cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21500262
title: Supplementary Material for: Risk Factors of Rapid FEV<sub>1</sub> Decline in a Real-World Chronic Obstructive Pulmonary Disease Cohort

description: <b><i>Background:</i></b> Rapid forced expiratory volume in 1 s (FEV<sub>1</sub>) decliners have been considered a unique subgroup of patients with chronic obstructive pulmonary disease (COPD). Rapid FEV<sub>1</sub> decline manifests early and is associated with poor prognosis. This necessitates the pre-emptive identification of risk factors for rapid FEV<sub>1</sub> decline. <b><i>Objectives:</i></b> We aimed to determine the risk factors and clinical outcomes in patients with COPD. <b><i>Methods:</i></b> This longitudinal, observational study was based on the Korea COPD Subgroup Study cohort (NCT02800499) from January 2012 to December 2019 across 54 medical centers in South Korea. Eligible patients were followed up for 3 years with serial spirometric tests. We calculated the annualized percentage change in FEV<sub>1</sub> from baseline. Rapid decliners were defined as the quartile of patients with the highest annualized percentage FEV<sub>1</sub> decline. <b><i>Results:</i></b> Of the 518 patients, 130 were rapid decliners who lost 6.2%/year and 100 mL/year of FEV<sub>1</sub>. The multivariable logistic regression identified male sex, current smoking, blood eosinophil count &lt;150/µL, and high forced vital capacity as the independent risk factors for rapid FEV<sub>1</sub> decline. Among rapid decliners, the lung function deteriorated more rapidly in current smokers and patients with severe dyspnea, while triple combination therapy attenuated lung function decline in comparison with mono-bronchodilator therapy. Rapid decliners had a higher rate of severe exacerbation than nonrapid decliners (0.2/year vs. 0.1/year, <i>p</i> value = 0.032). <b><i>Conclusions:</i></b> We identified the independent risk factors for rapid FEV<sub>1</sub> decline. This information may assist physicians in the early detection and pertinent management of rapid decline among patients with COPD.
DOI: 10.6084/m9.figshare.20066429
title: Supplementary Material for: Suitability of Different Diagnostic Platforms for Virological Testing of Blood Samples from Cornea Donors

description: <b><i>Background:</i></b> To minimize the risk of disease transmission in cornea transplantation, donor screening for blood-derived viral infections is mandatory. Ideally, pre-mortem blood samples are used, but based on availability, cadaveric blood samples of cornea donors may also be used. However, serological and nucleic acid amplification tests (NATs) need to be validated for the use of cadaveric specimens. <b><i>Methods:</i></b> Hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), human T-lymphotropic virus (HTLV) 1/2, and <i>Treponema pallidum</i> (syphilis)-specific serological and/or NAT assays were validated on different platforms (Abbott Alinity i, Alinity m, Roche Cobas 6800, and Roche Cobas AmpliPrep/Cobas TaqMan (CAP/CTM)) using (un)spiked paired pre- and post-mortem cornea donor blood samples from the same individual (up to 23.83 h after death) of 28 individuals in accordance with the specifications of the German Federal Institute for Vaccines and Biomedicines (Paul-Ehrlich-Institut [PEI]). In addition, routinely HBV-, HCV- and HIV-PCR-negative tested post-mortem blood samples of 24 individuals were used to assess NAT specificity. <b><i>Results:</i></b> For the majority of serological parameters on the Abbott Alinity i (HBsAg, anti-HBc, anti-HBs, anti-HCV, anti-HIV, anti-HTLV 1/2, and anti-<i>Treponema pallidum</i>), ratios of generated test results of (un)spiked paired pre- and post-mortem blood samples differed ≤25%, with an agreement of qualitative pre- and post-mortem test results ranging from 91.2 to 100%. For NAT parameters (HBV, HCV, and HIV) on the Cobas 6800, Alinity m, and CAP/CTM, no significant deviation in virus concentrations (factor &gt;5) of spiked pre- and post-mortem blood samples could be observed. Ct-values of corresponding internal controls did also not differ significantly (&gt;1.5 Ct-values). In addition, no false-positive test results were generated when specificity was assessed. <b><i>Conclusion:</i></b> Overall, fluctuations of test results for serological and NAT parameters in pre- and post-mortem blood samples examined in this study, were only limited and within the range of what is also observed when routinely testing fresh patient specimens. We conclude that all examined assays are eligible for the screening of blood samples taken up to about 24 h after the occurrence of death.
DOI: 10.6084/m9.figshare.21302898
title: Supplementary Material for: Evaluations of Skin Permeability of Cannabidiol and Its Topical Formulations by Skin Membrane-Based Parallel Artificial Membrane Permeability Assay and Franz Cell Diffusion Assay

description: <b><i>Introduction:</i></b> Cannabinoids including cannabidiol (CBD) have attracted enormous interest as bioactive ingredients for various dermatological and/or cosmeceutical uses. However, topical applications of cannabinoids might be limited without a fundamental understanding of their skin permeability. Herein, we aimed to evaluate the skin permeability of CBD and its topical formulations using artificial skin membrane assays. The solubility and stability of CBD in various surfactants that are commonly used in topical applications were also evaluated. <b><i>Methods:</i></b> CBD and two CBD-incorporated topical formulations (cream and gel) were prepared for this study. Computational predictions (SwissADME and DERMWIN™) and the parallel artificial membrane permeability assay (PAMPA) were used to evaluate the skin permeability of CBD isolate. The Franz cell diffusion (in vitro release testing) assay was used to evaluate the skin permeability of CBD formulations. The solubility and stability of CBD in surfactants were assessed by high-performance liquid chromatography and mass spectrometry analysis. <b><i>Results:</i></b> CBD isolate showed favorable skin permeability in the SwissADME and DERMWIN™ predictions (−Log Kp of 3.6 and 5.7 cm/s, respectively) and PAMPA (−LogPe value of 5.0 at pH of 6.5 and 7.4). In addition, CBD had higher solubility (378.4 μg/mL) in surfactant Tween 20 as compared to its solubility in polyisobutene. In an acidic environment (pH 5 and 6), Tween 20 maintained the CBD content at 81% and 70% over 30 days, respectively. CBD in the formulations of cream and gel also had moderate skin permeability in the Franz cell diffusion assay. <b><i>Conclusion:</i></b> Data from artificial membrane-based assays support that CBD is a skin permeable cannabinoid and the permeability and stability of its formulations may be influenced by several factors such as surfactant and pH environment. Findings from our study suggest that CBD may have suitable skin permeability for the development of dermatological and/or cosmeceutical applications but further studies using in vivo models are warranted to confirm this.
DOI: 10.6084/m9.figshare.21656357
title: Supplementary Material for: Tracking Chromosomal Origins in the Northern Italy System of Metacentric Races of the House Mouse

description: The Western European house mouse is chromosomally diverse, with diploid karyotypes ranging from the standard 40 telocentric chromosomes down to 22 chromosomes. Karyotypes are modified through Robertsonian (Rb) fusion of 2 telocentrics into a single metacentric, occurring repeatedly with fixation, and whole-arm reciprocal translocations (WARTs) generating additional novel karyotypes. Over 100 metacentric populations (chromosomal races) have been identified, geographically clustered into “systems.” Chromosomal races within systems often hybridise, and new races may emerge through this hybridisation (“zonal raciation”). We wished to determine the degree to which chromosomal races in a system have evolved independently or share common ancestry. Recombination between chromosomes from hybridising chromosomal races can erase the signals associated with a particular metacentric of interest, making inferences challenging. However, reduced recombination near the centromeres of chromosomal race-specific metacentrics makes centromere-adjacent markers ideal for solving this problem. For the Northern Italy System (NIS), we used microsatellite markers near the centromere to test previous hypotheses about evolutionary relationships of 5 chromosomal races. We chose markers from chromosomes 1, 3, 4, and 6, all of which comprise one arm of a metacentric in at least 2 of these NIS metacentric populations. We used estimates of F<sub>ST</sub> and R<sub>ST</sub>, as well as principal components analyses and neighbour-joining phylogenetic analyses, to infer evolutionary relationships between these 5 chromosomal races and neighbouring mice with the standard karyotype. We showed that the metacentric populations form a single grouping distinct from the standard populations, consistent with their common origin and consistent with a parsimonious sequence of chromosomal rearrangements to explain the relationship of the chromosomal races. That origin and evolution of the chromosomal races in the system would have involved Rb fusions, explaining the occurrence of chromosomal races with diploid numbers as low as 22. However, WARTs and zonal raciation have also been inferred, and the rare occurrence of chromosome 1 in different metacentrics in closely related chromosomal races is almost certainly explained by a WART. Our results with centromeric microsatellites are consistent with the above scenarios, illustrating, once again, the value of markers in the centromeric region to test evolutionary hypotheses in house mouse chromosomal systems.
DOI: 10.12751/g-node.qeeyfz
title: The physiological basis for contrast opponency in motion computation in Drosophila

description: This dataset contains traces (dF/F0) from in vivo two-photon calcium imaging from Tm1, tm2, Tm4, Tm9, CT1, and T5 neurons from responses to ONOFF fullfield flashes, ON and OFF bars, and moving sinewaves.
description: IsSupplementTo: Ramos-Traslosheros G., Silies, M. (2021). The physiological basis for contrast opponency in motion computation in Drosophila. Nature Communications. ()
description: IsSupplementTo: Ramos-Traslosheros G., Silies, M. (2021). The physiological basis for the computation of direction selectivity in the Drosophila OFF pathway. bioRxiv 2021.04.17.440268. (https://doi.org/10.1101/2021.04.17.440268)
DOI: 10.13020/y8ry-gm18
title: NCOMMS-21-11334 -- Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis

description: The data deposited here are raw files, R code and mass spec, associated with the results presented in the paper, "Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis." These data have been made publicly available in keeping with the journal's data availability policy.
description: R Code:
Supplementary Data 1. Code for running kinetics simulations
File name: Supplementary Data 1.R 

Mass Spectrometry .raw files:
Supplementary Figure 4a-c. Mass spectrometric analysis of split borosin coexpressions.
File name: 20200110_FSM1167_SonA+SonM_24.5min.raw
Supplementary Figure 4d-j. Mass spectrometric analysis of split borosin coexpressions.
File name: 20200909_KC1063_StrA+StrM_15min_redalk_18pm4.raw

Supplementary Figure 16. SonM in vitro reactions analyzed by LC-MS/MS and
compared to kinetic model simulations.
File names:
20200220_FSM1178_kineticmodeling_t=2.raw
20200220_FSM1179_kineticmodeling_t=2.raw
20200220_FSM1180_kineticmodeling_t=8.raw
20200220_FSM1181_kineticmodeling_t=8.raw
20200220_FSM1182_kineticmodeling_t=20.raw
20200220_FSM1183_kineticmodeling_t=20.raw
20200220_FSM1184_kineticmodeling_t=40.raw
20200220_FSM1185_kineticmodeling_t=40.raw
20200220_FSM1186_kineticmodeling_t=60.raw
20200220_FSM1187_kineticmodeling_t=60.raw

Supplementary Figure 25a. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190701_kc1007_His-SonA_Y93F.raw
Supplementary Figure 25b. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190515_fsm1155_his-SonA-sonMT-R67K.raw
Supplementary Figure 25c. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190515_fsm1154_his-sonA_sonMTR67A.raw
Supplementary Figure 25d. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190701_kc1008_His-SonA_Y58F.raw
Supplementary Figure 25e. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190515_fsm1156_his-sonA-SonMT-Y71F.raw
Supplementary Figure 25f. Mass spectrometric analysis of SonM mutant in vitro
reactions.
File name: 20190701_kc1009_His-SonA_DBLMUT.raw
DOI: 10.25914/k8zf-6g46
title: GloLake: Global historical and near real-time lake storage dynamics from 1984-present

description: The GloLake dataset provides historical and near real-time time series of relative (i.e., storage change) and absolute (i.e., total stored volume) storage for more than 25,000 lakes worldwide using multiple sources of satellite data, including laser and radar altimetry and optical remote sensing. This data can help us understand the influence of climate variability and anthropogenic activities on water availability and system ecology over the last four decades. The GloLake dataset will be updated regularly when new remote sensing data is available.
DOI: 10.5281/zenodo.5155575
title: 2D NMR HSQC spectra of proteins and mouse urine with peaks picked by DEEP Picker

description: 2D 15N-1H HSQC NMR spectra of Im7 and a-synuclein with peak lists produced by DEEP Picker. 2D 13C-1H HSQC NMR spectrum of mouse urine with peak lists determined by DEEP Picker.
DOI: 10.6084/m9.figshare.21118807
title: Supplementary Material for: Relationship between <b><i>Blastocystis</i></b> spp. with Accompanying Food Hypersensitivity and Chronic Spontaneous Urticaria

description: <b><i>Introduction:</i></b> The relationship between <i>Blastocystis</i> spp. and chronic spontaneous urticaria (CSU) is unclear. The aim of this study was to evaluate the role of this parasitic infection on CSU and to search for risky groups in CSU patients with this parasite. <b><i>Methods:</i></b> Seventy adult CSU patients with <i>Blastocystis</i> spp. in their stool samples forming Group A and 70 CSU patients without any parasite as Group B were prospectively compared regarding urticaria activity score-7 (UAS7), medication scores (MS), and laboratory parameters. All patients received CSU treatment, and additionally, those in group A received an antiparasitic antibiotic. Eight months later, the same parameters were compared between the ones in remission (group A1) and those still having CSU symptoms (group A2) in group A. <b><i>Results:</i></b> UAS7 and MS were lower in group A than in group B (<i>p</i>: 0.007, <i>p</i> &lt; 0.001) 8 months later, while the initial scores were similar. The presence of food hypersensitivity reactions (FHRs) was higher in group A than in group B (<i>p</i> &lt; 0.001) and was detected as a significant risk factor in the presence of <i>Blastocystis</i> spp. infection (<i>p</i>: 0.002, OR [CI] = 0.151 [0.045–0.502]). In group A, UAS7, MS, serum total IgE levels, and blood eosinophil counts decreased 8 months later (<i>p</i> &lt; 0.001, <i>p</i> &lt; 0.001, <i>p</i>: 0.003, <i>p</i>: 0.004, respectively). Additionally, total IgE levels and eosinophil counts decreased in group A1 (<i>p</i>: 0.033, <i>p</i>: 0.002) while they did not change in group A2. <b><i>Discussion/Conclusion:</i></b> The eradication of <i>Blastocystis</i> spp. can improve the disease activity in CSU and the presence of FHRs seems to be risky in CSU patients with <i>Blastocystis</i> spp.
DOI: 10.6084/m9.figshare.21310917
title: Supplementary Material for: Genetic Variants in <b><i>MIR3142HG</i></b> Contribute to the Predisposition of IgA Nephropathy in a Chinese Han Population

description: <b><i>Background:</i></b> The study aimed to evaluate the association of genetic variants in <i>MIR3142HG</i> with the predisposition of IgA nephropathy (IgAN) in a Chinese Han population. <b><i>Methods:</i></b> Six single-nucleotide polymorphisms (SNPs) in <i>MIR3142HG</i> were chosen for genotyping among 417 IgAN cases and 424 healthy controls using Agena MassARRAY technique. Logistic regression models adjusted for age and gender were used to calculate odds ratios (ORs) and 95% confidence intervals (CI). Haploview and multifactor dimensionality reduction analysis were used to analyze the role of combined SNPs in IgAN risk. <b><i>Results:</i></b> Rs17057846-AA genotype (OR = 2.11, 95% CI: 1.04–4.27, <i>p</i> = 0.039) and rs58747524-CC genotype (OR = 1.89, 95% CI: 1.06–3.38, <i>p</i> = 0.032) had the higher risk for IgAN developing in the overall. Interestingly, rs7727115 had a reduced risk for IgAN in females, while rs17057846, rs2961920, and rs58747524 were related to the increased susceptibility to IgAN in females and the subjects with age ≤35 years; moreover, rs17057846 and rs58747524 conferred to the higher risk for Lee’s grade ≥III IgAN (<i>p</i> &lt; 0.05 for all). Besides, the combination of rs1582417, rs7727115, and rs2961920 was the best model (testing accuracy = 0.5468, CVC = 10/10, <i>p</i> &lt; 0.001) to predict IgAN predisposition compared to the single SNP alone. <b><i>Conclusions:</i></b> Our study firstly indicated that rs17057846 and rs58747524 in <i>MIR3142HG</i> contributed to the elevated risk for IgAN in a Chinese Han population. These results might provide a new insight for the molecular mechanism in the progression of IgAN.
DOI: 10.6084/m9.figshare.21493593
title: Supplementary Material for: Analysis of Patients with Asthma and Mixed Granulocytic Inflammatory Pattern in Sputum

description: <b><i>Background:</i></b> Patients with asthma usually present airway inflammation classified as eosinophilic, neutrophilic, mixed granulocytic, and paucigranulocytic pattern according to sputum inflammatory cells. <b><i>Objective:</i></b> The aim of the study was to analyze clinical and biological characteristics of patients with asthma and mixed granulocytic pattern in comparison with the other groups. <b><i>Methods:</i></b> Induced sputum was used to assess airway inflammation; lung function was evaluated as well as blood leukocytes and disease control. History of comorbidities was collected. <b><i>Results:</i></b> We retrospectively analyzed 231 subjects with asthma; patients with mixed granulocytic pattern were more frequently male compared with paucigranulocytic subjects, older than eosinophilic and paucigranulocytic patients with increased number and vitality of sputum cells compared to eosinophilic and paucigranulocytic patients and higher cumulative illness rating score, related to increased age. Smoking history, age of disease onset, and ICS treatment were not associated with higher mixed granulocytic pattern occurrence. Subjects with neutrophilic inflammation (mixed granulocytic and neutrophilic patterns considered altogether) were more frequently obese. In subjects under 67 years of age (median of the enrolled subjects), arterial hypertension was the only comorbidity more frequent in mixed granulocytic than in the other groups. 137/231 subjects were re-valuated during follow-up. Lung function of patients with mixed granulocytic, neutrophilic, and paucigranulocytic patterns improved less than that of eosinophilic patients. <b><i>Conclusion:</i></b> Aging and presence of comorbidities, in particular obesity and hypertension, are characteristics of patients with asthma and mixed granulocytic pattern. They could respond less well to treatment than eosinophilic patients.
DOI: 10.6084/m9.figshare.21550797
title: Supplementary Material for: Development of Novel Tasks to Assess Outcome-Specific and General Pavlovian-to-Instrumental Transfer in Humans

description: <b><i>Introduction:</i></b> The emergence of Pavlovian-to-instrumental transfer (PIT) research in the human neurobehavioral domain has been met with increased interest over the past two decades. A variety of PIT tasks were developed during this time; while successful in demonstrating transfer phenomena, existing tasks have limitations that should be addressed. Herein, we introduce two PIT paradigms designed to assess outcome-specific and general PIT within the context of addiction. <b><i>Materials and Methods:</i></b> The single-lever PIT task, based on an established paradigm, replaced button presses with joystick motion to better assess avoidance behavior. The full transfer task uses alcohol and nonalcohol rewards associated with Pavlovian cues and instrumental responses, along with other gustatory and monetary rewards. We constructed mixed-effects models with the addition of other statistical analyses as needed to interpret various behavioral measures. <b><i>Results:</i></b> Single-lever PIT: both versions were successful in eliciting a PIT effect (joystick: <i>p</i> &lt; 0.001, η<sub>p</sub><sup>2</sup> = 0.36, button-box: <i>p</i> &lt; 0.001, η<sub>p</sub><sup>2</sup> = 0.30). Full transfer task: it was determined that the alcohol and nonalcoholic reward cues selectively primed their respective reward-associated responses (gustatory version: <i>p</i> &lt; 0.001, <i>r</i> = 0.59, and monetary version: <i>p</i> &lt; 0.001, <i>r</i> = 0.84). The appetitive/aversive cues resulted in a general transfer effect (gustatory: <i>p</i> &lt; 0.001, η<sub>p</sub><sup>2</sup> = 0.09, and monetary: <i>p</i> &lt; 0.001, η<sub>p</sub><sup>2</sup> = 0.17). <b><i>Discussion/Conclusion:</i></b> Single-lever PIT: PIT was observed in both task versions. We posit that the use of a joystick is more advantageous for the analysis of avoidance behavior. It evenly distributes movement between approach and avoid trials, which is relevant to analyzing fMRI data. Full transfer task: While gustatory conditioning has been used in the past to elicit transfer effects, we present the first paradigm that successfully elicits both specific and general transfers in humans with gustatory alcohol rewards.