cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1632726
title: The tyrosine-sorting motif of the vacuolar sorting receptor VSR4 from <i>Arabidopsis thaliana</i>, which is involved in the interaction between VSR4 and AP1M2, μ1-adaptin type 2 of clathrin adaptor complex 1 subunits, participates in the post-Golgi sorting of VSR4

description: μ1-Adaptin of adaptor protein (AP) 1 complex, AP1M, is generally accepted to load cargo proteins into clathrin-coated vesicles (CCVs) at the <i>trans</i>-Golgi network through its binding to cargo-recognition sequences (CRSs). Plant vacuolar-sorting receptors (VSRs) function in sorting vacuolar proteins, which are reportedly mediated by CCV. We herein investigated the involvement of CRSs of <i>Arabidopsis thaliana</i> VSR4 in the sorting of VSR4. The results obtained showed the increased localization of VSR4 at the plasma membrane or vacuoles by mutations in CRSs including the tyrosine-sorting motif YMPL or acidic dileucine-like motif EIRAIM, respectively. Interaction analysis using the bimolecular fluorescence complementation (BiFC) system, V10-BiFC, which we developed, indicated an interaction between VSR4 and AP1M2, AP1M type 2, which was attenuated by a YMPL mutation, but not influenced by an EIRAIM mutation. These results demonstrated the significance of the recognition of YMPL in VSR4 by AP1M2 for the post-Golgi sorting of VSR4. Clathrin AP1M2-recognizable tyrosine motif for plant VSR4 sorting.
DOI: 10.6084/m9.figshare.24057336.v1
title: Code smells and quality attributes dataset

description: This dataset contains over 1000 Java project instances where for each instance the relative frequency of 20 code smells has been extracted along with the value of eight software quality attributes. The data samples are used to train machine learning models predicting software quality attributes based on code smells.
DOI: 10.6084/m9.figshare.5387590.v1
title: Birnie-Gauvin et al. Hydrodam removal JEMA

description: Raw data on fish density estimates used to evaluate the effects of a small hydrodam removal.
DOI: 10.6084/m9.figshare.18700289.v1
title: PMEN3 assemblies

description: Assemblies of <i>S. pneumoniae </i>PMEN3 isolates, including the annotation of the reference isolate, RMV4.<br>
DOI: 10.6084/m9.figshare.21513765.v1
title: Untitled Item

description: The fMRI preprocessed bold time series data with 122 regions of the Brain using Bootstrap Analysis of Stable Clusters map using Nilearn. <br> This dataset was used in the paper: <br> Alves, Caroline, et al. "Diagnosis of autism spectrum disorder based on functional brain networks and machine learning." (2022).
DOI: 10.6084/m9.figshare.12656231.v1
title: Gene database of Synechococcus elongatus PCC 6301

description: <i>Synechococcus elongatus</i> is a cyanobacterium capable of rapid growth under autotrophic conditions in light. Such rapid growth holds implications for its potential use in biotechnology. This work sought to provide the genetic repertoire of <i>S. elongatus</i> in the form of an Excel database. Based on the annotated genome sequence of the cyanobacterium downloaded from Genbank, the database was parsed by an in-house MATLAB software. Comprising gene name, gene function and gene sequence, the resource should be useful for cloning genes from the cyanobacterium for heterologous expression in other biotechnological chassis for investigating how facile the cyanobacterium photosynthetic system could be transferred to another species.
DOI: 10.6084/m9.figshare.23932863.v1
title: DART-FISH (Kalhor, Chen et al) human brain motor cortex

description: This data set is associated with Kalhor, Chen et al (https://doi.org/10.1101/2023.08.16.553610). This repo contains the DART-FISH data on human brain presented in the paper.File descriptionM1C_cell_metadata.tsv: a data table containing the cell IDs, locations (xg and yg columns) and annotations (class and subclass columns)spots_table.tsv: a data table containing the information for all decoded spots, including location (xg and yg columns), gene, and the ID of the cell they were assigned to (cell_label column)brightfield.tif, DRAQ5.tif, RiboSoma_N9.tif: brightfield, nuclear stain, and RiboSoma stain for the entire imaged area, respectivelysegmentation_mask_custom.npy: Cell segmentation mask generated by a fine-tuned cellpose model<br>
DOI: 10.6084/m9.figshare.5129134.v1
title: Supplementary Material for: Atrial and Ventricular Arrhythmia-Associated Factors in Stable Patients with Chronic Obstructive Pulmonary Disease

description: <b><i>Background:</i></b> Supraventricular and ventricular premature complexes (SVPC and VPC, respectively) are associated with chronic obstructive pulmonary disease (COPD) and with increased mortality in COPD patients. However, there are few reports on the causes of arrhythmia in COPD patients. <b><i>Objectives:</i></b> This study explores the associations between cardiopulmonary dysfunction and COPD by comparing patients with defined arrhythmias (&gt;100 beats per 24 h) and those without, based on 24-hour electrocardiogram (ECG) recordings. <b><i>Methods:</i></b> Patients with arrhythmia underwent a 24-hour ECG and subsequent pulmonary function tests, computed tomography, ECG, 6-min walk test (6MWT), and BODE (body mass index, airflow obstruction, modified Medical Research Council Dyspnoea Scale, exercise capacity) index calculation. <b><i>Results:</i></b> Of 103 study patients (71 COPD patients and 32 at-risk patients), 36 had VPC, 45 had SVPC, 20 had both, and 42 had neither. The predicted post-bronchodilator forced expiratory volume in 1 s, the proportion of low-attenuation area on computed tomography, and BODE index values were significantly worse in the SVPC and VPC groups compared with the corresponding reference groups. Patients in the VPC group showed significantly increased right ventricular pressure and increased desaturation in the 6MWT compared with the reference group. In the multivariate analyses, bronchodilator use was a significant risk factor in the SVPC group, whereas in the VPC group, all parameters of the BODE index except for the dyspnoea score were identified as risk factors. <b><i>Conclusions:</i></b> Increased SVPC might be caused by bronchodilator use, whereas increased VPC is likely related to the peculiar pathophysiology of COPD.
DOI: 10.60893/figshare.jcp.26047618.v1
title: Supplementary information"

description: Supplementary information for paper "Perturbation theory in the complete degenerate active space (CDAS-PT2)."
DOI: 10.6084/m9.figshare.29132525.v1
title: Pathways Linking Social Support, Peer Influence, Substance Use, and Mental Health Among Youth: A Structural Equation Modelling Approach

description: This data supports the findings of the pathways linking social support, peer influence, substance use, and mental health among youth: A structural equation modelling approach<br><br>
DOI: 10.6084/m9.figshare.11310077.v1
title: Lichen Data

description: bFSingleStand.csv: this is a CSV file (241 rows, 41 columns) of the lichen composition on 21 balsam fir trees in a single stand. Column headers are TreeID (tree ID number); Aspect (N: north, S: south) and ladder.location (position up the lichen ladder). The remaining columns are 37 lichen species; the last column gives the sum.<br> bFDispersed.csv: this is a CSV file (211 rows, 31 columns) of the micro- and macro- lichen composition on 24 balsam fir trees dispersed within a 500 sq km ecoregoin. Column headers are TreeID (tree ID number); Aspect (N: north, S: south) and ladder.location (position up the lichen ladder). The remaining columns are 27 lichen species; the last column gives the sum.<br> yBDispersed.csv: this is a CSV file (211 rows, 35 columns) of the micro- and macro- lichen composition on 24 yellow birch trees dispersed within a 500 sq km ecoregoin. Column headers are TreeID (tree ID number); Aspect (N: north, S: south) and ladder.location (position up the lichen ladder). The remaining columns are 31 lichen species; the last column gives the sum.
DOI: 10.6084/m9.figshare.21122320.v1
title: Data & Scripts for the article: Same process different patterns: pervasive effect of evolutionary time on species richness in freshwater fishes

description: This dataset contains all the scripts used in this article to create the variables and replicate all the analyses presented, as well as the data generated for each freshwater taxon.
DOI: 10.6084/m9.figshare.21592443.v2
title: Paper 2 IFOMSSA SPSS Quantitative Data.sav

description: Dataset for IFOMSSA Senior Scholarship Evaluation 2014 to 2019
DOI: 10.6084/m9.figshare.28365836.v1
title: <b>The</b> <b>circular RNA </b><b><i>circbabo(5,6,7,8S)</i></b><b> regulates lipid metabolism and neuronal integrity via TGF-β/ROS/JNK/SREBP signaling axis in </b><b><i>Drosophila</i></b>

description: <b>Background</b>Lipid droplets (LDs) are dynamic cytoplasmic lipid-storing organelles that play a pivotal role in maintaining cellular energy balance, lipid homeostasis, and metabolic signaling. Dysregulation of lipid metabolism, particularly excessive lipogenesis, contributes to the abnormal accumulation of LDs in the nervous system, which is associated with several neurodegenerative diseases. Circular RNAs (circRNAs) are a new class of non-coding and regulatory RNAs that are widely expressed in eukaryotes. However, only a subset has been functionally characterized. Here, we identified and functionally characterized a new circular RNA <i>circbabo(5,6,7,8S)</i> that regulates lipogenesis and neuronal integrity in <i>Drosophila melanogaster.</i><b>Results</b><i>circbabo(5,6,7,8S) </i>is derived from the <i>babo</i> locus which encodes the type I receptor for transforming growth factor β (TGF-β). Depletion of <i>circbabo(5,6,7,8S)</i> in flies causes elevated lipid droplet accumulation, progressive photoreceptor cell loss and shortened lifespan, phenotypes that are rescued by restoring<i> circbabo(5,6,7,8S) </i>expression. In addition, RNA-seq and epistasis analyses reveal that these abnormalities are caused by aberrant activation of the SREBP signaling pathway. Furthermore, <i>circbabo(5,6,7,8S)</i>-depleted tissues display enhanced activation of the TGF-β signaling pathway and compromised mitochondrial function, resulting in upregulation of reactive oxygen species (ROS). Moreover, we provide evidence that <i>circbabo(5,6,7,8S)</i> encodes the protein circbabo(5,6,7,8S)-p, which inhibits TGF-β signaling by interfering with the assembly of babo/put receptor heterodimer complex. Lastly, we show that dysregulation of the ROS/JNK/SREBP signaling cascade is responsible for the LD accumulation, neurodegeneration, and shortened lifespan phenotypes elicited by <i>circbabo(5,6,7,8S)</i> depletion.<b>Conclusions</b>Our study demonstrates the physiological role of the protein-coding circRNA <i>circbabo(5,6,7,8S)</i> in regulating lipid metabolism and neuronal integrity.
DOI: 10.6084/m9.figshare.28524356.v1
title: Sample descriptions

description: Human lung adenocarcinoma cells (A549) and human monocytic cells (THP-1) were infected with H3N23 influenza virus A virus. Transcriptome analysis were performed by next generation RNA sequencing of three replicates each for infected A549 cells at 4, 8 and 24h p.i. and infected THP-1 cells at 4, 8, 12 and 24h p.i., and corresponding set of non-infected controls. The description of samples is provided here.
DOI: 10.6084/m9.figshare.5142466.v2
title: Pointing04 DB

description: One who wants to use this database needs to cite the following article:<br>N. Gourier, D. Hall, J. L. CrowleyEstimating Face Orientation from Robust Detection of Salient Facial FeaturesProceedings of Pointing 2004, ICPR, International Workshop on Visual Observation of Deictic Gestures, Cambridge, UK<br>For more details, please see the following web pageshttp://www-prima.inrialpes.fr/Pointing04/data-face.html<br>
DOI: 10.6084/m9.figshare.28942499.v1
title: RAD23B IP mass raw data.zip

description: After lysis of colorectal cancer SW480 cells, the co-immunoprecipitation experiment was conducted using RAD23B antibody. Then, the co-precipitation products were identified by mass spectrometry to search for proteins related to RAD23B.
DOI: 10.6084/m9.figshare.5123359.v1
title: Supplementary Material for: An in vitro Comparison of Detection Methods for Approximal Carious Lesions in Primary Molars

description: <i>Background/Aims:</i> This study aimed to compare and contrast in vitro six methods to determine the most accurate method for detecting approximal carious lesions in primary molars. <i>Methods:</i> Extracted primary molars (n = 140) were stored in 0.02% chlorhexidine solution and mounted in light-cured resin in pairs. The six carious lesion detection methods used by the three examiners to assess approximal carious lesions were visual inspection, digital radiography, two transillumination lights (SDI and NSK), and two laser fluorescence instruments (CDD and DDP). Five damaged teeth were discarded. The teeth (n = 135) were sectioned, serially ground, and examined under light microscopy using Downer’s histological (HST) criteria as the gold standard. Intra- and inter-examiner reliability, agreement with HST, specificity, sensitivity, receiver operating characteristic (ROC) curves, and areas under the curve were calculated. <i>Results:</i> This study found visual inspection to be the most accurate method when validated by histology. Transillumination with NSK light had the highest specificity, and digital radiography had the highest sensitivity for detecting enamel and/or dentinal carious lesions. Combining specificity and sensitivity into the area under ROC curves, enamel plus dentinal lesions were detected most accurately by visual inspection followed by digital radiography; dentinal lesions were detected most accurately by digital radiography followed by visual inspection. <i>Conclusions:</i> None of the four newly developed methods can be recommended as suitable replacements for visual inspection and digital radiography in detecting carious lesions on approximal surfaces of primary molars, and further developmental work is needed.
DOI: 10.6084/m9.figshare.20098124.v7
title: Human development and Tourism: Evidence from Ten Countries (Dataset)

description: Data of ten countries: seven countries are classified as ‘developing’ – Bolivia, Cambodia, Ecuador, Kazakhstan, Morocco, Nepal and Tanzania, while three countries – Hungary, Slovenia and USA are designated as ‘developed.’ These countries have the complete HDI and tourist arrivals’ data for the period 1996 – 2019. The study analyses the impact of tourism to human development in ten countries, that also include other variables: jobs, government effectiveness and political stability, using three different panel estimation techniques: random, fixed effect and Least-squares Dummy variables (LSDV).
DOI: 10.6084/m9.figshare.5067148.v1
title: Norwegian mobile downtime dataset from NorNet Edge

description: We use measurements collected by the NorNet Edge measurement infrastructure. NorNet Edge consists of hundreds of measurement nodes that are spread all over Norway. Each node connects to up to 4 mobile operators. We collect all downtime events (time periods without mobile connectivity) for each node on each operator.<br><br>This dataset includes downtime time series of each node (with a fixed Node ID) on each operator ("Net01-04"). The 0-1 time series are defined using 5-min bins, and each bin is marked as "1" if it include a part of a downtime event. The dataset here includes five periods of time with length 3 months: January 1-March 31 ("JFM") of 2014 and 2015, as well as July 1-September 30 ("JAS") of 2013, 2014 and 2015. When the time series in one data file is shorter than the full length of 3 months, it means that there is no more downtime event in the remaining time series (always "0" values).<br><br>Finally, "invalid_final.zip" contains the data of node invalid periods within the considered 5 stages. Each line in the text file includes 4 values of an invalid period: Node ID, Operator ID, starting time (Unix timestamp), and total time length in seconds. When we calculate the Pearson correlation between nodes, invalid periods should be excluded from the 0-1 time series firstly.<br><br><br><br>
DOI: 10.6084/m9.figshare.28187837.v1
title: Supplementary Material

description: The majority of exercise physiology research has been conducted in males, resulting in a skewed biological representation of how exercise impacts the physiological system. Extrapolating male-centric physiological findings to females is not universally appropriate and may even be detrimental. Thus, addressing this imbalance and taking into consideration sex as a biological variable is mandatory for optimization of precision exercise interventions and/or regimens. Our present analysis focused on establishing multiomic profiles in young, exercise-naïve males (n=23) and females (n=17) at rest and following acute exercise. Sex differences were characterized at baseline and following exercise using skeletal muscle and extracellular vesicle transcriptomics, whole blood methylomics, and serum metabolomics. Sex-by-time analysis of the acute exercise response revealed notable overlap, as well as divergent molecular responses between males and females. An exploratory comparison of two combined exercise regimens (high-intensity: HITT and traditional: TRAD) was then performed using singular value decomposition, revealing latent data structures that suggest a complex dose-by-sex interaction response to exercise. These findings lay the groundwork for an understanding of key differences in responses to acute exercise exposure between sexes. This may be leveraged in designing optimal training strategies, understanding common and divergent molecular interplay guiding exercise responses, and elucidating the role of sex hormones and/or other sex-specific attributes in responses to acute and chronic exercise.
DOI: 10.17632/cktyw4g9f7
title: Data for:Opioid Prescribing can be reduced in Oral Surgery practice.

description: Abstract Background: Pain management is one of the most critical aspects of practice in Oral and Maxillofacial Surgery. We performed a three year retrospective analysis of heavy opioid prescription in one practice after introduction of Office Protocol designed to decrease such prescriptions. Methods: We analyzed data available through Illinois Monitoring Service of patients who obtained hydrocodone/oxycodone prescriptions for qualified procedures routinely requiring heavy opioids. The number of procedures performed in each year, starting 2015 and ending 2017 was analyzed along with percentage of patients that filled prescription for heavy opioids in the same time frame. 95 % confidence intervals were used to analyze the data and compare between each year. Results: Based on the 95% confidence intervals, 56.6% of patients undergoing qualified surgical procedures required heavy opioid prescriptions in 2015. After introduction of Office Protocol for pain management that numbered fell to 15.2% in 2 years. Thus, we obtained a 3.7fold reduction in Hydrocodone/Oxycodone prescription in a three years interval. Conclusion: The Office Protocol utilized in this study that included use of NSAIDs, acetominophen and homeopathic Recovery Kit has effectively decreased the number of heavy opioids required for patients undergoing various oral surgery procedures.
DOI: 10.6084/m9.figshare.7723211.v4
title: National Culture, Research Performance Indicators, and Log GDP Per Capita

description: Dataset of National culture (taken from Geert Hofstede), Country level research performance indicators (taken from Scimago Journal & Country Rank), and Log GDP per capita (taken from the World Bank Open Data). All data were retrieved on <b>August 18, 2019</b>.<br><i>Notes on abbreviations:</i><br>DOC = Total Documents (1996-18 Aug 2019)<br>CITA = Citable Documents<br>CIT = Citations<br>SELF = Self-citations<br>CPD = Citations per Document<br>HINDEX = H index<br>PDI = Power Distance<br>IDV = Individualism (vs. Collectivism)<br>MAS = Masculinity (vs. Femininity)<br>UAI = Uncertainty Avoidance<br>LTOWVS = Long term (vs. Short term) Normative Orientation<br>IVR = Indulgence (vs. Restraint)<br>LogGDP = Natural Logarithm of Averaged (1993-2018) GDP per Capita<br>Research_Performance = Z-scores of Component 1 from PCA extraction (based on DOC, CITA, CIT, SELF, HINDEX)<br>Research_Impact = Z-scores of Component 2 from PCA extraction (based on CPD)<br>PCA = Principal Component Analysis
DOI: 10.34740/kaggle/dsv/12023071
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.6084/m9.figshare.11742792.v1
title: Analysing the cross-section of the AAA's neck and its effects on stent deployment - Data

description: The raw measurements taken from the study of 258 patients suffering from abdominal aortic aneurysm (AAA) are presented. 2 3D aortic angles along with 2 dimensional variables and 2 shape metrics for the aortic neck region are reported.
DOI: 10.6084/m9.figshare.19583446.v1
title: Mungbean(Vigna radiata) genome assembly and population resequencing

description: Mungbean is an economically important legume crop used as food, vegetable,ingredients and even medicine. To explore the genome diversity, we assembled a high-quality reference genome(Jilv 7) and pan-genome for mungbean by deeply sequencing a high yield variety and 217 accessions. Important agronomic traits, such as yield components, grain composition, morphology and insect resistance, were observed for these accessions and associated with their genome sequences. Significant SNPs and candidate genes were identified for almost all traits. These results would build a solid foundation for genomic breeding in mungbean.
DOI: 10.6084/m9.figshare.21091075.v1
title: Biomass and Composition 2022.csv

description: All fishes data with coordinates
DOI: 10.6084/m9.figshare.23939514.v1
title: sDrev.rds

description: All single-cell atlas of cigarette smoking lung. Seurat obj.
DOI: 10.6084/m9.figshare.25275595.v2
title: Data retrieval

description: Scientific production on physical activity and sustainable development goals. Data mining was perfomed on Scopus and the Web of Science databases.
DOI: 10.17632/n3vs7pkdx6
title: Data for: Dynamic Effect Analysis of Meteorological Conditions on Air Pollution: A Case Study from Beijing

description: The meteorological data of Beijing from November 1, 2013 to October 31, 2017. The variables include average humidity, extreme wind speed, sunshine duration, average wind speed and rainfall capacity and air quality index (AQI).
DOI: 10.6084/m9.figshare.19274777.v3
title: CarboGrove Glycan Binding Data

description: Data is three tables pulled from publication version of CarboGrove. These tables contain all the information available for the glycan binding data used in the analysis found in CarboGrove.<br>The main table "AllBindingData.csv" references DataID found in "AllDataInfo.csv" to link relevant dataset information (data source, glycan binding protein, and concentration) and GlycanID found in "AllGlycanInfo.csv" which gives the glycan structures both in raw format and several parsed/processed forms (IUPAC condensed, WURCS, and GlyTouCanID).<br>All references to data source are provided in "AllDataInfo.csv". Data can be found either as supplemental text to the papers linked, in the databases linked, or by searching available primscreen id in the CFG.<br>