cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21679874
title: Supplementary Material for: Interference with Lipoprotein Maturation Sensitizes Methicillin-Resistant <b><i>Staphylococcus aureus</i></b> to Human Group IIA-Secreted Phospholipase A<sub>2</sub> and Daptomycin

description: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) has been classified as a high priority pathogen by the World Health Organization underlining the high demand for new therapeutics to treat infections. Human group IIA-secreted phospholipase A<sub>2</sub> (hGIIA) is among the most potent bactericidal proteins against Gram-positive bacteria, including <i>S. aureus</i>. To determine hGIIA-resistance mechanisms of MRSA, we screened the Nebraska Transposon Mutant Library using a sublethal concentration of recombinant hGIIA. We identified and confirmed the role of <i>lspA</i>, encoding the lipoprotein signal peptidase LspA, as a new hGIIA resistance gene in both in vitro assays and an infection model in hGIIA-transgenic mice. Increased susceptibility of the <i>lspA</i> mutant was associated with enhanced activity of hGIIA on the cell membrane. Moreover, <i>lspA</i> deletion increased susceptibility to daptomycin, a last-resort antibiotic to treat MRSA infections. MRSA wild type could be sensitized to hGIIA and daptomycin killing through exposure to LspA-specific inhibitors globomycin and myxovirescin A1. Analysis of &gt;26,000 <i>S. aureus</i> genomes showed that LspA is highly sequence-conserved, suggesting universal application of LspA inhibition. The role of LspA in hGIIA resistance was not restricted to MRSA since <i>Streptococcus mutans</i> and <i>Enterococcus faecalis</i> were also more hGIIA-susceptible after <i>lspA</i> deletion or LspA inhibition, respectively. Overall, our data suggest that pharmacological interference with LspA may disarm Gram-positive pathogens, including MRSA, to enhance clearance by innate host defense molecules and clinically applied antibiotics.
DOI: 10.6084/m9.figshare.21680105
title: Supplementary Material for: Effect of Fludrocortisone on Intradialytic Hypotension: An Open-Label, Randomized, Crossover Study

description: <b><i>Introduction:</i></b> Intradialytic hypotension (IDH) is an important complication during chronic hemodialysis due to its adverse cardiovascular and hemodialysis outcomes. Case reports have demonstrated that administration of fludrocortisone before undergoing hemodialysis might increase intradialytic blood pressure. This study is a randomized crossover study aiming to evaluate the intradialytic hemodynamic effects of fludrocortisone. <b><i>Material and Methods:</i></b> A randomized, controlled two-period crossover trial was conducted at Lampang Hospital in stable chronic hemodialysis patients who experienced IDH &gt;30% in their sessions during the past 3 months. All participants have randomly received a single dose of 0.2-mg fludrocortisone 30 min before each hemodialysis session, or had no treatment for 4 weeks. After a 2-week washout period, the participants were then switched to the other treatment for 4 weeks. The primary outcome was the mean lowest intradialytic mean arterial pressure (MAP) during the hemodialysis session. <b><i>Results:</i></b> A total of 17 patients were recruited with a mean age of 61.7 ± 14.8 years. By analysis of crossover design, the mean lowest intradialytic MAP was not different between receiving fludrocortisone or with no treatment (76.1 ± 12.5 vs. 73.9 ± 11.5 mm Hg, <i>p</i> for treatment effect = 0.331, <i>p</i> for period effect = 0.855, <i>p</i> for sequence effect = 0.870). There was no difference in the incidence of IDH between the two groups (34.4% in fludrocortisone vs. 42.7% in no treatment, <i>p</i> = 0.137). However, in diabetic patients and patients with residual kidney function, the incidence of IDH was significantly lower when receiving fludrocortisone (30.8 vs. 52.6%, <i>p</i> &lt; 0.001, and 27.6 vs. 74.3%, <i>p</i> &lt; 0.001, respectively). <b><i>Conclusions:</i></b> In chronic hemodialysis patients who had IDH, fludrocortisone administration did not improve intradialytic hemodynamics and did not decrease the incidence of IDH.
DOI: 10.6084/m9.figshare.21680219
title: Supplementary Material for: Serum Calciprotein Monomers and Chronic Kidney Disease Progression

description: <b><i>Introduction:</i></b> Elevated levels of fibroblast growth factor-23 (FGF23) in chronic kidney disease (CKD) are associated with progression of CKD. FGF23 inhibits proximal tubular phosphate reabsorption, raising phosphate concentrations in the tubular fluid of functioning nephrons, predisposing to spontaneous precipitation of calcium phosphate crystals and resultant tubular injury. Calciprotein monomers (CPM) form spontaneously in biological fluids when clusters of calcium phosphate ions are bound by the liver-derived glycoprotein fetuin-A. Serum CPM are elevated in CKD and are postulated to trigger FGF23 secretion. CPM are also readily filtered at the glomerulus into the tubular fluid, suggesting that higher CPM levels could be associated with progression of CKD via FGF23-mediated increased phosphate load but also through direct effects in the proximal tubule. <b><i>Methods:</i></b> ACADEMIC was a prospective observational study of 200 stable outpatients with CKD stages 3 and 4. Participants were followed until commencement of dialysis or death. In this study, we examined a sub-cohort of 189 participants who had baseline serum available for measurement of CPM. Cox proportionate hazard regression models were used to examine the association between CPM and a composite kidney disease outcome (commencement of dialysis or reduction in estimated glomerular filtration rate [eGFR] &gt;30%). Linear regression models were used to examine the association between CPM and annualized eGFR slope. <b><i>Results:</i></b> Relative to the lowest tertile, the highest tertile of CPM was associated with increased risk of the composite kidney disease outcome in univariate models and after sequential adjustment for conventional risk factors for progression of CKD (adjusted hazard ratio 4.22; 95% confidence interval [CI] 1.91, 9.33, <i>p</i> &lt; 0.001). Natural log-transformed CPM was also inversely associated with eGFR slope in univariate and multivariate adjusted models (adjusted β-coefficient −1.66, 95% CI: −3.10, −0.22, <i>p</i> = 0.024). In exploratory mediation analysis, the association between serum CPM and eGFR slope was partially mediated by iFGF23; however, the majority of the association was direct and independent of the iFGF23 pathway. <b><i>Conclusion:</i></b> Elevated levels of CPM are associated with the progression of CKD. This association was partially mediated via FGF23, consistent with recent evidence that FGF23 predisposes to spontaneous precipitation of calcium phosphate crystals leading to tubular injury. However, serum CPM also appeared to have a direct association with eGFR slope, raising the possibility that CPM may also be associated with progression of CKD through additional pathways.
DOI: 10.17632/vvtfdgfk76.1
title: A broad-spectrum antiviral molecule, protoporphyrin IX, acts as a moderator of HIV-1 capsid assembly by targeting the capsid hexamer

description: Information of drug library used and The results of drug screening.
DOI: 10.6084/m9.figshare.21069808
title: Supplementary Material for: Common Variants in Neuraminidase Genes Contribute to Predisposition to and Progression of Chronic Heart Failure

description: <b><i>Introduction:</i></b> The role of neuraminidases in cardiovascular disease has recently gained increasing attention. However, the association between neuraminidase gene polymorphisms and heart failure (HF) has not yet been investigated. <b><i>Methods and Results:</i></b> Genotyping of nine single-nucleotide polymorphisms (SNPs) in the NEU2/NEU3/NEU4 genes was performed in 610 HF patients and 600 healthy controls from the Southwest Han Chinese population using TaqMan SNP Genotyping Assay. Individuals carrying the A allele of rs11545301 had decreased risk of HF (additive model: OR = 0.704, 95% CI = 0.511–0.97; <i>p</i> = 0.032). However, the C allele of rs2293763 increased the risk of HF in the recessive model (OR = 1.486, 95% CI = 1.095–2.012; <i>p</i> = 0.011). Rs2233384, rs2233394, and rs2293763 were significantly associated with the mortality risk of HF in the dominant model, both with and without adjustment for conventional risk factors (HR = 0.686, 95% CI = 0.52–0.906, <i>p</i> = 0.008 for rs2233384, HR = 1.357, 95% CI = 1.035–1.78, <i>p</i> = 0.027 for rs2233384, and HR = 0.76, 95% CI = 0.592–0.975, <i>p</i> = 0.031 for rs2293763). <b><i>Conclusion:</i></b> Our findings demonstrated the association between a series of variants in NEU2/NEU4 genes and the risk or prognosis of HF in the Han Chinese population. These data suggested an important role of NEU2 and NEU4 in the pathogenesis of HF.
DOI: 10.5066/p9wbfr1t
title: Machine-learning model predictions and groundwater-quality rasters of specific conductance, total dissolved solids, and chloride in aquifers of the Mississippi embayment

description: Groundwater is a vital resource in the Mississippi embayment of the central United States. An innovative approach using machine learning (ML) was employed to predict groundwater salinity - including specific conductance (SC), total dissolved solids (TDS), and chloride (Cl) concentrations - across three drinking-water aquifers of the Mississippi embayment. A ML approach was used because it accommodates a large and diverse set of explanatory variables, does not assume monotonic relations between predictors and response data, and results can be extrapolated to areas of the aquifer not sampled. These aspects of ML allowed potential drivers and sources of high salinity water that have been hypothesized in other studies to be included as explanatory variables. The ML approach integrated output from a groundwater-flow model and water-quality data to predict salinity, and the approach can be applied to other aquifers to provide context for the long-term availability of groundwater resources.The Mississippi embayment includes two principal regional aquifer systems; the surficial aquifer system, dominated by the Quaternary Mississippi River Valley Alluvial aquifer (MRVA), and the Mississippi embayment aquifer system, which includes deeper Tertiary aquifers and confining units. Based on the distribution of groundwater use for drinking water, the modeling focused on the MRVA, middle Claiborne aquifer (MCAQ), and lower Claiborne aquifer (LCAQ). Boosted regression tree (BRT) models (Elith and others, 2008; Kuhn and Johnson, 2013) were developed to predict SC and Cl to 1-kilometer (km) raster grid cells of the National Hydrologic Grid (Clark and others, 2018) for 7 aquifer layers (1 MRVA, 4 MCAQ, 2 LCAQ) following the hydrogeologic framework of Hart and others (2008). TDS maps were created using the correlation between SC and TDS. Explanatory variables for the BRT models included attributes associated with well location and construction, surficial variables (such as soils and land use), and variables extracted from a MODFLOW groundwater flow model for the Mississippi embayment (Haugh and others, 2020a; Haugh and others, 2020b). Prediction intervals were calculated for SC and Cl by bootstrapping raster-cell predictions following methods from Ransom and others (2017). For a full description of modeling workflow and final model selection see Knierim and others (2020).
DOI: 10.6084/m9.figshare.12083889.v1
title: TCGA Pan-Cancer immune gene TPMs (mRNA)

description: Including Pan-Cancer TPMs of 114 TIMER-based B cell marker genes and MS4A1
DOI: 10.6084/m9.figshare.12084678.v1
title: ssGSEA scores of immune cells in TCGA HNSC, LUAD, CESC, LGG and KIPR

description: ssGSEA scores of immune cells in TCGA-HNSC, LUAD, CESC, LGG and KIRP.
DOI: 10.6084/m9.figshare.12824897
title: Data for Self-propelling and rolling of a sessile-motile bacterial aggregate (published)

description: Source data for figures.
DOI: 10.6084/m9.figshare.21687482
title: Supplementary Material for: Which Health-Related Quality of Life Items Most Affect Acne Patients?

description: <b><i>Background:</i></b> Health-related quality of life (HRQoL) assessment in patients with acne is recommended by several national guidelines. There are several acne-specific HRQoL instruments. <b><i>Objectives:</i></b> Participants of the European Academy of Dermatology and Venereology (EADV) Task Forces (TFs) on QoL and Patient Oriented Outcomes (PO) and Acne, Rosacea, and Hidradenitis Suppurativa (ARHS) agreed to scrutinize aspects of existing acne-specific HRQoL instruments for their relevance in international study. <b><i>Methods:</i></b> Consensus agreement on items related to QoL was reached after an independent assessment by seven experts from the EADV TFs on QoL and PO, and a list of 97 items was prepared and proposed to a group of acne patients. In order to have data from patients to check if any important topics were overseen, another group of acne patients from participating countries was asked to list how acne influenced different aspects of their lives. <b><i>Results:</i></b> Based on results obtained from 601 acne patients from nine countries, most of the items and topics showed low relevance for acne patients especially during the previous month or shorter time periods. Based on percentage of relevance and factor analysis, short (6 items) and long (45 items) lists of the most relevant topics were formed. <b><i>Conclusion:</i></b> Most of the items and topics from the initial list showed low relevance for acne patients. None of the identified acne-specific HRQoL instruments contain all the items that were deemed most relevant to acne patients. For this reason, participating members of the EADV TFs on QoL and PO, and ARHs are in the process of developing a new acne-specific HRQoL instrument.
DOI: 10.21227/ccgv-5329
title: CCAP

description: Chest CT of COVID-19
DOI: 10.22008/fk2/dqzif7
title: Camp Century: Global Navigation Satellite System measurements

description: Global Navigation Satellite System (GNSS) measurements collected at Camp Century. This includes the CEN-GPS station, which continuously recorded during 2019-2021. This also includes the seven-stake strain network (S1, S2, S3, S4, S5, S6 and S7) that was measured in summer 2017, as well as the spring 2019 re-measurement of stake S5. These data are primary data from the GNSS receivers.
DOI: 10.25375/uct.12472739
title: H4:IC31 and BCG induced immune responses in a prevention of M. tuberculosis infection efficacy trial

description: Immunogenicity responses from the C040-404 clinical trial were measured by whole blood intracellular cytokine staining at baseline and 70 days after vaccination with H4:IC31 (subunit vaccine containing Ag85B and TB10.4), Bacille Calmette-Guerin (BCG, a live attenuated vaccine) or placebo (n=~30 per group) using flow cytometry.
DOI: 10.25835/0090041
title: COVID-19 Image Repository

description: This project aims to create an anonymized data set of COVID-19 cases with a focus on radiological imaging. This includes images with extensive metadata, such as admission-, ICU-, laboratory-, and patient master-data. This repository contains image data from the Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany.
DOI: 10.5281/zenodo.3979446
title: Selecting third-party libraries: The practitioners' perspective

description: Online appendix: Selecting third-party libraries: The practitioners' perspective, published in the Proceedings of the 28th ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering, November 8--13, 2020, Virtual Event, USA.
DOI: 10.5281/zenodo.6795994
title: Data for "Where does the dust deposited over the Sierra Nevada snow come from?"

description: This is the data prepared for submission of the manuscript "<strong>Where does the dust deposited over the Sierra Nevada snow come from?</strong>". Three folders are included: 1) The WRF-Chem simulation results with 4 SOM clustering; 2) The MERRA-2 reanalyses with 4 SOM clustering 3) The ERA5 reanalyses for wind and geopotential height
DOI: 10.5517/cc6ntrd
title: CCDC 198764: Experimental Crystal Structure Determination

description: Related Article: C.Siedschlag, G.Szeimies, K.Polborn|2002|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.19618971
title: Supplementary Material for: GDF15 Suppresses Lymphoproliferation and Humoral Autoimmunity in a Murine Model of Systemic Lupus Erythematosus

description: Growth and differentiation factor 15 (GDF15), a divergent member of the transforming growth factor-β superfamily, has been associated with acute and chronic inflammatory conditions including autoimmune disease, i.e., type I diabetes and rheumatoid arthritis. Still, its role in systemic autoimmune disease remains elusive. Thus, we studied GDF15-deficient animals in Fas-receptor intact (C57BL/6) or deficient (C57BL/6<sup><i>lpr/lpr</i></sup>) backgrounds. Further, lupus nephritis (LN) microdissected kidney biopsy specimens were analyzed to assess the involvement of GDF15 in human disease. GDF15-deficiency in lupus-prone mice promoted lymphoproliferation, T-, B- and plasma cell-expansion, a type I interferon signature, and increased serum levels of anti-DNA autoantibodies. Accelerated systemic inflammation was found in association with a relatively mild renal phenotype. Splenocytes of phenotypically overall-normal <i>Gdf15−/−</i> C57BL/6 and lupus-prone C57BL/6<sup><i>lpr/lpr</i></sup> mice displayed increased in vitro lymphoproliferative responses or interferon-dependent transcription factor induction in response to the toll-like-receptor (TLR)-9 ligand CpG, or the TLR-7 ligand Imiquimod, respectively. In human LN, GDF15 expression was downregulated whereas type I interferon expression was upregulated in glomerular- and tubular-compartments versus living donor controls. These findings demonstrate that GDF15 regulates lupus-like autoimmunity by suppressing lymphocyte-proliferation and -activation. Further, the data indicate a negative regulatory role for GDF15 on TLR-7 and -9 driven type I interferon signaling in effector cells of the innate immune system.
DOI: 10.6084/m9.figshare.19713487
title: Supplementary Material for: HMGB1-Like Dorsal Switch Protein 1 Triggers a Damage Signal in Mosquito Gut to Activate Dual Oxidase via Eicosanoids

description: Several mosquitoes transmit human pathogens by blood feeding, with the gut being the main entrance for the pathogens. Thus, the gut epithelium defends the pathogens by eliciting potent immune responses. However, it was unclear how the mosquito gut discriminates pathogens among various microflora in the lumen. This study proposed a hypothesis that a damage signal might be specifically induced by pathogens in the gut. The Asian tiger mosquito, <i>Aedes albopictus</i>, encodes dorsal switch protein 1 (<i>Aa-DSP1</i>) as a putative damage-associated molecular pattern (DAMP). Aa-DSP1 was localized in the nucleus of the midgut epithelium in naïve larvae. Upon infection by a pathogenic bacterium, <i>Serratia marcescens</i>, Aa-DSP1 was released to hemocoel and activated phospholipase A<sub>2</sub> (PLA<sub>2</sub>). The activated PLA<sub>2</sub> increased the level of prostaglandin E<sub>2</sub> (PGE<sub>2</sub>) in the gut and subsequently increased Ca<sup>2+</sup> signal to produce reactive oxygen species (ROS) via dual oxidase (Duox). Inhibition of Aa-DSP1 via RNA interference or specific inhibitor treatment failed to increase PGE<sub>2</sub>/Ca<sup>2+</sup> signal upon the bacterial infection. Thus, the inhibitors specifically targeting eicosanoid biosynthesis significantly prevented the upregulation of ROS production in the gut and enhanced mosquito mortality after the bacterial infection. However, such inhibitory effects were rescued by adding PGE<sub>2</sub>. These suggest that Aa-DSP1 plays an important role in immune response of the mosquito gut as a DAMP during pathogen infection by triggering a signaling pathway, DSP1/PLA<sub>2</sub>/Ca<sup>2+</sup>/Duox.
DOI: 10.6084/m9.figshare.19867654
title: Supplementary Material for: Regulation of TLR10 Expression and Its Role in Chemotaxis of Human Neutrophils

description: Toll-like receptors are innate immune receptors that play a critical role in pathogen-associated molecular pattern recognition. TLR10 was recently identified and very limited data are available on its expression, mechanisms that regulate its expression, and its role in primary immune cells. To study the expression pattern of TLR10 in primary immune cells, we examined TLR10 protein expression in naive and <i>Escherichia coli</i> lipopolysaccharide (LPS)-activated human neutrophils. Human neutrophils challenged with LPS showed a decrease in total and surface TLR10 expression at 90 min. TLR10 in LPS-activated neutrophils colocalized with flotallin-1, a lipid raft marker, and EEA-1, an early endosomal marker, to suggest its endocytosis. There was increased colocalization of TLR10 with TLR4 at LPS 60 min followed by decrease at later LPS treatment times. Treatment with TLR4 neutralizing antibody decreased cytoplasmic localization of TLR10 in LPS-treated neutrophils. Reactive oxygen species (ROS) depletion and neutralization of p65 subunit of NF-κB in LPS-treated neutrophils decreased TLR10 expression. Live cell imaging of LPS-activated neutrophils showed TLR10 translocation in the leading edge and TLR10 knockdown in neutrophils reduced their fMLP-induced chemotaxis and the number of neutrophils with pseudopodia but without affecting the expression of key proteins of actin nucleation process, ARP-3 and Diap1. Taken together, our findings show that neutrophil activation alters TLR10 expression through ROS production and NF-κB regulation, and TLR10 knockdown reduced neutrophil chemotaxis.
DOI: 10.6084/m9.figshare.20265942
title: Supplementary Material for: miR-181a Improved Renal Inflammation by Targeting TNF-α in a Diabetic Nephropathy Animal Model

description: <b><i>Introduction:</i></b> Recent studies have elucidated that miR-181a plays a vital role in various inflammation-associated diseases; however, its role in the pathogenesis of diabetic nephropathy (DN) has not been elucidated clearly. Hence, we investigated the involvement of miR-181a in the pathogenesis of DN in patients and animal models. <b><i>Methods:</i></b> miR-181a levels were measured in the kidneys of DN patients and a DN mouse model (db/db mice) by RT-PCR. The interaction of miR-181a with the 3′-UTR of potential target transcripts was investigated using luciferase reporter assays. miR-181a-GFP-AAV and miR-181a inhibitor were used to overexpress or downregulate miR-181a in the kidney of db/db mice, respectively. The expression of inflammatory proteins and target genes was measured in the kidneys of the animals. <b><i>Results:</i></b> In DN patients and DN mouse models, expression analyses showed a significant decrease in miR-181a levels in the kidney. In addition, a negative linear correlation between miR-181a and proinflammatory gene (IL-1β and TNF-α) levels was observed in the kidneys of DN patients. Overexpression of miR-181a reduced IL-1β and TNF-α expression, whereas suppression of miR-181a worsened these changes, which was attenuated by combined treatment with TNF-α neutralizing antibody in db/db mice. Moreover, luciferase assays revealed that TNF-α is a direct target of miR-181a. <b><i>Conclusion:</i></b> Our data emphasized the anti-inflammatory actions of miR-181a by targeting TNF-α in the context of renal inflammation in DN. Hence, we concluded that miR-181a could be a potential therapeutic option for minimizing renal inflammation in DN.