cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20047763.v1
title: Supplementary Material for: <b><i>DAXX</i></b>, <b><i>ATRX</i></b>, and MSI in PanNET and Their Metastases: Correlation with Histopathological Data and Prognosis

description: <b><i>Introduction:</i></b> Studies on pancreatic neuroendocrine tumors (PanNETs) regarding loss of <i>ATRX</i>, <i>DAXX</i>, or frequency of microsatellite instability (MSI) show inconclusive results. So far, data on corresponding metastaseshave not been published. <b><i>Methods:</i></b> We performed immunohistochemistry (IHC) of <i>ATRX</i>, <i>DAXX</i>, <i>MSH2</i>, <i>MSH6</i>, <i>MLH1</i>, and <i>PMS2</i> on 74 PanNETs and 19 metastases. <i>ATRX-</i> and <i>DAXX</i>-negative PanNETs were further sequenced for mutations. We used polymerase chain reaction for MSI on cases with IHC loss of <i>MSH2</i>, <i>MSH6</i>, <i>MLH1</i>, and <i>PMS2</i>. <b><i>Results:</i></b> Immunohistochemical loss of <i>DAXX</i> and <i>ATRX</i> was observed in 8/74 (11%) and 6/74 (8%) PanNETs. Loss of <i>DAXX</i> immunoreactivity was statistically associated with higher tumor grade and showed a tendency toward a decreased overall survival. Sequencing of <i>DAXX-</i> (7/11 [64%]) and <i>ATRX-</i>negative (5/11 [45%]) PanNETs revealed a mutation in 6/7 (86%) and 2/5 (40%). The specificity of immunohistochemical loss of <i>DAXX</i> and <i>ATRX</i> for mutation was 80% and 67%, respectively. The expression status of <i>DAXX</i> compared to primary tumor differs in 2/12 (17%) lymph node metastases. We further identified 3/74 (4%) tumors as MSI, associated with a poor prognosis. <b><i>Discussion/Conclusion:</i></b> Our study supports the hypothesis that a loss of <i>DAXX</i> immunoreactivity can identify a more aggressive subtype of PanNET with high confidence, while <i>ATRX</i> loss is a weaker indicator. Our results also strengthen the role of <i>DAXX</i> immunolabeling as a prognostic marker. We could show that <i>ATRX</i> might be less suitable as a surrogate for sequencing. Our results indicate that IHC of <i>DAXX</i> and <i>ATRX</i> may identify PanNET subtypes as targets for more aggressive therapy.
DOI: 10.6084/m9.figshare.16881964.v1
title: Supplementary Material for: Guideline-Directed Medical Therapy in Patients with Chronic Kidney Disease Undergoing Peripheral Vascular Intervention

description: <b><i>Introduction:</i></b> Guideline-directed medical therapy (GDMT) is imperative to improve cardiovascular and limb outcomes for patients with critical limb ischemia (CLI), especially amongst those at highest risk for poor outcomes, including those with comorbid chronic kidney disease (CKD). Our objective was to examine GDMT prescription rates and their variation across individual sites for patients with CLI undergoing peripheral vascular interventions (PVIs), by their comorbid CKD status. <b><i>Methods:</i></b> Patients with CLI who underwent PVI (October 2016–April 2019) were included from the Vascular Quality Initiative (VQI) database. CKD was defined as GFR &lt;60 mL/min/1.73 m<sup>2</sup>. GDMT included the composite use of antiplatelet therapy and a statin, as well as an angiotensin-converting enzyme inhibitor or angiotensin receptor blocker if hypertension was present. The use of GDMT before and after the index procedure was summarized in those with and without CKD. Adjusted median odds ratios (MORs) for site variability were calculated. <b><i>Results:</i></b> The study included 28,652 patients, with a mean age of 69.4 ± 11.7 years, and 40.8% were females. A total of 47.5% had CKD. Patients with CKD versus those without CKD had lower prescription rates both before (31.7% vs. 38.9%) and after (36.5% vs. 48.8%) PVI (<i>p</i> &lt; 0.0001). Significant site variability was observed in the delivery of GDMT in both the non-CKD and CKD groups before and after PVI (adjusted MORs: 1.31–1.41). <b><i>Discussion/Conclusion:</i></b> In patients with CLI undergoing PVI, patients with comorbid CKD were less likely to receive GDMT. Significant variability of GDMT was observed across sites. These findings indicate that significant improvements must be made in the medical management of patients with CLI, particularly in patients at high risk for poor clinical outcomes.
DOI: 10.6084/m9.figshare.1365432.v1
title: Risk-taking behavior in a computerized driving task: brain activation correlates of decision-making, outcome, and peer influence in male adolescents

description: 1) a supplementary table for questionnaire and task performance data 2) fMRI data in the form of contrast files used in the second-level analyses
DOI: 10.6084/m9.figshare.20332692.v1
title: Supplementary data for "Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies"

description: Supplementary data for "Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies" <br> It includes the raw data, results, and code to reproduce the results.
DOI: 10.6084/m9.figshare.22656730.v1
title: Supplementary Material for: Unusual cause of thrombocytopenia and renal failure in a 14-year-old boy (MYH9-associated disorders)

description: MYH9-associated disorders represent rare group of autosomal dominant diseases and are caused by pathogenic mutations in the MYH9 gene. Clinically are represented by macro-platelet-thrombocytopenia, various degrees of renal dysfunction, hearing loss and early-onset cataracts. We describe the case of 14-year-old boy in medical follow-up from birth for thrombocytopenia. Systolic hypertension and nephrotic proteinuria were detected at preventive health check. Renal biopsy revealed sing of segmental glomerulosclerosis. Dialysis treatment was needed. Before transplantation due to the finding of chronic tonsillitis with positive bacterial capture in the culture examination, tonsillectomy was indicated. Postoperative period was complicated with arterial post-tonsillectomy haemorrhage. Six months after tonsillectomy the patient underwent primary deceased-donor kidney transplantation without complication. Blood platelets showed fluctuating character in the zone of sever thrombocytopenia. However, no signs of bleeding were present. Three months after successful transplantation gene sequencing of whole exon was performed. The presence of the variant c.2105G&gt; A [p. (Arg702HIS)] in exon 17 of the MYH9 gene has been detected. The variant c.2105G&gt;A may be clinically manifested by progressive proteinuria with rapid deterioration of renal function. This case is an example of the delayed diagnosis of rare disease and highlights the usefulness of genetic testing.
DOI: 10.6084/m9.figshare.28579784.v1
title: raw data.zip

description: Lung cancer remains highly malignant worldwide, with rising incidence rates. This study aims to develop a predictive model using cell lines resistant to EGFR-tyrosine kinase inhibitors (EGFR-TKIs) to create a risk score predicting outcomes in lung cancer patients on EGFR-TKI therapy.
DOI: 10.6084/m9.figshare.28638233.v1
title: Supplementary Material for: Caffeine Consumption, Psychological Distress, and Insomnia in a Cohort of Individuals with Depression

description: Objective: Caffeine is a widely consumed psychoactive compound that can cause anxiety and sleep difficulties, in part due to genetic variation. We investigated the association between caffeine consumption, psychological distress, and sleep difficulties in a genetically informative cohort of individuals with a history of depression.

Methods: Survey data and genetic information were sourced from the Australian Genetics of Depression Study (AGDS (n = 20,689, �male = 75%, mean age 43±15 years)). Associations between caffeine consumption and symptoms of distress and sleep disturbance, as well as 9 genetic variants associated with caffeine consumption behaviour, were assessed using linear regression.

Results: The highest consumers of caffeine reported higher psychological distress measured by the Kessler 10 scale (β = 1.21, SE = 0.25, p = 1.4 x 10-6) compared to the lowest consumers. Consumption was associated with 2 genetic variants with effect sizes ~0.35 additional caffeinated drinks/day between opposite homozygotes (p &lt; 0.005). A deletion near MMS22L/POU3F2 was associated with 10% increased odds of reporting caffeine susceptibility (OR = 1.1 per deletion (95% CI 1.04 – 1.17), p = 0.002). 

Conclusions: Higher rates of caffeine consumption were associated with higher levels of psychological distress, but not insomnia, in individuals with a history of depression. While the direction of causality is unclear, caffeine consumption may be a modifiable factor to reduce distress in individuals susceptible to mental health problems. Some of the previous findings of single gene associations with caffeine consumption and susceptibility were replicated.
DOI: 10.6084/m9.figshare.5005346.v1
title: sysBio v1.0.0

description: A first version of sysBio, an open source package for modeling and simulation of biological systems. It provides ability to convert reactions into ordinary differential equations (ODEs) and ability to solve them via numerical integration or stochastic simulation.
DOI: 10.17632/28rryvwn63
title: Handgrips strength review

description: Dataset for review of handgrip strength methods in CKD
DOI: 10.17632/tycj43cfnk
title: WhatsApp Effectiveness measure

description: This dataset captures valuable information about student engagement, belonging, and interaction within university settings through WhatsApp groups. The data aims to shed light on the impact of digital communication platforms on students' academic experiences, social integration, and overall well-being. The dataset is organized into several tables, each providing specific insights into different aspects of student engagement and participation.
The data was collected from 2022 first entering students after a period of time interacting on whatsapp.
DOI: 10.6084/m9.figshare.23617197.v3
title: Generation time and spatial population synchrony R code and data sources

description: Generation time and spatial population synchrony data processing code <br> R code for processing data and running synchrony calculations Data sources for abundance time-series and life history trait data <br> Ellen C. Martin, Brage Bremset Hansen, Aline Magdalena Lee & Ivar Herfindal. 2023. Generation time and seasonal migration explain variation in spatial population synchrony across European bird species. Journal of Animal Ecology. In press. <br> Contact: ecmartin33@gmail.com
DOI: 10.6084/m9.figshare.25055645.v1
title: meas_MID00221_FID94179_DE_TRUFI_SAX_MOCO_30avg.demo.gz

description: Cardinal MRI Dataset Demonstration for SCC(Surface Coil Intensity Correction (SCC)): Please be advised that this dataset has been derived from Siemens raw data with all sensitive information meticulously removed. While the structural integrity of the data is preserved, it may not be compatible with standard Siemens raw data tools.
DOI: 10.6084/m9.figshare.7813412.v1
title: Supplementary Material for: Overweight and Obesity in the Russian Population: Prevalence in Adults and Association with Socioeconomic Parameters and Cardiovascular Risk Factors

description: <b><i>Objective:</i></b> To evaluate the prevalence and geographic distribution of overweight and obesity in Russian adults aged 25–64 years as well as the association between chronic risk factors and obesity. <b><i>Methods:</i></b> Data were obtained from the survey “Epidemiology of Cardiovascular Diseases and Its Risk Factors in Some Regions of the Russian Federation” (ESSE-RF). This is a large cross-sectional multicenter population-based study that included interviews and medical examination (anthropometry, blood pressure [BP] measurement, and laboratory analysis) applied in 2012–2014. <b><i>Results:</i></b> The sample included 20,190 adults (response rate 79.4%) aged 25–64 years. Approximately one third of participants (30.3%) had obesity and another third (34.3%) were classified as overweight. BMI increased with age in both sexes. The prevalence of obesity between regions ranged from 24.4 to 35.5%. Overweight and obesity levels decreased with higher education (men only). Overall obesity rates were higher in rural than urban populations, but rates of overweight were similar in rural and urban populations. Participants with obesity were more likely to have BP &gt; 160/100 mm Hg (odds ratio &gt; 2.0) and also &gt; 140/90 mm Hg, raised blood glucose, and high triglycerides. <b><i>Conclusion:</i></b> The prevalence of overweight and obesity in Russian adults aged 25–64 years is not evenly distributed geographically, but it is comparable to that of other European countries. Individuals with obesity were also more likely to have indicators of poor cardiovascular and metabolic health.
DOI: 10.17632/8275525mh8
title: Multimodal x-ray and electron microscopy of the Allende meteorite

description: This dataset contains (1) spectroscopic Scanning Transmission X-ray Microscopy (STXM), (2) HAADF-STEM and (3) Electron Dispersive Spectroscopy (EDS) tomography data from Allende meteorite grain.
DOI: 10.26188/26534182.v2
title: Deidentified with participantID_2024 Consolidated Matched _ARC Public Schools Family Unit, Resilience and Wellbeing.csv

description: This data set is used to determinethe effectiveness of a positive education program in a state secondary school environment. Assessing the levels of resilience and well-being for Year 10 students group by Positive Education Program (PEP) and Well-being As Usual (WBAU) and by family unit.
DOI: 10.17632/f2cwvmmzfs
title: Data for: Classification of South Korean coastal sediments based on textural and geochemical characteristics and their major oceanographic constraints

description: South Korean coastal sediment data including textural and geochemical compositions (Mz, POC, CoCO3, Al, Mg, Si, REEs, Zr, etc.)
DOI: 10.6084/m9.figshare.13363502.v1
title: Scalable Integration and Querying of Nested Biological Data

description: Raw runtimes for the program performance for burden based analyses, driver gene analysis, and clinical exploratory programs.
DOI: 10.6084/m9.figshare.19754332.v1
title: Supplementary Material for: Serum Thyrotropin Elevation and Coronary Artery Calcification in Hemodialysis Patients

description: Introduction: Hypothyroidism is highly prevalent in end-stage kidney disease (ESKD) patients, and emerging data show that lower circulating thyroid hormone levels lead to downregulation of vascular calcification inhibitors and coronary artery calcification (CAC) in this population. To date, no studies have examined the association of serum thyrotropin (TSH), the most sensitive and specific single biochemical metric of thyroid function, with CAC risk in hemodialysis patients. Methods: In secondary analyses of patients from the Anti-Inflammatory and Anti-Oxidative Nutrition in Hypoalbuminemic Dialysis Patients (AIONID) trial, we examined serum TSH levels and CAC risk assessed by cardiac CT scans collected within a 90-day period. We evaluated the relationship between serum TSH with CAC Volume and Agatston scores (defined as &gt;100 mm3 and &gt;100 Houndsfield Units [HU], respectively) using multivariable logistic regression. Results: Among 104 patients who met eligibility criteria, higher TSH levels in the highest tertile were associated with moderately elevated CAC Volume and Agatston scores in case-mix adjusted analyses (ref: lowest tertile): adjusted ORs (aORs) (95%CIs) 4.26 (1.18, 15.40) and 5.53 (1.44, 21.30), respectively. TSH levels &gt;3.0 mIU/L (ref: ≤3.0 mIU/L) were also associated with moderately elevated CAC Volume and Agatston scores. In secondary analyses, point estimates of incrementally lower direct free thyroxine levels trended towards elevated CAC Volume and Agatston scores, although associations did not achieve statistical significance. Conclusions: In hemodialysis patients, higher serum TSH was associated with elevated CAC Volume and Agatston scores. Further studies are needed to determine if thyroid hormone supplementation can attenuate CAC burden in this population.
DOI: 10.17632/99w7bb2p5v
title: Basic life support knowledge among junior medical students dataset
DOI: 10.6084/m9.figshare.25680162.v1
title: Widely targeted metabolomics reveal the distribution of primary and secondary metabolites in pomegranate fruit

description: A total of 858 metabolites belonging to 11 classes were identifiedin pomegranate peel, seed and aril.Of which 647 metabolites showed statistically significant differences between the groups. Flavonoids mainly up-regulated in peel and aril; as were phenolic acids and amino acids in aril; tannins and terpenoids in peel; and lipids and alkaloids in seed. Some functional antioxidants, such as 10,16-dihydroxypalmitic acid, 3-O-methylellagic acid, and 3,3'-O-dimethylellagic acid, were first identified in pomegranate fruits.
DOI: 10.17632/cg3xsrfpy8
title: Niiya, Jiang, & Yakin (2000) JRP: Compassionate goals and dissent

description: Niiya, Y., Jiang, T., & Yakin S. (2020). Compassionate goals predict greater and clearer dissent expression to ingroups through collectively oriented motives in Japan and the U.S. Journal of Research in Personality, (online first) doi: 10.1016/j.jrp.2020.104057. (http://www.sciencedirect.com/science/article/pii/S009265662030146X) Abstract: Although compassionate goals often result in harmonious relationships, people with higher compassionate goals expressed dissent toward their ingroup, both directly (Study 1) and indirectly, through higher collectively oriented motives (Studies 2-4). They expressed dissent in clearer and less harmful ways, and were more likely to take ownership of their opinions (Studies 2-4). In contrast, the goals to project a desirable self-image showed mixed associations with the degree and methods of dissent expression. Similar results emerged in two contrasting socio-cultural contexts, namely Japan (Studies 1, 2, and 3) and the U.S. (Studies 3 and 4). Unlike interdependent cultural orientation, which involves the avoidance of confrontation, compassionate goals dissent expression to ingroup members by highlighting the benefit of dissent for the group. Keywords: compassionate goals; self-image goals; dissent; conformity; interdependence
DOI: 10.6084/m9.figshare.28811672.v1
title: HIP ABD ROM

description: Hip abduction range of motion in infants aged 0-3 months
DOI: 10.17632/699nwtvshn
title: Corrected ISICSoo class version

description: Abstract The Coster–Kronig enhancement factor calculation for M _3 shell x-ray production cross sections was found to be incorrect in both ISICSoo class (Batič et al. (2012) [1]) and isics program (Cipolla (2013) [2]). The affected functions of ISICSoo class have been corrected. The resulting X-ray production cross sections are modified by less than 15%, while ionization cross sections are unchanged. Title of program: ISICSoo Catalogue Id: AEKN_v1_1 Nature of problem Ionization and X-ray production cross section calculations for ion-atom collisions. Versions of this program held in the CPC repository in Mendeley Data AEKN_v1_0; ISICSoo; 10.1016/j.cpc.2011.10.004 AEKN_v1_1; ISICSoo; 10.1016/j.cpc.2013.02.018 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.26188/28720421.v1
title: Incorporated Chinese Community Voluntary Associations in Victoria, Australia

description: This database contains comprehensive information on 715 formally incorporated Chinese Voluntary Associations (CVAs) in the State of Victoria, Australia. Victoria is home to one of the largest and most vibrant ethnic Chinese communities in Australia, making this dataset particularly significant. The information provided includes organisation names, year of registration, membership numbers, deregistration years (where applicable), and mission statements (for some organisations). This rich collection of data offers researchers a unique opportunity to study the evolution and characteristics of Chinese community organisations in a key area of Chinese settlement and community development in Australia.While the database is based on self-reported information and may not perfectly reflect reality, it nonetheless provides a robust and detailed picture of the formally incorporated Chinese community organisations in Victoria. The dataset's strengths lie in its comprehensive coverage of registered CVAs and the inclusion of both active and deregistered organisations. However, it is important to note that informal, unincorporated associations are not included in this database.This valuable resource can support various research applications, including analyses of trends in organisation formation, patterns in organisational missions, membership dynamics, and comparative studies with other regions or ethnic communities. By making this database available, researchers can gain deeper insights into the Chinese diaspora's civic engagement and community-building efforts in one of Australia's most significant Chinese population centres, contributing to a better understanding of multicultural society and immigrant integration in urban contexts.
DOI: 10.6084/m9.figshare.13643144.v1
title: Supplementary files for "A Four Gene-based Immune Signature Predicts Dedifferentiation and Immune Exhaustion in Dedifferentiated Thyroid Cancer."

description: Supplementary files for "A Four Gene-based Immune Signature Predicts Dedifferentiation and Immune Exhaustion in Dedifferentiated Thyroid Cancer."
DOI: 10.6084/m9.figshare.16573118.v1
title: Feed Efficiency Genomics in Tilapia

description: Three type of files are available : phenotypic files, genomic file and pedigree file in view to perform genomic predictions.
DOI: 10.6084/m9.figshare.3512921.v1
title: Appendix A. Chaparral and coastal sage scrub mapped near Santa Ana, California, by the Weislander Vegetation Type Map survey in 1940 matches a similar distribution of this shrubland vegetation mapped in 1887.

description: Chaparral and coastal sage scrub mapped near Santa Ana, California, by the Weislander Vegetation Type Map survey in 1940 matches a similar distribution of this shrubland vegetation mapped in 1887.
DOI: 10.6084/m9.figshare.9917087.v1
title: CavBench datasets

description: CavBench's protein cavity datasets, which include cavities output by the following cavity detection methods: Fpocket, KVFinder, GHECOM, and Gaussian Finder. It is clear that ground truth dataset of protein cavities is also included.
DOI: 10.6084/m9.figshare.26148565.v1
title: Dataset: A novel approach for calculating prediction uncertainty when using acoustic indices and machine learning algorithms to monitor animal communities

description: Mammides, C., Huang, G., Sreekar, R., Ieronymidou, C., & Papadopoulos, H. (2024). A novel approach for calculating prediction uncertainty when using acoustic indices and machine learning algorithms to monitor animal communities. https://doi.org/10.21203/rs.3.rs-4494063/v1"BIOMON: Using passive acoustic monitoring methods to survey bird communities in biodiverse agricultural farmlands in the EU"https://cordis.europa.eu/project/id/1010902731/6/2022 - 31/5/2024
DOI: 10.6084/m9.figshare.3189775.v1
title: QCSsquirelindirecteffctFigshare.xlsx

description: We present here a case study to to measure short-term indirect effects between co-occurring plant species mediated by seed scatter-hoarding rodents in a subtropical forest in Southwest China using a replacement design and tracked the fate of individually-tagged seeds in experimental patches. We manipulated the benefits to rodents by using low-tannin dormant chestnuts (<i>Castanea henryi</i>) as palatable food and high-tannin non-dormant acorns (<i>Quercus variabilis</i>) as unpalatable food.
DOI: 10.6084/m9.figshare.3551505.v1
title: Full Archive

description: Full Archive