cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/46npy3y2zg
title: Attenuating neural threat expression with imagination. Reddan et al

description: Neuroimaging and behavioral data and analysis scripts to reproduce the figures in Reddan, Wager, Schiller (2018) Attenuating neural threat expression with imagination. Neuron. Please contact first author marianne.reddan@gmail.com if you have questions or requests
DOI: 10.17632/p7y5wmschg
title: Machine Learning and Network Medicine approaches for Drug Repositioning for COVID-19. Santos et al.

description: Supplemental Items used in "Machine Learning and Network Medicine approaches for Drug Repositioning for COVID-19" by Suzana 
de Siqueira Santos, Mateo Torres, Diego Galeano, María del Mar Sánchez, Luca Cernuzzi, and Alberto Paccanaro. The items include 
input datasets, and predictions by our matrix decomposition model and network medicine approach.

Predictions by our matrix decomposition model are shown in Supplementary File 1. Two out of three interactomes used by our 
network medicine approach were mapped to SwissProt proteins and shown in Supplementary Files 
2 (Luck et al., 2020, DOI: 10.1038/s41586-020-2188-x), and 3 (Cheng et al., 2018, DOI: 10.1038/s41467-018-05116-5). 
For these two interactomes, we used drug-target associations in Supplementary File 4, and 336 host proteins 
(UniProt accession numbers) in Supplementary File 5. For the Gysi el al. interactome 
(Gysi et al., 2021, DOI: 10.1073/pnas.2025581118), we used Entrez IDs of the 336 host proteins shown in Supplementary File 6. 
Supplementary File 7 shows the ATC categories of DrugBank drugs. DrugBank entries with effect against SARS-CoV-2 according to
 CMAP, in vitro, and clinical trials evidence are shown in Supplementary Files 8, 9, and 10, respectively. Predictions by our network
 medicine approach are shown in Supplementary File 11. The weights assigned to the host proteins by the kernel-based methods are 
shown in Supplementary File 12.
DOI: 10.6084/m9.figshare.16847707.v1
title: Table S3 edgeR results.xlsx

description: Supplementary table 2, containing full results from edgeR RNA-sequencing differential expression analysis of <i>B. malayi </i>microfilariae controls compared to treatment with tetracyclines, used in the associated manuscript for drawing conclusions. Full details on data generation are available in the related manuscript.<br>
DOI: 10.6084/m9.figshare.24013908.v1
title: Supplementary Material for: Development and validation of a nomogram for predicting all-cause mortality in patients with hemodialysis having pulmonary hypertension

description: Introduction: Patients with end-stage renal disease receiving hemodialysis (HD) have a high morbidity and mortality rate associated with pulmonary hypertension (PH). A nomogram was developed to predict all-cause mortality in HD patients with PH. In this study, we aimed to validate the usefulness of this nomogram. Methods: A total of 274 HD patients with PH were hospitalized at the Affiliated Hospital of Xuzhou Medical University between January 2014 and June 2019 and followed up for 3 years. Echocardiography detected PH when the peak tricuspid regurgitation velocity (TRV) was more than 2.8 m/s. To evaluate the all-cause mortality for long-term HD patients with PH, Cox regression analysis was performed to determine the factors of mortality that were included in the prediction model. Next, the area under the receiver-operating characteristic curve (AUC-ROC) was used to assess the predictive power of the model. Calibration plots and decision curve analysis (DCA) were used to assess the accuracy of the prediction results and the clinical utility of the model. Results: The all-cause mortality rate was 29.1% throughout the follow-up period. The nomogram comprised six commonly available predictors: age, diabetes mellitus, cardiovascular disease, hemoglobin, left ventricular ejection fraction, and TRV. The 1-year, 2-year, and 3-year AUC-ROC values were 0.842, 0.800, and 0.781, respectively. The calibration curves revealed an excellent agreement with the nomogram, while the DCA demonstrated favorable clinical practicability. Conclusion: The first developed nomogram for predicting all-cause mortality in HD patients with PH could guide clinical decision-making and intervention planning.
DOI: 10.6084/m9.figshare.24006267.v1
title: Supplementary Material for: Refining a multifaceted model of perceived utility of genomic sequencing results

description: Introduction: Research on the perceived utility of genomic sequencing has focused primarily on pediatric populations and on individuals and families with rare genetic diseases. Here, we evaluate how well a multifaceted perceived utility model developed with these populations applies to a diverse, adult population aged 18-49 at risk for hereditary cancer and propose new considerations for the model. Methods: Participants received clinical genomic sequencing in the Cancer Health Assessments Reaching Many (CHARM) study. Semi-structured qualitative interviews were conducted with a subset of participants at one and six months after results disclosure. We used an approach influenced by grounded theory to examine perceptions of the utility of genomic sequencing and analyzed how utility in CHARM mapped to the published multifaceted perceived utility model, noting which domains were represented or absent, and which were most salient to our population. Results: Participants’ discussions of utility often involved multiple domains and revealed the variety of ways in which receiving sequencing results can impact one’s life. Results demonstrated that an individual’s perception of utility can change over the life course when sequenced at a relatively young age and may be influenced by the resources available to them to act on the results. Discussion/Conclusion: Our findings demonstrate the relevance of a multifaceted perceived utility model for a diverse adult population at risk for hereditary cancer. We identified refinements that could make the model more robust, including emphasizing the overlapping nature of the domains, and the importance of life stage and personal resources to the perception of utility.
DOI: 10.6084/m9.figshare.25398451.v1
title: Metagenome-assembled genomes (MAGs)

description: The MetaWRAP pipeline was employed for genome assembly and binning. Specifically, MEGAHIT was used to assemble sequences and generate contigs. Prodigal was used to predict open reading frames (ORFs) in each contig. MetaBAT2 and MaxBin2 were used to perform genome binning of assembled contigs, and the assembled bins were subsequently verified with the Bin_refinement module. The consolidated bins were improved by the Reassemble_bins module to generate final metagenome-assembled genomes (MAGs).
DOI: 10.6084/m9.figshare.3526907.v1
title: Appendix B. A description of protocol for calculation of wave exposure.

description: A description of protocol for calculation of wave exposure.
DOI: 10.17632/yzyn6rxksh
title: Supplementary data files regarding antimicrobial resistance in commensal E. coli from healthy Australian dairy cattle

description: Supplementary data files for the study titled “Epidemiology of antimicrobial resistance in commensal E. coli from dairy cattle on a Mediterranean pasture-based system of Australia: A cross-sectional study”, authored by M. Tree, T.J.G.M. Lam, S. McDougall, D.S. Beggs, I.D. Robertson, A.L. Barnes, A. Chopra, R. Ram, C.A. Stockman, T.C. Kent, J.W. Aleri. This study assessed antimicrobial resistance for 891 commensal E. coli isolated from healthy adult lactating cow and calf faeces collected from 26 Western Australian dairy farms. Supplementary Table 1 presents the STROBE-Vet checklist. Supplementary Table 2 presents the number and (percentage)1 of E. coli isolated from the faecal samples collected on each WA dairy farm. Supplementary Table 3 provides the AMR and virulence genes identified to be present within the genome of MDR E. coli isolated from the faecal samples collected on WA dairy farms.
DOI: 10.6084/m9.figshare.17075978.v2
title: fig wasps' DNA marker

description: Sanger sequencing
DOI: 10.6084/m9.figshare.20301108.v1
title: Supplementary Material for: Atezolizumab Plus Bevacizumab vs Sorafenib for Unresectable Hepatocellular Carcinoma: Results From Older Adults Enrolled in the IMbrave150 Randomized Clinical Trial

description: Introduction The efficacy of systemic first-line treatments in older adults with unresectable hepatocellular carcinoma (HCC) has not been well-studied. We compared the safety and efficacy of atezolizumab plus bevacizumab vs sorafenib as a first-line treatment in younger vs older patients with unresectable HCC. Methods This global, phase 3, open-label, randomized clinical trial (IMbrave150) recruited patients aged ≥18 years with locally advanced metastatic or unresectable HCC, an Eastern Cooperative Oncology Group performance status score of 0 or 1, and Child-Pugh class A liver function who had not previously received systemic therapy for liver cancer. Patients received either 1200 mg atezolizumab plus 15 mg/kg bevacizumab intravenously every 3 weeks or 400 mg sorafenib orally twice daily until loss of clinical benefit or unacceptable toxicity. Primary endpoints were overall survival (OS) and progression-free survival (PFS). Secondary outcomes were incidence of adverse events and time to deterioration of patient-reported outcomes (PROs). This subgroup analysis evaluated safety and efficacy endpoints in patients &lt;65 years, ≥65 to &lt;75 years, and ≥75 years. Results Of 501 patients, 165 patients were randomized to sorafenib and 336 were randomized to atezolizumab plus bevacizumab (175 patients &lt;65 years; 106 patients ≥65 to &lt;75 years; 55 patients ≥75 years). Across all age groups, patients receiving atezolizumab plus bevacizumab had longer median OS (&lt;65: 18.0 vs 12.2 months [HR, 0.57; 95% CI, 0.40-0.82]; ≥65 to &lt;75: 19.4 vs 14.9 months [HR, 0.80; 95% CI, 0.52-1.23]; ≥75: 24.0 vs 18.0 months [HR, 0.72, 95% CI, 0.37-1.41]) and PFS than those receiving sorafenib. Time to deterioration for multiple PROs was delayed for patients receiving atezolizumab plus bevacizumab, including older adults. There were no clinically meaningful differences in toxicity between age groups. Conclusion Atezolizumab plus bevacizumab is safe and effective in adults &lt;65, ≥65 to &lt;75, and ≥75. Treatment was well-tolerated even in elderly patients.
DOI: 10.6084/m9.figshare.22269487.v1
title: agri_canola.tif

description: canola straw map
DOI: 10.6084/m9.figshare.24601854.v2
title: oranigbr-BATB-BRTR-P10P.zip

description: Zip files include four scenarios: Scenario 1: Increase of 10 p.p. in the taxation of the sector from 2023;Scenario 2: Increase of 20 p.p. in the taxation of the sector from 2023;Scenario 3: Increase of 30 p.p. in the taxation of the sector from 2023;Scenario 4: Gradual increase from 10 to 30 p.p. in the taxation of the sector between the years 2023 and 2025.
DOI: 10.6084/m9.figshare.24901584.v7
title: <b>Frontal midline theta transcranial alternating current stimulation </b><b>enhances early consolidation of episodic memory</b>

description: Evidence implicating theta rhythms in declarative memory encoding and retrieval, together with the notion that both retrieval and consolidation involve memory reinstatement or replay, suggests that post-learning theta rhythm modulation can promote early consolidation of newly formed memories. Building on earlier work employing theta neurofeedback, we examined whether theta-frequency transcranial alternating stimulation (tACS) can engender effective consolidation of newly formed episodic memories, compared with beta frequency stimulation or sham control conditions. We compared midline frontal and posterior parietal theta stimulation montages, and examined whether benefits to memory of theta upregulation are attributable to consolidation rather than to retrieval processes by using a washout period to eliminate tACS after-effects between stimulation and memory assessment. Four groups of participants viewed object pictures followed by a free recall test during three study-test cycles. They then engaged in tACS (frontal theta montage / parietal theta montage / frontal beta montage / sham) for a period of 20 minutes, followed by a 2-hour break. Free recall assessments were conducted after the break, 24 hours later, and 7 days later. Frontal midline theta-tACS induced significant off-line retrieval gains at all assessment time points, relative to all other conditions. This indicates that theta upregulation provides optimal conditions for consolidation of episodic memory, independent of mental-state strategies.
DOI: 10.6084/m9.figshare.25013312.v1
title: Supplementary Material for: Magnetic resonance imaging-based Classifications for Symptom of Adenomyosis

description: Objectives: To identify an optimal magnetic resonance imaging (MRI)-based classification for the severity of adenomyosis and explore the factors associated with disease severity (dysmenorrhea or menorrhagia).
Design and Participants: Several classifications based on MRI have been proposed, and their phenotypes are reported to be associated with the severity of adenomyosis. However, a consensus classification based on MRI findings has not yet been reached. Our study was designed to retrospectively analyze data from a cohort of patients in the Affiliated Nanchong Central Hospital of North Sichuan Medical College from June 2017 to December 2021 before focused ultrasound ablation surgery (FUAS), to identify the optimal classification of adenomyosis severity from different classification criteria and explore factors associated with the presence of symptoms.
Methods: The proportions of disease severity among different classification groups were compared to obtain the one generating the most considerable chi-square value, which was identified as the optimal classification for informing disease severity. A logistic regression model was constructed to explore factors associated with disease severity.
Results: Classification of Kobayashi H (classification 4) concerning the affected areas and size (volumes of lesions) was recognized as the optimal one, which identified dysmenorrhea (χ2=18.550, p-value=0.002) and menorrhagia (χ2=15.060, p-value=0.010) secondary to adenomyosis. For volumes of uterine wall &lt;2/3, the dysmenorrhea rate in subtype-4 was higher than that in subtype-1 (χ2=4.114, p-value=0.043), and the dysmenorrhea rate in subtype-5 was higher than that in subtype-2 (χ2=4.357, p-value=0.037). Age (OR=0.899, 95%CI=0.810～0.997, p-value=0.044) and external phenotype (OR=3.588, 95%CI=CI 1.018～12.643, p-value=0.047) were associated with dysmenorrhea. Concerning volumes of uterine wall ≥2/3, the menorrhagia rate in subtype-3 remarkably increased compared with that in subtype-6 (χ2=9.776, p-value=0.002), and internal phenotype was identified as an independent factor associated with menorrhagia (OR=1.706, 95%CI=1.131～2.573, p-value=0.011).
Limitations: Patients in our study were all included before FUAS, which limited our result interpretation for the general patient population.
Conclusions: MRI-based classification 4 is identified as an optimal classification for informing the severity of adenomyosis. The phenotype of classification is the main characteristic associated with disease severity.
DOI: 10.6084/m9.figshare.25393273.v1
title: Wastewater Taxonomic Abundance Matrices

description: Taxonomic abundance data across classifiers.<br><br>xtree -- the numbers separated by an underscore at the total genome and "unique portion of the genome" coverage cutoffs, respectively, used to mask the data. All aligned reads below those cutoffs are set to 0.<br><br>kraken -- confX refers to the --confidence flag setting, 0 or 0.2<br>MetaPhlAn4 was run with the default settings.<br><br>decontam vs nodecontam refers to if a dataframe were decontaminated (using the decontam package in R).<br>k, d, p, c, o, g, s refer to clade ranks. Viruses (PVC) are only reported here at the species level. For viral taxonomic annotations, please refer to the PVC: https://figshare.com/projects/The_Pan_Viral_Compendium/185977
DOI: 10.17632/jjky2k38kp
title: Scoring rubric for the modified version of the Environment and Policy Assessment and Observation-Self Report (EPAO-SR) tool, used to assess the nutrition and physical activity environment in Family Child Care services

description: Scoring rubric for the modified version of the Environment and Policy Assessment and Observation-Self Report (EPAO-SR) tool, used to assess the nutrition and physical activity environment in Family Child Care services
DOI: 10.6084/m9.figshare.25003727.v3
title: code

description: <b>code for review</b>2D FPF in Example 1
DOI: 10.6084/m9.figshare.13258595.v1
title: Generated MCBJ datasets

description: Generated MCBJ datasets accompanying the manuscript 'Benchmark and application of unsupervised classification approaches for univariate data' and used for the benchmark in the main text
DOI: 10.6084/m9.figshare.28330997.v1
title: Dataset of FADD Deficiency Cases

description: FADD deficiency is a rare autosomal recessive inborn error of immunity characterized by impaired apoptosis, dysregulated immune activation, and susceptibility to recurrent infections, autoinflammation, lymphoproliferation, and autoimmune manifestations. This dataset was compiled as part of a systematic review analyzing all reported cases of FADD deficiency in the literature. Inclusion criteria encompassed original human clinical studies and non-experimental observational studies, while studies involving non-FADD mutations or in vitro research were excluded. The systematic literature search identified eight relevant articles for review. The reviewed cohort comprised 13 patients. The dataset includes demographic details, genetic findings (FADD gene mutations and inheritance patterns), clinical presentations (fever-related encephalopathy, invasive pneumococcal disease, lymphoproliferation, and organ dysfunction), immunological parameters (lymphocyte apoptosis defects, antibody deficiencies, and double-negative T-cell counts), neuroimaging findings, and treatment outcomes.Metadata:MMR – Measles, Mumps, and Rubella vaccineVZV – Varicella-Zoster VirusHHV-6 – Human Herpesvirus 6CMV – CytomegalovirusEBV – Epstein-Barr VirusCT – Computed TomographyMRI – Magnetic Resonance ImagingIPD – Invasive Pneumococcal Disease (a severe infection caused by <i>Streptococcus pneumoniae</i>, including conditions like meningitis and bacteremia)<br>The data were extracted from the following sources:Bolze A, Byun M, McDonald D, Morgan NV, Abhyankar A, Premkumar L, et al. Whole-exome-sequencing-based discovery of human FADD deficiency. American Journal of Human Genetics. 2010;87(6):873-81.Meer E, Solanes F, Kohn L, Kuo CY, Wong DA, Pineles S, et al. Ocular findings associated with FADD deficiency resemble familial exudative vitreoretinopathy. American Journal of Ophthalmology case reports. 2022;25:101305.Kohn LA, Long JD, Trope EC, Kuo CY. Novel Compound Heterozygote Variations in FADD Identified to Cause FAS-Associated Protein with Death Domain Deficiency. Journal of Clinical Immunology. 2020;40(4):658-61.Vogel B, Boyd NK, Kuo CY, Kohn LA, Soldatos A, Santoro JD. Immunotherapy responsive neuroinflammation in a child with FAS‐associated death‐domain mutation. Clinical Genetics. 2023;103(2):252-3.Setia P, Bargir UA, Shanmukhaiah C, Jodhawat N, Gaikwad P, Vedpathak D, et al. Expanding the clinical phenotype of FADD deficiency with a novel mutation and its role in Fas-mediated apoptotic pathway. British Journal of Haematology. 2023;202(2):e11-e5.Giovannini G, Giannoccaro MP, Cioclu MC, Orlandi N, Liguori R, Meletti S. FADD gene pathogenic variants causing recurrent febrile infection-related epilepsy syndrome: Case report and literature review. Epilepsia. 2024;65(7):e119-e24.Savic S, Parry D, Carter C, Johnson C, Logan C, Gutierrez BM, et al. A new case of Fas-associated death domain protein deficiency and update on treatment outcomes. The Journal of Allergy and Clinical Immunology. 2015;136(2):502-5.e4.<br>
DOI: 10.6084/m9.figshare.5732328.v1
title: ipinyou.contest.dataset season2

description: iPinYou Global RTB Bidding Algorithm Competition Dataset
DOI: 10.17632/g7cxfygc3j
title: REWO Study - Supplementary material Appendix 1-3

description: Supplementary Material for the article: Acute cholecystitis – a cohort study in a real-world clinical setting (REWO study) Digital Content
DOI: 10.17632/mstcx94xyj
title: Parasitized & unparasitized Manduca mass over time

description: This compares weight of both parasitized and unparasitized Manduca, demonstrating the reduction in feeding in the later stages of parasitism.
DOI: 10.6084/m9.figshare.28748915.v1
title: Main_Document.doc

description: Genes important for research and breeding new plant varieties are crucial for the survival and development of human civilization. Seeds of cereal germplasm are maintained in gene banks (GBs) and grain viability of GB accessions must be regularly restored by seed multiplication. During related operations human errors result in contaminated or mislabelled accessions and thus in genotype non-authenticity, and such mistakes accumulate. The detection of non-authentic genotypes in GBs has been a major topic of our research. In this article 289 accessions of 93 winter barley varieties were studied, each obtained from several of the total of nine GBs (on average 3.1). Five single seed progenies (SSPs) were usually harvested from an accession and their genes of specific powdery mildew resistance were postulated. In 1,412 analysed lines 22 known resistance genes and 60 of their combinations were identified. Variety accessions from different GBs were compared; 40 (13.8%) were mislabelled and 102 (35.3%) heterogeneous, both containing a minimum of 276 SSPs (19.7%) carrying non-authentic genotypes. In 93 varieties 273 genotypes were found; 68 (73.1%) varieties were heterogeneous, containing from two to eight, (on average 3.6) genotypes. Misrepresented varieties in GBs are a great problem for research projects, especially those aimed at finding new (e.g. molecular) varietal characteristics, and in breeding programmes as the required gene combination of bred varieties cannot be achieved. A suggested way to allot responsibility for use of authentic genotypes is proposed.
DOI: 10.6084/m9.figshare.19576117.v2
title: Multiple sequence alignments and HMMs of the four core virion proteins of eukaryotic bamfordviruses

description: Multiple sequence alignments of the major capsid proteins, minor capsid proteins, protease and ATPase found in the bamfordviruses that infect eukaryotes. These include a concatenated alignment and an alignment with <em>E. coli </em>phage PRD1 as an outgroup. <br> Files also include 38 HMM models used to search for protein homologoues.
DOI: 10.6084/m9.figshare.14748384.v4
title: The MOISCRUST dataset

description: The MOISCRUST dataset is a 14-yr continuous dataset of surface soil moisture measurements from multiple microsites (vegetated and open areas with different degree of biocrust development) gathered from the Aranjuez Experimental Station, a semi-arid grassland in Central Spain.
DOI: 10.17632/fcyd9c42dg
title: Supplementary data - manuscript "Supervised learning-based 3D imaging from single grayscale image"

description: 3D reconstruction of a dynamic scene. 
This video shows the advanced technique of integrating structured-light and deep learning to deliver the single-shot 3D reconstruction of dynamic object.
DOI: 10.6084/m9.figshare.28151450.v1
title: Annotation results( <i>Ilisha elongata</i> )

description: These are annotation result files of the <i>Ilisha elongata</i>.
DOI: 10.6084/m9.figshare.1249718.v1
title: CFMT Dataset for Cho et al., 2014

description: This is the data (collected online and in the lab) for the following article: Cho, Sun-Joo, Wilmer, J., Herzmann, G., McGugin, R.W., Fiset, D., Van Gulick, A.E., Ryan, K, & Gauthier, I. (in press). Item Response Theory Analyses of the Cambridge Face Memory Test (CFMT). Psychological Assessment.