Results:</i></b> PD-L1 expression did not affect growth characteristics of BNL-MEA cells but downregulated the expression of genes related to T-cell activation in the tumor microenvironment. Co-culture of PD-L1-expressing BNL-MEA cells with CD8+ T cells reduced T-cell proliferation and expression of cytokines IFNγ and TNFα. Tumors with PD-L1 expression showed better response to anti-PD1 therapy and depletion of CD8+ T cells abolished the antitumor effect. The difference in treatment response between parental and PD-L1-expressing tumors disappeared when a combination of anti-PD1 and sorafenib was given. <b><i>Conclusions:</i></b> PD-L1 expression in HCC cells may inhibit T-cell function in the liver tumor microenvironment. Anti-PD1 therapy appeared more effective in PD-L1-expressing than nonexpressing tumors, but the difference was diminished by the addition of sorafenib.
DOI: 10.6084/m9.figshare.25285408.v1
title: Raw data for Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics"

description: Supplementary data repository for the study by Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics".This repository includes raw data used from the companion paper based on the Stiller et al. 2024 study (in press in Nature). The main analysis from this study is based on 63430 loci obtained from intergenic regions, maximum likelihood analysis, and coalescent-based species tree estimation, which are included in this repository. For more data analyses specific to this paper, please refer to https://zenodo.org/records/10699424Files and explanation of content:<br>* 63430.alignments.tar.gz Alignments in FASTA format for which gene trees were built* 63430.gene.trees.gz Gene trees in newick format with support as aLRT values.* 63430.aLRT-0.95-collapsed.gene.trees.gz 63430 gene trees after collapsing branches with aLRT values below 0.95. This file was used as input for ASTRAL analysis.* 63430.named.gene.trees.gz Gene trees, with 1st column is name of the underlying locus, 2nd column is tree in newick format in order to match gene trees to alignments.* 63430.aLRT-0.95-collapsed.gene.trees.gz* 63430.ASTRAL.species.tre Main species tree resulting from ASTRAL analysis.* 63430.timetree.tre The time calibrated species tree.
DOI: 10.4121/uuid:88ff16b7-73bd-4728-9f99-cd7408c23664
title: Parasuicide Pre and Post Intervention Data

description: The data set is for adolescents who had attempted suicide. The variables in the data set are hope, self esteem, resilience and suicidal behaviours. study implemented an intervention aimed at reducing repeat suicidal behaviours after a parasuicide. The study utilized a quantitative approach with a pre-post test design without a control group with five participants.
DOI: 10.6084/m9.figshare.20310924.v1
title: Environmental magnetic parameters of a sediment core in the tropical Western Pacific

description: This dataset provides the environmental magnetism, geochemical elements, and clay minerals of a sediment core (H10) in the tropical Western Pacific. The analysis on the dataset was submitted to <em>Paleogeography, Paleoclimatology, Paleoecology</em>, titled “Asian summer monsoon evolution during glacial cycles since MIS8: Evidence from environmental magnetic records of tropical Western Pacific sediment.”
DOI: 10.6084/m9.figshare.13379816.v2
title: The Middle Cumberland Region

description: The Middle Cumberland Region is a unique area of Mississippian period (ca. 1000-1500 CE) culture focused along the Cumberland River watershed of central Tennessee. This ArcGIS shapefile presents a polygon of the Middle Cumberland Region, based on archival research of both published and unpublished data on file at the Tennessee Division of Archaeology (Nashville, TN). The boundary is visualized in ArcMap 10.8.1 primarily using 10-digit Hydrologic Unit (HU-10) USGS Watershed Boundary data.