cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22188748.v1
title: Supplementary Material for: Clear Cell Renal Cell Carcinoma: A Comprehensive in Silico Study in Searching for Therapeutic Targets

description: Introduction: Clear cell renal cell carcinoma is recognized as one of the leading causes of illness and death worldwide. Understanding the molecular mechanisms in clear cell renal cell carcinoma pathogenesis is crucial for discovering novel therapeutic targets and developing efficient drugs. With the application of a comprehensive in silico analysis of the clear cell renal cell carcinoma-related array sets, the main objective of this study was to discover the top molecules and pathways in the pathogenesis of this cancer. Methods: Clear cell renal cell carcinoma microarray datasets were downloaded from the Gene Expression Omnibus database, and after quality checking, normalization, and analysis using the Limma algorithm, differentially expressed genes (DEGs) were identified, considering the adjusted p-value &lt; 0.049. The intensity values of the identified DEGs were introduced to the WGCNA algorithm to construct co-expression modules. Functional enrichment analyses were performed using the DEGs in the disease-correlated module, and hub genes were identified among the top genes in a protein-protein interaction network and the disease-most correlated module. The expression analysis of hub genes was done by utilizing GEPIA, and the GSCA server was used to compare the expression patterns of hub genes in clear cell renal cell carcinoma and other cancers. DGIdb database was utilized to identify the hub genes-related drugs. Results: Three datasets, including GSE11151, GSE12606, and GSE36897, were retrieved, merged, normalized, and analyzed. Using WGCNA, the DEGs were clustered into eight different modules. Translocation of ZAP-70 to immunological synapse, endosomal/vacuolar pathway, cell-surface interactions at the vascular wall, and immune-related pathways were the topmost enriched terms for the clear cell renal cell carcinoma correlated DEGs. Twelve genes including PTPRC, ITGAM, TLR2, CD86, PLEK, TYROBP, ITGB2, RAC2, CSF1R, CCR5, CCL5, and LCP2 were introduced as hub genes. All the 12 hub genes were up-regulated in clear cell renal cell carcinoma samples and showed a positive correlation with the infiltration of different immune cells. According to the DGIdb database, 127 drugs, including tyrosine kinase inhibitors, glucocorticoids, and chemotaxis targeting molecules, were identified to interact with the hub genes. Conclusion: By utilizing an integrative bioinformatics approach, this experiment shed light on the underlying pathways in the pathogenesis of clear cell renal cell carcinoma and introduced several potential therapeutic targets for repurposing or developing novel drugs for an efficient treatment of this cancer. Our next step would be to assess the gene expression profiles of the identified hubs in different cell populations in the tumor microenvironment.
DOI: 10.6084/m9.figshare.24061428.v1
title: Agrarose Gels (Compressed file)related to "A conserved nutrient responsive axis mediates autophagic degradation of miRNA-mRNA hybrids in blood cell progenitors"Manuscript No: NAR-00264-X-2023.R1

description: File Contains raw gel images of the paper titled "<b>A conserved nutrient responsive axis mediates autophagic degradation of miRNA-mRNA hybrids in blood cell progenitors</b>" .
DOI: 10.17632/88g8kcwj9r
title: C4ISTAR technologies

description: The dataset contains the list of the technologies in the context of a defence related domain, C4ISTAR. C4ISTAR, in general indicated as “Command and Control” or “C2”, is an acronym used in Defence for Command, Control, Communication, Computer, Information/Intelligence, Surveillance, Target Acquisition, and Reconnaissance. The technologies are automatically mapped using a Text Mining technique, callled as Named Entity Recognition (NER). The approach to NER used in this article is twofold: a gazetteer based (or terminological-driven NER) approach and a rule-based approach. The text mining techniques are applied to a collection of the C4ISTAR documents, we collected English documents (166 documents) from diverse sources published from 2000 to 2020. The method applied allow us to map the C4ISTAR domain and to identify a list of 1090 technologies. The dataset published in this artiche contains the completed list of the technologies extracted in the C4ISTAR domain.
DOI: 10.6084/m9.figshare.12058728.v1
title: CBX8 phosphorylation.xlsx

description: 我们进行了CBX8的体外磷酸化，并使用质谱法鉴定了PKD1-CA磷酸化了CBX8的哪个残基。质谱分析了包括Ser219，Ser236和Ser256在内的三个磷酸化丝氨酸位点
DOI: 10.6084/m9.figshare.25248256.v1
title: Behavioral Data

description: Behavioral data supporting the manuscript "Lightening the Mind: Comparing Audiovisual Stimulation and Meditation for Mood and Cognition Enhancement".<br><br>This description will be updated upon peer-review with a full detail of all variable names.
DOI: 10.6084/m9.figshare.28103435.v1
title: SNAI2 cooperates with MEK1/2 and HDACs to suppress BIM- and BMF-dependent apoptosis in TERT promoter mutant cancers.pzfx

description: Raw data with analysis for Western blots and CHIP-RT-PCR in the manuscript.
DOI: 10.6084/m9.figshare.29084303.v1
title: "Longitudinal cutaneous changes and adverse events during T-DM1 therapy"dermatological imaging protocol (Canon EOS 90D DSLR camera with 18-55mm macro lens, fixed ISO 400, f/5.6 aperture, and 1/60s shutter speed under uniform lighting).Symptoms were evaluated ≤48 hours post-infusion by a clinical oncologist through structured interviews and physical examinations.

description: dermatological imaging protocol (Canon EOS 90D DSLR camera with 18-55mm macro lens, fixed ISO 400, f/5.6 aperture, and 1/60s shutter speed under uniform lighting).<br>Symptoms were evaluated ≤48 hours post-infusion by a clinical oncologist through structured interviews and physical examinations.
DOI: 10.6084/m9.figshare.4996220.v1
title: Supplementary Material for: Persistently Altered Metabolic Phenotype following Perinatal Excitotoxic Brain Injury

description: Excitotoxicity plays a key role during insults to the developing brain such as neonatal encephalopathy, stroke, and encephalopathy of prematurity. Such insults affect many thousands of infants each year. Excitotoxicity causes frank lesions due to cell death and gliosis and disturbs normal developmental process, leading to deficits in learning, memory, and social integration that persist into adulthood. Understanding the underlying processes of the acute effects of excitotoxicity and its persistence during brain maturation provides an opportunity to identify mechanistic or diagnostic biomarkers, thus enabling and designing possible therapies. We applied mass spectrometry to provide metabolic profiles of brain tissue and plasma over time following an excitotoxic lesion (intracerebral ibotenate) to the neonatal (postnatal day 5) mouse brain. We found no differences between the plasma from the control (PBS-injected) and excitotoxic (ibotenate-injected) groups over time (on postnatal days 8, 9, 10, and 30). In the brain, we found that variations in amino acids (arginine, glutamine, phenylananine, and proline) and glycerophospholipids were sustaining acute and delayed (tertiary) responses to injury. In particular, the effect of the excitotoxic lesion on the normal profile of development was linked to alterations in a fingerprint of glycerophospolipids and amino acids. Specifically, we identified increases in the amino acids glutamine, proline, serine, threonine, tryptophan, valine, and the sphingolipid SM C26:1, and decreases in the glycerophospholipids, i.e., the arachidonic acid-containing phosphatidylcholine (PC aa) C30:2 and the PC aa C32:3. This study demonstrates that metabolic profiling is a useful approach to identify acute and tertiary effects in an excitotoxic lesion model, and generating a short list of targets with future potential in the hunt for identification, stratification, and possibly therapy.
DOI: 10.17632/xw7w5ns649
title: Global Database of Foraminiferal Organic Linings: ForamL Version 1.2

description: This database is a collection of references to illustrations of Foraminiferal Organic Linings (FOLs) published in available scientific literature. FOLs are extracted from recent marine samples and sedimentary rocks worldwide. The analysis of the publications led to the collection of 155 scientific reports that illustrate 614 foraminiferal organic linings. All linings have been assigned to supraordinal groups of Foraminifera (Pawlowski et al. 2013), as well as to basic morphologic types of chamber arrangements. The database consists of three tables that cover the whole Phanerozoic split to the Cenozoic, Mesozoic, Paleozoic, and then to systems/periods, i.e. Quaternary, Neogene, Paleogene, Cretaceous, Jurassic, Triassic and older intervals. For each system, scientific publications are referenced chronologically, according to a publication year. The main principle to collect the data was the preparation method based on palynological procedures. The procedures included treating samples with hydrochloric acid (HCl) to remove carbonates, following with hydrofluoric acid (HF) to remove silicates from the sample. The next step was to sieve the extracted organic matter through a 10 or 15 or 20 μm sieve to separate larger organic particles, including palynomorphs with foraminiferal organic linings, for further preparation of palynological slides. Most researchers identified organic residues in palynological slides under optical microscopes equipped in either analogue or digital cameras. Some authors used a scanning electron microscope (SEM) as a supplementary method of documentation. The purpose of gathering the data is to extend scientific knowledge on the origin, taphonomy, and phylogenetic patterns of these fossilizable organic foraminiferal structures. The most recent review of the knowledge on foraminiferal organic linings is presented by Tyszka et al. (2021). The ForamL database will be further supplemented by available records of foraminiferal organic linings, therefore, any new graphic contribution of published and unpublished specimens of FOLs is welcome.
DOI: 10.6084/m9.figshare.20517036.v4
title: Social responses to the natural loss of individuals in Barbary macaques

description: Data and the corresponding R codes used in the Fedurek et al. 2022 paper 'Social responses to the natural loss of individuals in Barbary macaques.' <br> IDs names in the matrices are as follows: <br> FS-female survivor FN-female non-survivor MS-male survivor mn-male non-survivor
DOI: 10.6084/m9.figshare.22109012.v1
title: Datasets of adult whitefles on tomato leaflets

description: This repository provides datasets of adult whiteflies on tomato leaflet for "Effect of image resolution on automatic detection of whitefly (Hemiptera: Aleyrodidae) species on tomato leaflets using deep learning."
DOI: 10.6084/m9.figshare.29115639.v1
title: Additional file 13 of Lung lipids associated with smoking and ECIG use in a cross-sectional study and clinical trial

description: Supplementary material 13.
DOI: 10.17632/27kgpf8kkp
title: G-code for bioprinting

description: G code needed to 3D bioprint Y shaped structures
DOI: 10.17632/5sb8j2mypg
title: Box C/D snoRNP autoregulation by a cis-acting snoRNA in the NOP56 pre-mRNA

description: In the manuscript 'Box C/D snoRNP autoregulation by a cis-acting snoRNA in the NOP56 pre-mRNA' by Lykke-Andersen et al. we report that the human intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor and master switch controlling levels of the limiting snoRNP core protein NOP56, which together with other proteins functions to produce mature Box C/D snoRNPs, which is important for proper ribosome biogenesis. Our results support a model where snoRD86 adopts different RNP conformations that dictate the usage of nearby alternative splice donors in the NOP56 pre-mRNA. Excess snoRNP core proteins prevent further production of NOP56, and instead trigger generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway. Our findings reveal a feedback mechanism based on RNA structure that controls the precise coordination between box C/D snoRNP core proteins and global snoRNA levels. All raw data of Northern blots, Western blots, IF images, Flow cytometry, FACS and PCR gels presented within the paper are collected within this data set. To understand data please use the descriptions presented within the figure legends in the paper. A description of the order of samles is presented for each data file together with a figure ID related to the paper.
DOI: 10.17632/j2gwxb8pbg
title: Temperature and gas generation experimental data

description: Temperature and gas generation experimental data for the paper titled Preventing fertiliser fires through NOx scavenging and better ventilation.
DOI: 10.17632/r6d7xmgdgk
title: Body image dissatisfaction and social media use among adolescent athletes in Sri Lanka

description: The present study sought to investigate the magnitude of body image dissatisfaction (BID) among adolescent athletes in Sri Lanka and to explore its relationship with selected activities on social media. A total of 478 adolescents (53.7% male), aged 13 to 19 years, who were currently engaged in athletics, were recruited. BID was assessed using the Adolescent Body Image Satisfaction Scale. Time spent on social media, and the frequency of selfie-taking, selfie-posting and photo manipulation were assessed using ordinal scales. Weight and height were measured and body mass index was calculated. In the sample, 51.3% were reportedly active on social media. Social media use was higher among boys and older adolescents. While 20.9% of the adolescents articulated a positive body image, almost all the others (78.7%) reported mild BID. Higher body mass index was associated with greater BID, after adjusting for age and gender. Gender and age were not significant predictors of body image concerns. Among the social media activity parameters, only selfie-taking frequency was positively correlated with BID. Photo manipulation was significantly associated with body image concerns, only among girls.
DOI: 10.6084/m9.figshare.15059814.v1
title: COVID-19 Data base.csv

description: Clinical data from 102 Japanese patients with COVID-19.
DOI: 10.6084/m9.figshare.1044282.v8
title: The Impact of Visual Attributes on Online Image Diffusion

description: Data collected and used on the article "The Impact of Visual Attributes on Online Image Diffusion", published at the Web Science 2014 conference.
DOI: 10.6084/m9.figshare.25036799.v1
title: Tables S1–S6 Gas compositions and helium flux.zip

description: Gas samples were collected from natural springs in the form of warm springs to boiling springs and geysers in southern Tibet and the Himalayas. The dataset includes sample locations, physical and chemical properties, gas compositions and noble gas isotope values of hydrothermal fluids, which were used for calculation of upward fluid flow rate, transit time and helium flux.
DOI: 10.6084/m9.figshare.26343748.v1
title: Multi-location Traffic Flow Dataset: Stockton and Oakland California

description: This dataset supports the research detailed in "A Hybrid Deep Learning Approach with GEH-based Loss Function and Evaluation Metric for Multi-location Traffic Flow Forecasting" containing traffic flow measurements from Stockton and Oakland, California. The dataset is organized into four sub-folders: 'Oakland-raw', 'Oakland-processed', 'Stockton-raw', and 'Stockton-processed'. The raw data folders ('Oakland-raw' and 'Stockton-raw') include the initial traffic measurements as collected directly from traffic sensors, providing a granular view of traffic patterns without any modifications. The processed data folders ('Oakland-processed' and 'Stockton-processed') contain data that has been cleaned and structured, making it more suitable for analytical tasks and modeling purposes.
DOI: 10.17632/63gdkbhdtx
title: CAE model of Total Knee Replacement with knee joint at standing position

description: Total Knee Replacement (TKR) is a permanent solution for arthritis in the knee joint; the infected knee is replaced with biocompatible components of TKR. After this surgery the patient can resume everyday activities with normal functioning of the knee. Total Knee Replacement has three components- femoral component, bearing, and tibial component. These components are fixed to Femur and Tibia with a strong cement (Kanyal, 2020). Finite element analysis or CAE analysis can be used to simulate the dynamics of TKR with knee joint. The CAE model of a posterior-stabilized, fixed bearing total knee prosthesis, PFC Sigma (De Puy, Johnson & Johnson, Leeds, UK) assembled along with Femur and Tibia bones is presented here. Kanyal(2021) developed a CAD model for TKR components with knee joint which could be used to further develop a finite element model of the TRK components with knee joint, however, an already meshed CAE model is presented here representing the same CAD as Kanyal(2021) developed which will help to save time and effort; brick or hex meshing (meshing a solid with brick elements or hex elements) takes considerable time and effort. The bearing component is the most critical component in a TKR as it is prone to wear and therefore failure. Godest et al (2002), and Zelle et al (2009) also used hex elements to mesh bearing component in CAE analysis. Meshing of Femur bone, Tibia bone, and Femoral component is done with three noded tria elements, however the Tibial component is meshed with hex elements. The meshing of TKR components, Femur and Tibia bones is executed in Hypermesh 13 (Altair Engineering, Inc., Troy, MI, USA). The CAE meshed model(cae.hm) can be opened in Hypermesh 13 (Altair Engineering, Inc., Troy, MI, USA) for further model development like defining material properties, section properties, contact definitions etc. , then it can be exported to a CAE solver as .inp file for analysis and post processing. All dimensions are in mm.
DOI: 10.17632/y33zc8shj2
title: GeoViS—Relativistic ray tracing in four-dimensional spacetimes

description: Abstract The optical appearance of objects moving close to the speed of light or orbiting a black hole is of interest for educational purposes as well as for scientific modeling in special and general relativity. The standard approach to visualize such settings is ray tracing in four-dimensional spacetimes where the direction of the physical propagation of light is reversed. GeoViS implements this ray tracing principle making use of the Motion4D library that handles the spacetime metrics, the integrat... Title of program: GeoViS Catalogue Id: AESY_v1_0 Nature of problem First-person visualization of four-dimensional spacetimes in the theory of relativity. Versions of this program held in the CPC repository in Mendeley Data AESY_v1_0; GeoViS; 10.1016/j.cpc.2014.04.013 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.6084/m9.figshare.1109972.v1
title: MTT assay raw data

description: MTT Cell Proliferation Assay kit from ATCC (Cat. No. 30-1010K). The assay is based upon measuring the reduction of tetrazolium salts to examine changes in cell proliferation. The yellow tetrazolium MTT (3-(4, 5dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) is reduced by metabolically active cells, in part by the action of dehydrogenase enzymes, to generate reducing equivalents such as NADH and NADPH. The resulting intracellular purple formazan crystals that form in metabolically active cells can be solubilized using a detergent solution and quantified by spectrophotometric means.
DOI: 10.6084/m9.figshare.12886694.v1
title: Supplementary Material for: Podocyte Involvement in Renal Thrombotic Microangiopathy: A Clinicopathological Study

description: <b><i>Background:</i></b> The current study aimed to evaluate the associations between podocyte injury and clinicopathological features in renal thrombotic microangiopathy (TMA) based on a Chinese cohort, which might be underscored in this disease. <b><i>Methods:</i></b> The clinical, laboratory, and renal histopathological data of patients with renal biopsy-proven TMA from 2000 to 2015 in our institute were collected. Foot process effacement (FPE) was quantified by foot process width (FPW) by electron microscopy. Podocytes in the renal specimens were also detected by stainings for podocyte-specific markers, including Wilms tumor 1 (WT-1), synaptopodin, and podocalyxin. The associations between FPW and clinico-histopathological data were further analyzed. A composite end-point was defined by all-cause death or end-stage renal disease to address the predictive value of FPW. <b><i>Results:</i></b> Sixty-three patients with renal biopsy-proven TMA were enrolled. The FPW of renal TMA patients was 1,090 ± 637 nm (range, 572–4,748 nm), which was significantly higher than the normal range in our center (<i>p</i> = 0.005). By immunohistochemistry and immunofluorescence assays, we found decreased expressions of synaptopodin, podocalyxin, and WT-1 and continued stainings of WT-1 in some podocytes without detectable synaptopodin stainings in the areas of sclerotic tufts and cellular crescents. The FPW value was correlated with the serum albumin concentration (<i>r</i><sub>s</sub> = −0.281, <i>p</i> = 0.026), proteinuria amount (<i>r</i><sub>s</sub> = 0.255, <i>p</i> = 0.047), serum creatinine levels (<i>r</i><sub>s</sub> = 0.339, <i>p</i> = 0.007), and eGFR (<i>r</i><sub>s</sub> = −0.335, <i>p</i> = 0.007). According to ROC curve analysis, the optimal cutoff level of FPW for predicting the composite end-point was 869 nm. In patients with FPW ≥ 869 nm, FPW levels were further correlated with the severity of mesangiolysis (<i>r</i><sub>s</sub> = 0.351, <i>p</i> = 0.033) and glomerulosclerosis (<i>r</i><sub>s</sub> = 0.369, <i>p</i> = 0.025) in pathological evaluations. Patients without clinical remission also had higher FPW than those with remission (1,240 ± 793 vs. 925 ± 344 nm, <i>p</i> = 0.013). The multivariate Cox hazard model showed that FPW ≥ 869 nm was an independent risk factor for the composite end-point (hazard ratio: 3.64, 95% CI: 1.37–9.66, <i>p</i> = 0.009). <b><i>Conclusion:</i></b> The podocyte injury was prevalent and the FPW levels were closely associated with clinicopathological features, especially prognosis, in renal TMA patients.
DOI: 10.6084/m9.figshare.1603537.v1
title: cytokines

description: not real data!
DOI: 10.6084/m9.figshare.6962810.v2
title: Dataset for "A continental system for forecasting bird migration"

description: This submission contains data and code associated with the following journal article:<br>A continental system for forecasting bird migration<br>Benjamin M. Van Doren and Kyle G. Horton<br>Published in <i>Science</i>http://doi.org/10.1126/science.aat7526<br>Abstract: Billions of animals cross the globe each year during seasonal migrations, but efforts to monitor them are hampered by the unpredictability of their movements. We developed a bird migration forecast system at a continental scale by leveraging 23 years of spring observations to identify associations between atmospheric conditions and bird migration intensity. Our models explained up to 81% of variation in migration intensity across the United States at altitudes of 0-3000 m, and performance remained high when forecasting events 1-7 days in advance (62-76% variation explained). Avian migratory movements across the United States likely exceed 500 million individuals per night during peak passage. Bird migration forecasts will reduce collisions with buildings, airplanes, and wind turbines, inform a variety of monitoring efforts, and engage the public.<br>