cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26335894.v2
title: <b>Gastric cytology: a supplement to early diagnosis of gastric malignancies</b>

description: <b>Introduction</b>: Gastric cancer is the fifth most common malignancy worldwide with high morbidity and mortality. Endoscopic gastric cytology and biopsy aid in early diagnosis and management. This study evaluates the diagnostic yield of gastric cytology in diagnosing gastric lesions with histopathology as the gold standard.<b>Methods</b>: This retrospective, cross-sectional study was conducted in the Department of Pathology for a period of 3.5 years. The cases with clinical suspicion of gastric malignancy and those who have had both cytology and histopathology examination were included. Cytology results were reported as positive for malignancy, suspicious for malignancy, atypical cells- favor reactive and negative for malignancy. The cytology and histopathology results were correlated, and descriptive statistics were used to analyze data.<b>Results</b>: Among 118 patients included in the study, 103 cases were malignant and 15 were nonmalignant. Out of 103 malignant cases, 89 cases were detected in cytology. False positive cases consisted of 4 gastritis with florid reactive atypia and one with moderate dysplasia. False negative cases were seen more often in diffuse and intestinal subtype of adenocarcinoma, followed by non-Hodgkin lymphoma. Sensitivity and specificity were found to be 86.41% and 66.67% respectively. Positive predictive value of 94.68% with 41.67% negative predictive value and diagnostic accuracy of 83.90%.<b>Conclusion</b>: Gastric cytology is a reliable screening and diagnostic tool with a high positive predictive value and acceptable sensitivity. Negative cytology in endoscopically suspected cases of gastric malignancy should always be correlated with biopsy reports. Gastric malignancy is known to be present as diffuse thickening of gastric wall, like diffuse subtype of adenocarcinoma and non-Hodgkin lymphoma is a pitfall on cytology because of low cellularity. Gastric cytology is a cost effective and rapidly performed technique with high positive predictive value, sensitivity and diagnostic accuracy.
DOI: 10.6084/m9.figshare.28259369.v1
title: Faculty Perspectives on Using Kimi and DouBao

description: Faculty Perspectives on Using Kimi and DouBao
DOI: 10.6084/m9.figshare.12026940.v1
title: Figure 3_MosquitoCollections.xls

description: Data underlying Figure 3. <i>Wolbachia </i>infection prevalence in local <i>Aedes aegypti </i>mosquito populations, in Indriani et al (2020) <i>Gates Open Research (submitted)</i>. Lines show the percentage of <i>Aedes aegypti </i>collected from intervention areas (closed circles; solid line) and untreated control areas (open circles; dashed line) that <i>Wolbachia </i>infected, each week since the start of deployments until September 2019. For the intervention areas, week 0 is the week in which deployment commenced (between 15 August and 18 September 2016, see Table 2). For the control areas, week 0 is the week in which the first deployments commenced in the intervention area (15 August 2016). Shaded area indicates release period.
DOI: 10.6084/m9.figshare.17121464.v1
title: Datasets and R scripts for "Reduced physiological plasticity in a fish adapted to stable temperatures"

description: All scripts and datasets (including raw data) for the article "Reduced physiological plasticity in a fish adapted to stable temperatures"
DOI: 10.6084/m9.figshare.18665642.v1
title: Grassland Monitoring Team Data_Ratcliffe et al. 2022

description: This repository contains data and replication code for "Invasive species do not exploit early growing seasons in burned tallgrass prairies" by Ratcliffe, Hugh; Ahlering, Marissa; Carlson, Daren; Vacek, Sara; Allstadt, Andrew; Dee, Laura. <br> <br>The included data is a subset of the Grassland Monitoring Team dataset, collected from 2008 - 2019. These data were collected as part of a collaborative project which included the Minnesota Department of Nature Resources, the Nature Conservancy, and the US Fish and Wildlife Service. Data are included for public record and are available for public use.<br><br><b>Repository Contents</b><br>1. <b>GMT Analysis.Rmd </b>- Contains all R code used to implement regressions. Instructions included within.<br>2. <b>Ratcliffe et. al 2022_GMT Data.csv</b> - Includes all data necessary to replicate results from scratch.<br>3. <b>Ratcliffe et al. 2022_GMT Metadata.xlsx - </b>Accompanying metadata and variable definitions for all variables found in Ratcliffe et. 2022_GMT Data.csv.<br>4. <b>2013_dnr_plant_status.xls </b>- Supplemental file from the Minnesota Department of Natural Resources used to differentiate native versus invasive species.<br>5. <b>2013_dnr_plant_checklist.xls </b>- Supplemental file from the Minnesota Department of Natural Resources used to identify indicator species.<br>6. <b>Vacek 2012 - GMT Protocols</b> - Protocol used for the collection of the vegetation data. <br>Vacek, S., M. Cornett, D. Carlson, and M. Ahlering. 2016. Grassland Monitoring Team Standardized Monitoring Protocol. https://ecos.fws.gov/ServCat/Reference/Profile/26773 <br>For questions or use please contact the owner of this figshare repository, Hugh Ratcliffe, at hugh.ratcliffe@gmail.com.
DOI: 10.6084/m9.figshare.24025008.v1
title: What are the perspectives of General Practitioners regarding the provision of suicide prevention in primary care? – a scoping review protocol

description: This is a scoping review protocol regarding the perspectives of GP's in relation to suicide prevention in Primary Care. Suicide is a major public health issue and is the largest killer of men under the age of 50 in the UK. (1) Individuals who display suicidal behaviour are more likely to visit their General Practitioner (GP) in the months leading up to the event. (2, 3) The objective of this scoping review is to map the current research on the experiences of GP’s regarding suicide prevention and to identify knowledge gaps within this area. This will help to inform further related work within the research department. This scoping review protocol will follow the methodologies set out by Arksey and O’Malley (2005) and the Joanna Briggs Institute’s (JBI) manual for reporting scoping reviews.(4, 5) A search of Pubmed/MEDLINE and Web of Science will be performed. Included studies will be qualitative, English-language and focus on GP’s perspectives of suicide prevention in primary care. Abstracts and titles of relevant articles will be screened and articles at full-text review will be assessed for their inclusion in the review against pre-determined eligibility criteria. Data will be extracted using a standardised form. The characteristics of the studies included will be displayed in tabular format and a narrative description of the main themes from the included studies will be provided.This work will be written up as a report to map the current research describing the experiences of GP’s regarding suicide prevention and to identify knowledge gaps within this area. This will assist in producing a focussed and relevant research question for a related research project. Ethical approval was not needed for the development of this scoping review.
DOI: 10.17632/wxfdf7nyg2
title: MDR-TB patients Data in the six geopolitical zones of Nigeria from January 2013 to December 2017 with treatment outcomes

description: The aim of the study was to determine the rate of distribution, risk factors and treatment outcomes associated with multidrug-resistant tuberculosis (MDR-TB) in patients admitted to different specialized treatment centres in Nigeria between January, 2013 and December, 2017. This was a multi-center, hospital-based retrospective study designed to identify the pattern of prevalence, the factors predisposing individuals and the outcome of treatment of multidrug resistant tuberculosis in Nigeria. The medical records of bacteriologically and clinically confirmed MDR - TB patients that were registered, admitted and treated in twelve special MDR-TB treatment centres from across the six geopolitical zones in Nigeria between January, 2013 and December, 2017 were used for the study. These patients’ folders/files were reviewed and data were collected using a purposively designed proforma. Treatment outcome of patient’s were determined and recorded in their medical records by the health team following standard WHO definitions of MDR-TB treatment performance indicator.
DOI: 10.6084/m9.figshare.13490379.v1
title: Data S17-21

description: EEG Data
DOI: 10.6084/m9.figshare.22301365.v1
title: Shrimp Predator Harassment (groups of 5)

description: Predator approach behavior in grass shrimp <em>Palaemon pugio</em>. 15 minute experimental trials in tanks with individual blue crabs (<em>Callinectes sapidus</em>). Groups of 5 shrimp were tagged and monitored on video.
DOI: 10.6084/m9.figshare.28742006.v1
title: Data_and_script_mistletoe_frenchNFI

description: Script and data files used for the analysis of mistletoe occurrences in french forests. Please refer to the manuscript "<i>Viscum album</i> in French forests: distribution, environmental drivers and impacts on tree health and growth" for further information on the methods.
DOI: 10.17632/bctc4dh2ck
title: Data for: Dataset on application of electrochemical and photochemical processes for sulfacetamide antibiotic elimination in water

description: This file contains raw data on the application of electrochemical and photochemical processes for sulfacetamide antibiotic elimination in water. All experiments were developed at lab-scale.
DOI: 10.17632/z4gxnhchky
title: Supporting documentation for time-dependent concrete material models in OpenSees

description: This dataset contains supporting documentation explaining the use of time-dependent concrete material models TDConcrete, TDConcreteEXP, TDConcreteMC, and TDConcreteMC10NL in OpenSees.
The dataset contains a manual explaining the use and features of the models, an Excel table for calculating model input parameters and example files using the material model TDConcreteMC10NL on a specific example.
DOI: 10.6084/m9.figshare.12089367.v1
title: Big data analytics and innovation

description: The fieldwork was carried out between September 2018 and October 2018.
DOI: 10.6084/m9.figshare.16725745.v2
title: Benchmark datasets of US-align

description: MMalign_dataset : 200 dimers, 200 trimers, 200 tetramers, 129 pentamers, 200 hexamers, 60 heptamers and 134 octamers for protein oligomer structure alignment.<br>RNAalign_dataset : 637 chains for monomeric RNA structure alignment.<br>TMalign_dataset : 1000 SCOPe domains for monomeric protein structure alignment.<br>TMdock_dataset : 439 protein-RNA complex structures for protein-RNA docking.<br>mTMalign_dataset : 31 groups of RNAs for multiple structure alignment.
DOI: 10.6084/m9.figshare.28208450.v1
title: <b>Attenuation of an original novel goose parvovirus strain NMG21 via serial cell passage</b>

description: In China, drastic losses in the economy have been caused by the novel goose parvovirus (N-GPV), the causative agent of the beak atrophy and dwarfism syndrome (BADS), to the duck-raising industry. In this study, an original, highly virulent N-GPV strain NMG21 was serially passaged in duck embryo fibroblast cells (DEFs). The virus titers and virulence of selected passages in 1-day-old ducklings were examined. Increased virus titer was observed at the 5th passage (P5). Compared with the parent strain NMG21, P35 (NMG21-35 strain) has a clear decrease in pathogenicity for ducklings, with less tissue damage. The NMG21-35 also had relatively low tissue replication rates and higher antibody levels. Collectively, the virulence of N-GPV strain NMG21 was reduced via serial cell passage. Our research successfully prepared a N-GPV attenuated variant which might serve as a potential attenuated live vaccine candidate against N-GPV infection. Producing a live attenuated vaccine candidate against N-GPV infection in China is essential to reducing the economic impact of N-GPV on the duck-raising industry.
DOI: 10.17632/2n95sn7t6v
title: Economic impact of Certifications in Colombia - TRANSSUSTAIN

description: Original dataset containing cross-sectional data on the economic impact of industry and company-led certifications in two cooperatives in Colombia's coffee belt (n=612). The household-level data was collected in 2016 and the recall period was year 2015.
DOI: 10.6084/m9.figshare.28707107.v1
title: Source data for AJP-GI manuscript

description: Source data for AJP-GI manuscript.
DOI: 10.6084/m9.figshare.853801_d7
title: SPI_NLDAS.zip

description: The Global Integrated Drought Monitoring and Prediction System (GIDMaPS) provides near real-time drought information based on multiple drought indicators and input data sets (http://drought.eng.uci.edu/). In this package, the folder names indicate the drought index and the source of data (INDEX_SOURCE). Index options are: 1-PSI: Multivariate Standardized Drought Index (MSDI) based on Precipitation (P) and Soil Moisture (S). 2-SSI: Standardized Soil Moisture Index 3-SPI: Standardized Precipitation Index. In each folder the files are named as INDEXYYYYMM.asc, where YYYY= year; MM= month, and INDEX = PSI, SSI, SPI.
<br>
GIDMaPS is presented in [Hao et al, 2014]. The deatails of MSDI, SSI and SPI are discussed in [Hao and AghaKouchak 2013a, 2013b]. GIDMaPS data has been used in [Damberg and AghaKouchak, 2013].
 
<strong>References</strong>
[1] Hao Z., AghaKouchak A., Nakhjiri N., Farahmand A., 2014, Global Integrated Drought Monitoring and Prediction System, Scientific Data, 1: 140001, doi: 10.1038/sdata.2014.1.
<br>
[2]  Hao Z., AghaKouchak A., 2013a, A Nonparametric Multivariate Multi-Index Drought Monitoring Framework,Journal of Hydrometeorology, doi:10.1175/JHM-D-12-0160.1.
<br>
[3]  Hao Z., AghaKouchak A., 2013b, Multivariate Standardized Drought Index: A Parametric Multi-Index Model,Advances in Water Resources, 57, 12-18, doi: 10.1016/j.advwatres.2013.03.009.
<br>
[4]  Damberg L., AghaKouchak A., 2013, Global Trends and Patterns of Droughts from Space, Theoretical and Applied Climatology, doi: 10.1007/s00704-013-1019-5. 
<br>
DOI: 10.6084/m9.figshare.25400398.v3
title: Supplementary Information for "Mildly explosive eruptions at Martian low-shield volcanoes"

description: This repository contains supplementary materials for "Mildly explosive eruptions at Martian low-shield volcanoes".This repository includes Supplementary Information comprising four supplementary tables and seventeen supplementary figures which constitute an extension of the results included in the main manuscript related to the mapped vent-proximal pyroclastic deposits. In addition, this repository hosts the produced digital elevation models (DEMs) using the MarsSI system that were used for 3D visualizations and providing topographical cross-sections of mapped pyroclastic ramparts. This repository includes also shapefiles of dated areas, mapped impact craters, and CraterStats files for the entire set of dated areas.
DOI: 10.6084/m9.figshare.25932409.v2
title: A semi-labelled dataset for fault detection in air handling units from a large-scale office

description: Fault detection and diagnosis (FDD) in Air Handling Units (AHUs) systems ensure optimal performance, energy efficiency, and occupant comfort by quickly identifying and diagnosing faults. Combining deep learning with FDD has demonstrated high generalization ability in this field. To develop deep learning models, this research constructed a dataset sourced from real data collected from a large-scale office in South Korea. The raw AHU data were extracted from a building management system (BMS) at 1 hour interval, spanning from November 2023 to May 2024. The dataset was partially labeled by annotation experts, categorizing the data into four types: normal, fan fault, sensor fault, and valve fault. The main contributions of this dataset to the field are twofold. First, it represents a unique dataset sourced from the real operational data of a large-scale office, which is currently non-existent in this domain. Second, the dataset's expert labeling adds significant value by ensuring accurate fault classification. Therefore, we hope that this dataset will encourage the development of robust FDD techniques that are more suitable for real-world applications.
DOI: 10.6084/m9.figshare.3568512.v1
title: Appendix A. Overview of the annual Serengeti wildebeest migration including maps of the point locations of GPS collared wildebeest and zebra (by season) and a table summarizing the mean number of days tracked and distance moved per individual.

description: Overview of the annual Serengeti wildebeest migration including maps of the point locations of GPS collared wildebeest and zebra (by season) and a table summarizing the mean number of days tracked and distance moved per individual.
DOI: 10.6084/m9.figshare.7996397.v1
title: Global analysis of chaperone effects using a reconstituted cell-free translation system

description: Protein folding is often hampered by protein aggregation, which can be prevented by a variety of chaperones in the cell. A dataset that evaluates which chaperones are effective for aggregation-prone proteins would provide an invaluable resource not only for understanding the roles of chaperones, but also for broader applications in protein science and engineering. Therefore, we comprehensively evaluated the effects of the major Escherichia coli chaperones, trigger factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation-prone cytosolic E. coli proteins, using a reconstituted chaperone-free translation system. Statistical analyses revealed the robustness and the intriguing properties of chaperones. The DnaK and GroEL systems drastically increased the solubilities of hundreds of proteins with weak biases, whereas trigger factor had only a marginal effect on solubility. The combined addition of the chaperones was effective for a subset of proteins that were not rescued by any single chaperone system, supporting the synergistic effect of these chaperones. The resource, which is accessible via a public database, can be used to investigate the properties of proteins of interest in terms of their solubilities and chaperone effects.
DOI: 10.6084/m9.figshare.19603744.v2
title: Parsivel data

description: Rain rate, DSD from Parsivel
DOI: 10.6084/m9.figshare.27225894.v1
title: Dataset

description: Data from Federal Territory of Sirius, typical developed children aged 3-6.<br>Behavioral data: PLS-5 raw and standart scores, Levenstein distance (speech in noise paradigm), pseudowords repetitionEEG-data: mean amplitude of sustained wave (SW) (F3 and F4, 250-550ms), laterality index of SW, mean ITPC of ASSR (Fz, 39-41Hz, 0-500ms)
DOI: 10.6084/m9.figshare.29120102.v1
title: METHYLATION SITE ANALYSIS USING methylKit

description: SUMMARY<br>This script processes bisulfite sequencing data to identify significantly methylated CpG sitesacross multiple developmental timepoints and conditions in <i>Nasonia vitripennis</i>. It performs:- Read filtering- Merging methylation data- Binomial testing per sample- FDR correction- Site selection- Methylation profile visualization<br>ORIGIN<br>Script developed using `methylKit` for differential methylation analysis on whole-genome bisulfitedata from the Erin Diapause project.<br>KEY STEPS<br>1. Read methylation data (`*.cov` files) using `methRead()`2. Filter CpGs by minimum and maximum coverage thresholds3. Merge all samples into a common methylation object using `unite()`4. Conduct one-tailed binomial tests (p &gt; background) per CpG site for each sample5. Apply Benjamini-Hochberg FDR correction per sample6. Filter for significant sites (FDR &lt; 0.05)7. Collate significant sites across all samples8. Extract a methylBase object from the merged sites9. Export CpG-level data to `Total_Methylated_Bases.txt`10. Generate correlation, clustering, and PCA plots across all retained samples<br>INPUT FILES<br>- `*.CpG_report.merged_CpG_evidence.cov`: Methylation files from Bismark (one per sample)<br>SAMPLES<br>- 40 samples representing combinations of treatment (Control/Diapause) and timepoint (6d to 30d), with replicates- Sample names: D6C1, D6D1, D12C1, ..., D6C4- Treatment vector: `treat_conditions` defines relative order<br>OUTPUT FILES<br>- `step1meth.RData`, `step2meth.RData`, `step3meth.RData`, `finalmeth.RData`: R environments at major steps- `Total_Methylated_Bases.txt`: Final table of significant methylated sites across all samples- `CpG_Correlation.pdf`: Pairwise methylation correlation matrix- `CpG_Cluster.pdf`: Hierarchical clustering dendrogram- `CpG_PCA.pdf`: PCA plot of CpG methylation patterns<br>SOFTWARE REQUIREMENTS<br>- R package: `methylKit` (v1.22.1+ recommended)- Additional packages: `stats`, `utils`, `grDevices` (base R)<br>NOTES<br>- Filtering is performed with `mincov=10` and high-coverage threshold at 99.9th percentile- Binomial tests are one-tailed (test for greater-than-background methylation)- Each sample uses a slightly adjusted p-value threshold (e.g., 0.004–0.005)- Data are not destranded or normalized at this stage<br>LIMITATIONS<br>- Statistical tests are applied per sample; no groupwise differential analysis is performed here- Only CpGs passing FDR &lt; 0.05 are retained- Manual sample-by-sample processing of 40 timepoints; automation is possible for scalability<br><br><br>CONTACT<br>Eamonn Mallon ebm3@le.ac.uk<br>
DOI: 10.6084/m9.figshare.5127670.v1
title: Supplementary Material for: Increased Cerebral Cannabinoid-1 Receptor Availability Is a Stable Feature of Functional Dyspepsia: A [<sup>18</sup>F]MK-9470 PET Study

description: <b><i>Background:</i></b> Functional dyspepsia (FD) is a prevalent functional gastrointestinal disorder (FGID) defined by chronic epigastric symptoms in the absence of organic abnormalities likely to explain them. Comorbidity with mood and anxiety disorders as well as with other FGIDs and functional somatic syndrome (FSS) is high. FD is characterized by abnormal regional cerebral activity in cognitive/affective pain modulatory circuits, but it is unknown which neurotransmitter systems are involved. The authors aimed to assess and compare in vivo cerebral cannabinoid-1 (CB<sub>1</sub>) receptor availability between FD patients and age-, gender- and BMI-matched healthy controls (HC). <b><i>Methods:</i></b> Twelve FD patients and 12 matched HC were investigated using positron emission tomography (PET) with the CB<sub>1</sub> receptor radioligand [<sup>18</sup>F]MK-9470. Nine of the patients received a second PET scan after a naturalistic follow-up period of 36 ± 9.6 months (range: 25.2-50.4 months). <b><i>Results:</i></b> FD patients had significantly higher CB<sub>1</sub> receptor availability in the cerebral regions involved in (visceral) nociception (brainstem, insula, anterior cingulate cortex) as well as in the homeostatic and hedonic regulation of food intake [hypothalamus, (ventral) striatum] (p &lt; 0.05 corrected for multiple testing, region of interest analysis), which persisted after a follow-up period of 36 ± 9.6 months. <b><i>Conclusions:</i></b> Although these findings need replication in larger samples, they suggest that the abnormal brain activity in several of these regions, previously demonstrated in FD, may be due to a sustained endocannabinoid system dysfunction, identifying it as a potential novel target for treatment and warranting further studies to elucidate whether it is also a feature of other FGIDs or FSSs.
DOI: 10.6084/m9.figshare.12808343.v2
title: Genotypes

description: BovineSNP50K genotypes of 96 crossbred Vrindavani cattle collected from ICAR-IVRI farm at Bareilly, India.
DOI: 10.6084/m9.figshare.7492520.v1
title: CLM tundra file code and model results

description: CLM code modifications and run files; CLM output files
DOI: 10.6084/m9.figshare.22059383.v1
title: Long-term dynamics of wild primate populations across forests with contrasting protection in Tanzania

description: Primate group detections 2002-2020 in two forests, 8 transects, and for three arboreal species.