cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20409096.v1
title: COVID-19 Associated Pulmonary Aspergillosis Isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses

description: Secondary infections caused by the pulmonary fungal pathogen <em>Aspergillus fumigatus</em> are a significant cause of mortality in patients with severe COVID-19. Even though epithelial cell damage and aberrant cytokine responses have been linked with susceptibility to coronavirus associated pulmonary aspergillosis (CAPA), little is known about the mechanisms underpinning co-pathogenicity. Here, we analysed the genomes of 11 <em>A. fumigatus</em> strains from patients with CAPA in four different clinical settings. CAPA isolates are genomically diverse but are phenotypically similar across infection-relevant stresses. Phenotypically, CAPA strains are more similar to the <em>A. fumigatus</em> A1160 reference strain except for interactions with human immune cells wherein macrophage responses were similar to those induced by the Af293 reference strain. In contrast to previous reports, CAPA strains did not cluster based on geographic origin. A larger number of isolates from CAPA patients should be studied to identify genetic drivers of co-pathogenicity in patients with COVID-19. <br> This dataset contains the genome assemblies and annotations used in the manuscript.
DOI: 10.6084/m9.figshare.1299156.v1
title: Format technology analysis groups

description: This dataset contains property value pairs for three analysis groups. HTMLS - defines mime types and format version for the HTML and XHTML file format family. PDFS - defines mime type and format versions for PDF file format family. PDFS_software - defines mime type for the PDF and different Adobe distiller versions used to produced PDF files.
DOI: 10.6084/m9.figshare.14325866.v3
title: National Database of Medical Students from Argentina

description: This Database comes from a national survey of Medical Students from Argentina. If you would like to work with this database, please contact Maximo Rousseau Portalis (maximorp@campus.fmed.uba.ar).<br>We will be honored to share the information and collaborate with you.<br>Cheers.
DOI: 10.6084/m9.figshare.28696490.v1
title: Differences in Ct values in qPCR tests for the diagnosis of mpox

description: Database of mpox virus results using PCR in the population with social security.
DOI: 10.17632/pspr389m7c.1
title: Research Data

description: data for research (dataset)
DOI: 10.6084/m9.figshare.9938114.v1
title: Supplementary Material for: Southeast Asian Pharmacogenomics Research Network (SEAPharm): Current Status and Perspectives

description: Pharmacogenomics (PGx) is increasingly being recognized as a potential tool for improving the efficacy and safety of drug therapy. Therefore, several efforts have been undertaken globally to facilitate the implementation process of PGx into routine clinical practice. Part of these efforts include the formation of PGx working groups working on PGx research, synthesis, and dissemination of PGx data and creation of PGx implementation strategies. In Asia, the Southeast Asian Pharmacogenomics Research Network (SEAPharm) is established to enable and strengthen PGx research among the various PGx communities within but not limited to countries in SEA; with the ultimate goal to support PGx implementation in the region. From the perspective of SEAPharm member countries, there are several key elements essential for PGx implementation at the national level. They include pharmacovigilance database, PGx research, health economics research, dedicated laboratory to support PGx testing for both research and clinical use, structured PGx education, and supportive national health policy. The status of these essential elements is presented here to provide a broad picture of the readiness for PGx implementation among the SEAPharm member countries, and to strengthen the PGx research network and practice in this region.
DOI: 10.6084/m9.figshare.13475463.v1
title: Supplementary Material for: Weight Status and BMI-Related Traits in Adolescent Friendship Groups and Role of Sociodemographic Factors: The European IDEFICS/I.Family Cohort

description: <b><i>Background:</i></b> During adolescence, health behaviors and weight status are increasingly influenced by friendship and peer networks. This paper examines resemblances in weight-related characteristics and how they differ by sociodemographic factors. <b><i>Methods:</i></b> Over 3,000 friendships were reported by 1,603 adolescents, aged 11–16 years, who participated in the school-based I.Family study in 6 European countries. Each “source child” named 1–10 friends for whom standardized weight-related traits were available in the same survey. The mean value of the friends’ traits weighted by time spent together was calculated, and related to the source child’s trait. Country, age and sex of the source child, parental education, and immigrant background were considered for confounding and moderation. <b><i>Results:</i></b> Source children’s <i>z</i>-scores of body fat percent and BMI were positively associated with their friends’ characteristics, in particular if they had highly educated parents. Positive associations were also found regarding the frequency of fast-food consumption, impulsivity, screen time, preference for sugar-sweetened foods, and hours spent in sports clubs, in increasing order of effect size. Additionally, correlations were observed between friends’ cognitive and school functioning and being bullied. No associations were seen for a preference for high-fat foods, weight concerns, and health-related quality of life. Finally, parental education and immigrant background were associated between friends in all countries except Sweden, where no associations were observed. <b><i>Conclusion:</i></b> Adolescent friends shared a number of weight-related characteristics. For weight measures per se, positive associations with friends’ characteristics were only observed in adolescents with high parental education. Associations regarding energy-balance behaviors and indicators of school-related well-being did not differ by parental education. Parental education and immigrant background correlated positively in friends in most countries showing that social aggregation is already occurring in adolescence. The wide spectrum of friendship associations in weight-related traits and behaviors suggests that health promotion initiatives in adolescents should be directed towards peer groups in both school-related and leisure-time environments. <b><i>ISRCTN Registry:</i></b> Pan-European IDEFICS/I.Family children cohort (ID ISRCTN62310987; https://doi.org/10.1186/ISRCTN62310987).
DOI: 10.6084/m9.figshare.1276050.v1
title: Vienna RNA subopt++

description: This package contains all parts of the code necessary to run the Vienna RNA folding programs, including the modifications made to the Wuchty algorithm for optional multibranch loops, global constraints on the minimum number and length of helices, conditional chemical probing constraints, and an energy-independent lonely pairs filter. The starting point was the Vienna RNA websuite 1.8.3. Refer to the Vienna website http://www.tbi.univie.ac.at/RNA/ for the most current version fo the Vienna RNA package and also all previous versions. Please cite Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26. This modified package is also available at http://adenosine.chem.ou.edu/software.html. Have fun folding RNA!
DOI: 10.6084/m9.figshare.25707654.v2
title: Data and code for "Strong and consistent effects of waterbird composition on HPAI H5 occurrences across Europe"

description: Study abstract:Since 2014, highly pathogenic avian influenza (HPAI) H5 viruses of clade 2.3.4.4 have been dominating the outbreaks across Europe, causing massive deaths among poultry and wild birds. However, the factors shaping these broad-scale outbreak patterns, especially those related to waterbird community composition, remain unclear. In particular, we do not know whether these risk factors differ from those of other H5 clades. Addressing this knowledge gap is important for predicting and preventing future HPAI outbreaks. Using extensive waterbird survey datasets from about 6,883 sites, we here explored the effect of waterbird community composition on HPAI H5Nx (clade 2.3.4.4) spatial patterns in 2016/17 and 2020/21 epidemics in Europe, and compared it with 2005/06 HPAI H5N1 (clade 2.2) epidemic. We showed that HPAI H5 occurrences in wild birds in the three epidemics were strongly associated with very similar waterbird community attributes, which suggested that, in nature, similar interspecific transmission processes operate between the HPAI H5 subtypes or clades. Importantly, community phylogenetic diversity consistently negatively affected H5 occurrence in all three epidemics, suggesting a dilution effect of phylogenetic diversity. In contrast, waterbird community variables showed much weaker associations with HPAI H5Nx occurrence in poultry. Our results demonstrate that models based on previous epidemics can predict future HPAI H5 patterns in wild birds, implying that it is important to include waterbird community factors in future HPAI studies to predict outbreaks and improve surveillance activities.File descriptions:"1 Analyzed Data.xlsx": The processed dataset for the regression analysis"FigData2 Single-variable Results.csv": The dataset used to generate the Figure 2."FigData3 variance partitioning.csv": The dataset used to generate the Figure 3."FigData4 Multi-variable results.csv": The dataset used to generate the Figure 4."1 Regression Analyses.R": The R code used for the regression analysis."Fig 2 Codes.R": The R code for generating Figure 2."Fig 3 Codes.R": The R code for generating Figure 3."Fig 4AC Codes.R": The R code for generating Figure 4."Distance_matrix_of_survey_locations.RData": The R data contains the locations of bird survey sites.<br><br>
DOI: 10.6084/m9.figshare.7416317.v1
title: Dataset of the paper "Manifold Learning of Four-dimensional Scanning Transmission Electron Microscopy "

description: Dataset of the paper:Li, X., Dyck, O.E., Oxley, M.P., Lupini, A.R., McInnes, L., Healy, J., Jesse, S. and Kalinin, S.V., 2019. Manifold learning of four-dimensional scanning transmission electron microscopy. <i>npj Computational Materials</i>, <i>5</i>(1), p.5.<br>DOI: https://doi.org/10.1038/s41524-018-0139-y
DOI: 10.6084/m9.figshare.28079978.v1
title: appendix (2).docx

description: This study examines the factors affecting ADL and IADL disabilities of hypertensive patients of India.
DOI: 10.6084/m9.figshare.23143250.v1
title: Supplementary Material for: Intrarenal Anti-Leptin Treatment Attenuates Ischemia and Reperfusion Injury

description: Introduction: Renal ischemia and reperfusion (IR) injury introduces cellular stress and is the main cause of acute kidney damage. Renal cells exposed to noxious stress induce the expression of the pleiotropic hormone leptin. As we have previously revealed a deleterious stress-related role for leptin expression, these results suggested that leptin is also involved in pathological renal remodeling. The systemic functions of leptin preclude the study of its local effects using conventional approaches. We have therefore designed a method to locally perturb leptin activity in specific tissues without affecting its systemic levels. This study explores whether local anti-leptin strategy is reno-protection in a post-IR porcine kidney model. Methods: We induced renal IR injury in pigs by exposing kidneys to ischemia and revascularization. Upon reperfusion, kidneys instantly received an intraarterial bolus of either a leptin antagonist (LepA) or saline solution. Peripheral blood was sampled to assess systemic leptin, IL-6, creatinine, and BUN levels, and post-operative tissue samples were analyzed by H&E histochemistry and immunohistochemistry. Results: Histology of IR/saline kidneys exhibited extensive necrosis of proximal tubular epithelial cells, as well as elevated levels of apoptosis markers and inflammation. In contrast, IR/LepA kidneys showed no signs of necrosis or inflammation, with normal IL-6 and TLR4 levels. LepA treatment led to upregulation in mRNA levels of leptin, leptin receptor, ERK1/2, STAT3, and transport molecule NHE3. Conclusions: Local, intrarenal post-ischemic LepA treatment at reperfusion prevented apoptosis and inflammation and was reno-protective. Selective intrarenal administration of LepA at reperfusion may provide a viable option for clinical implementation.
DOI: 10.17632/cymmbkjbjs.1
title: Replication folder for paper titled "Sectoral exposure and its impact on bank risk: Evidence from India"

description: This replication package contains the sample data and the codes to reproduce the results, tables, and figures in the manuscript and its appendices. Please refer to the README of this repository for a walkthrough of the reproduction of the paper's results.
DOI: 10.6084/m9.figshare.17306831.v1
title: Supplementary Material for: PSA and PSA Kinetics as Predictors for 18F-Fluciclovine PET/CT Positivity in Biochemically Recurrent Prostate Cancer

description: <b><i>Introduction:</i></b> <sup>18</sup>F-Fluciclovine PET/CT is one of the imaging techniques currently employed to restage prostate cancer (PCa). Due to the conflicting results reported in the literature, it is not yet known at what PSA threshold <sup>18</sup>F-fluciclovine PET/CT could reliably demonstrate the presence of recurring disease. We explored the association between <sup>18</sup>F-fluciclovine PET/CT positivity and prescan PSA, PSA doubling time, and PSA velocity in patients with biochemical recurrence (BCR) of PCa after curative-intent treatment. <b><i>Methods:</i></b> Data from 59 patients who underwent <sup>18</sup>F-fluciclovine PET/CT for BCR after radical prostatectomy or radiotherapy were retrieved from a single institution database. Patients already undergone salvage treatments at the time of PET/CT, with newly diagnosed PCa or with initial diagnosis of metastatic PCa were excluded. A 2-sided independent samples Bayesian <i>t</i> test and Bayesian Mann-Whitney U test were used to assess the association between PET/CT and prescan PSA, PSA doubling time, and PSA velocity. <b><i>Results:</i></b> Evidence for no difference between PET/CT-positive and -negative patients for log-transformed PSA was found (BF<sub>01</sub> 3.61, % error: 0.01). Robustness check and sequential analysis showed stability across a wide range of prior distribution specifications. The hypothesis of no difference in terms of PSA-dt and for PSA-vel between groups was found to be more likely compared to the alternative hypothesis (BF<sub>01</sub> of 3.44 and 3.48, respectively). <b><i>Conclusion:</i></b> PSA and PSA kinetics are unlikely to be associated with <sup>18</sup>F-fluciclovine PET/CT positivity in patients with BCR, and none of these serum biomarkers might be used as single predictors of PET/CT detection. Larger studies might be needed to evaluate the role of different predictors.
DOI: 10.6084/m9.figshare.25963867.v3
title: Floods inventory of HMA

description: This flood data is compiled from sources such as public databases, flood yearbooks, media reports, and literature.
DOI: 10.6084/m9.figshare.26893276.v1
title: Supplementary Material for: The association between preserved-ratio impaired spirometry and depression: results from a prospective population-based study

description: Introduction: The relationship between preserved-ratio impaired spirometry (PRISm) and depression remains unclear. This study aimed to assess the bidirectional relationship between PRISm and depression using data from a national cohort.
Methods: Data from Wave 2 (2004–2005) to Wave 4 (2008–2009) of the English Longitudinal Study of Ageing (ELSA) were analyzed. Lung function and depressive symptoms were measured at baseline and follow-up. Cox proportional hazard models were used to calculate the hazard ratio (HR) of PRISm with depression (Study 1) and depression with PRISm (Study 2).
Results: Studies 1 and 2 included 2,934 and 2,277 participants, respectively. The follow-up period extended from Wave 2 to Wave 4. In univariate analyses, a bidirectional association between PRISm and depression was observed, with unadjusted HRs of 1.49 (95% confidence interval [CI], 1.12-1.99; P=0.007) in Study 1 and 1.69 (95% CI, 1.13-2.52; P=0.010) in Study 2. However, in multivariable Cox models, baseline PRISm was not associated with subsequent depression development (adjusted HR 1.26; 95% CI, 0.94-1.69; P=0.128). Conversely, participants with depression had a significantly higher risk of developing PRISm compared to those without depression (adjusted HR 1.54; 95% CI, 1.03-2.32; P=0.038). These findings were consistent with z-score-based interpretive strategies, with an adjusted HR of 1.30 (95% CI, 0.95-1.77; P=0.105) in Study 1 and 1.59 (95% CI, 1.03-2.47; P=0.038) in Study 2.
Conclusions: Depression was associated with an increased risk of developing PRISm, whereas PRISm did not increase the risk of developing depression. Physicians should be vigilant for potential PRISm development in patients with depression.
DOI: 10.6084/m9.figshare.3528503.v1
title: Supplement 1. Matlab files for conducting applications and examples.

description: File List Humanopen.txt <br> SERsens.txt <br> numSERsens.txt <br> lampj.txt <br> lampreal.txt <br> StripedBass.txt <br> LHSERSproj.txt <br> AMCO1.txt <br> BLTI1.txt <br> KIPE1.txt <br> LEKE1.txt <br> LSGO1.txt <br> NOFU1.txt <br> PAJA1.txt <br> SOAL1.txt <br> SPOW1.txt <br> WAAL1.txt<br> Supplement.zip – All files at once Description The .txt files are designed for use in Matlab. First, open the .txt files in the Matlab Editor and save them as .m files in order to make the code more user-friendly. Then, save all the .m files in a folder. Each file is designed for conducting one, or several, of the applications and examples appearing in the main text or online appendices. Their intended use is described in the following: Age-related dynamics of inertia in a population open to migration Humanopen.txt – (main file for conducting example) SERsens.txt – (matlab function for use in Humanopen.txt) lampj.txt – (matlab function for use in Humanopen.txt) Appendix D: Illustration of population inertia sensitivities in a source-sink metapopulation StripedBass.txt – (main file for conducting example) lampj.txt – (matlab function for use in StripedBass.txt) Appendix E: Illustration of population inertia sensitivities across life history strategies LHSERSproj.txt – (main file for conducting example) SERsens.txt – (matlab function for use in LHSERSproj.txt) numSERsens.txt – (matlab function for use in LHSERSproj.txt) lampreal.txt – (matlab function for use in LHSERSproj.txt) AMCO1.txt – (data file for use in LHSERSproj.txt) BLTI1.txt – (data file for use in LHSERSproj.txt) KIPE1.txt (data file for use in LHSERSproj.txt) LEKE1.txt (data file for use in LHSERSproj.txt) LSGO1.txt (data file for use in LHSERSproj.txt) NOFU1.txt (data file for use in LHSERSproj.txt) PAJA1.txt (data file for use in LHSERSproj.txt) SOAL1.txt (data file for use in LHSERSproj.txt) SPOW1.txt (data file for use in LHSERSproj.txt) WAAL1.txt (data file for use in LHSERSproj.txt)
DOI: 10.6084/m9.figshare.26978521.v1
title: Supplementary Figures and Code R markdown from Immunological feedback loops generate parasite persistence thresholds that explain variation in infection duration

description: R markdown file containing all code necessary to reproduce the results presented in the main text, as well as to produce supplemental figures.
DOI: 10.6084/m9.figshare.c.3799384_d3.v1
title: Additional file 3: of CottonFGD: an integrated functional genomics database for cotton

description: List of used WGS resequencing data. Including 96 analyses containing 79Â G. hirsutum strains and 83 analyses containing 52Â G. barbadense strains. (XLSX 31 kb)
DOI: 10.4121/12709127.v2
title: Receipt phase of an environmental permit application process (WABO), CoSeLoG project

description: This data originates from the CoSeLoG project executed under NWO project number 638.001.211. Within the CoSeLoG project the (dis)similarities between several processes of different municipalities in the Netherlands has been investigated. This event log contains the records of the execution of the receiving phase of the building permit application process in an anonymous municipality.
DOI: 10.6084/m9.figshare.24239725.v1
title: Supplementary material for: Pirowski, T., Szypuła B., 2023 "Dasymetric population mapping using building data"

description: This paper uses data on residential buildings from the nationwide vector database. Attribute information on buildings (location, volume, function, etc.) provides opportunities to estimate the number of residents. The recalculation of the population from the urban units into new spatial units was based on the area-weighted aggregation method. The location of buildings constituted a limiting variable, while the total square meterage (calculated as the area of the buildings and the number of their floors) constituted the binding variable. The introduction of additional binding variables related to the type of building and its location, as well as various methods of determining the square meterage per building type, resulted in the creation of a total of 19 maps of Cracow’s population. The results of the recalculation of population were related to demographic data compiled by the organisation Statistics Poland (GUS) relating to the 1x1 km grid. Comparison of the results with demographic data relating to other reference units allowed the reduction of subjective interpretation and the refining of input data conversion methods. As a result, correct methods for segmenting buildings were identified, useful optimisation criteria were selected, and the accuracy of population maps developed based on the database was calculated. For the input data, based solely on the amount of population in urban units, the calculated value of the mean absolute percentage error (MAPE) in the 1x1 km grid was 310.8%, and for the root mean square error (RMSE) was 1476 people. In the dasymetric method, directly associating the population with the volume of buildings, the errors fell to 21.9% and 632 people, respectively. Among the remaining 18 variants introducing the segmentation of buildings from the database, the best result was obtained for the variant based on minimizing the RMSE, associating the number of residents to single-family buildings (2.88 people/building) and associating the number of residents to the square footage in multi-family buildings (37.1m2/person) (MAPE=19.2%, RMSE=556 people).