cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8202314.v2
title: Global kinome profiling reveals abnormal active kinases in human skeletal muscle from obese insulin resistant participants

description: <b>ABATRACT</b> <b>Context:</b> Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in key signaling steps including insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global active kinases remain less understood. <b>Objective: </b>To investigate abnormal active kinase responsible for OIR in human skeletal muscle. <b>Design: </b>Stable isotopic labeling-based quantitative proteomics analysis and affinity-based active enzyme probes to profile <i>in vivo</i> active kinases. <b></b> <b>Participants: </b>Eight lean control and eight OIR but non-diabetic human participants who underwent hyperinsulinemic euglycemic clamp with muscle biopsy.<b></b> <b>Results: </b>We identified the 1st active kinome comprised of 54 active protein kinases in human skeletal muscle. The activities of 23 kinases were different in OIR compared to Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the two groups. The activities of multiple kinases involved in AMPK and p38 signaling were lower in OIR compared to Lean. On the contrary, multiple kinases in JNK signaling pathway exhibited higher activity in OIR vs. Lean. The kinase-substrate-prediction based on experimental data further confirmed a potential down-regulation of insulin signaling (e.g., inhibited phosphorylation of IRS1 and AKT1/2). <b>Conclusions: </b>These findings provide a global view of the active kinome in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in multiple signaling pathways important for skeletal muscle insulin resistance and provide potential drug targets (i.e., abnormal active kinase) to prevent and/or reverse skeletal muscle insulin resistance in humans.
DOI: 10.6084/m9.figshare.878038.v6
title: ij-non-local-means: ImageJ Plugin for Non-Local-Means Filtering

description: IJNLMeans is an ImageJ Plugin for denosing images via the non-local-means algorithm descriped by Buades et al.: Antoni Buades, Bartomeu Coll, and Jean-Michel Morel, Non-Local Means Denoising, Image Processing On Line, vol. 2011. including the changes proposed by "FAST NONLOCAL FILTERING APPLIED TO ELECTRON CRYOMICROSCOPY" By Darbon et al. It works with 8 Bit, 16 Bit, 32 Bit and RGB images/stacks. Since version 1.2 it is numerically optimized
DOI: 10.17632/nj72kmdj77
title: Forage biomass of different pasture management systems in Western Region of São Paulo State, Brazil

description: The objective of this dataset was to present the forage biomass production over time in different pasture management systems. We selected two farms located in the Western region of São Paulo State, Brazil. Pasture field data collection was carried out in two farms during three dates (June and November 2018 and March 2019) over two seasons (wet and dry). Samples were regularly taken through time to monitor forage biomass. These fields represent a wide variety of pasture management, as follow: Farm 1 (Santa Clara): i) traditional, low forage productivity, cattle rotation; ii) traditional, intermediate forage productivity, fertilized, cattle rotation; iii) intensified pasture, high forage productivity, reformed, cattle rotation. Farm 2 (Poderosa): i) traditional degraded*, recently reformed with millet + grass, cattle rotation; ii) traditional, low forage productivity, signs of degradation, fertilized, cattle rotation. *degraded was based on visual analysis of pasture area with sparse grass and exposed soil in some areas. With the support of NDVI images from the MODIS sensor, sample pixels were used to allocate the sample points. The areas of these pixels were divided into nine sampling points and in each of these points, the forage biomass was collected. Soil analyses were also carried out in two seasons (June 2018 and March 2019). The data files were organized in three folders. Each folder represents one field campaign. These folders have a shapefile of all the fields, the same file in kml extension (to open on Google Earth) and a zip file with photography of each field during the field campaign. The attribute table of the shapefile has a description of the fields and biomass. Excel files show the same information of the attribute table and a description of the items. A figure with the template of the biomass collection scheme is also available. Soil analyses are in the folders 'June 2018' and 'March 2019'. A more detailed description and discussion about these data and their association with soil chemical analysis were described in a scientific report (available by request). The biomass collection allowed the analysis of the forage production and better diagnoses about resource utilization strategies over the different pasture systems. This work was funded by the São Paulo Research Foundation (process numbers 2018/10770-1, 2017/06037-4, 2016/08741-8, 2017/08970-0, 2018/11052-5 and 2014/26767-9) as part of the Global Sustainable Bioenergy Initiative.
DOI: 10.6084/m9.figshare.25488814.v2
title: Bond strength of Polyalkasite cements with various surface preparations

description: This study aimed evaluate the effect of different surface treatments on the repair bond strength between existing and new Cention N restorative material. A total of 48 Cention N blocks each measuring 4 mm depth and 8mm diameter were fabricated. The samples were randomly divided into 8 groups (n = 6) according to the surface treatment applied. Group I-Surface preparation by bur, Group II- Surface treatment by laser, Group III- Adper Single Bond 2 adhesive application, Group IV- Scotchbond Universal adhesive application, Group V-Bur preparation followed by Adper Single Bond 2 adhesive application, Group VI- Bur preparation followed by Scotchbond Universal adhesive application, Group VII- Laser preparation followed by Adper Single Bond 2 adhesive application, Group VIII- Laser preparation followed by Scotchbond Universal adhesive application. The surface prepared specimens of all the groups were restored with freshly prepared Cention N. All samples were then subjected to repair bond strength testing using a universal testing machine. ANOVA with post-hoc Games Howell test and two-way ANOVA with post-hoc Bonferroni test were done to evaluate the role of surface preparation and bonding on repair bond strength.
DOI: 10.6084/m9.figshare.28172009.v1
title: Structural variants within NMR

description: Structural variants within NMR
DOI: 10.6084/m9.figshare.4880657.v1
title: Latitudinal gradient in insect immunity

description: Among-population differences of two parameters reflecting constitutive immunity – phenoloxidase (PO) and lytic activity – using common garden design on three distantly related moth species represented by populations ranging from northern Finland to Georgia (Caucasus). <br>
DOI: 10.6084/m9.figshare.21748160.v8
title: Carbon reduction targets in the NDCs

description: Unlocking the Power of Carbon Reduction Targets: Empirical Evidence from 1<sup>st</sup> Nationally Determined Contributions
DOI: 10.6084/m9.figshare.28295520.v1
title: Dysfunction of Endothelial Cell-Mediated Intercellular Communication and Metabolic Pathways in Age-Related Macular Degeneration

description: Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, but the therapies are not satisfactory. This study aimed to find AMD specific features through the analysis of high-throughput sequencing. In this study, we integrated six projects containing single-cell RNA sequencing (scRNA-seq) data to perform a comprehensive analysis for AMD samples in the tissues of retina and retinal pigment epithelium/choroid, and in the positions of macula and periphery. Differentially expressed genes (DEGs) were analyzed and crucial signaling pathways were identified across cell types and between the macula and periphery. The intercellular signaling transduction among cell types were inferred by "CellChat" to build cell–cell communication network under normal and AMD conditions, and verified at the transcriptional level. The CD31+ endothelial cells were obtained to evaluate the enrichment of KEGG pathways in atrophic and neovascular AMD, and GSVA was adopted to discover differential metabolic signals in each AMD type. Thirteen major cell types were identified in the integrated scRNA-seq data. Although no disease-specific cell type or differential cell proportion was found, DEGs and enriched pathways were shown in cell-type- and position-dependent manners. Severe impairment of endothelial cell-mediated cell interactions was found in the signaling transduction network of the macula, and compromised cell interactions were observed in the periphery. Furthermore, distinct signaling pathways and metabolic states were uncovered in atrophic and neovascular AMD. Striking reduction in energy metabolism, lipid metabolism, and oxidative stress was indicated in the atrophic AMD. Conclusively, we discover aberrant signals and metabolic pathways in AMD samples, providing insight into mechanisms and potential therapeutic targets for the AMD treatment.
DOI: 10.6084/m9.figshare.28531958.v3
title: SVs of Agaricus bisporus

description: SVs location information obtained by aligning 14 Agaricus bisporus samples to the reference genome(A33_62).
DOI: 10.17632/jwws9z8f2p
title: Dataset: The courtship song of voles: Male ultrasound vocalizations modulate female receptivity in two vole species

description: This dataset includes raw data for the article. The file contains the data from both vole species (bank voles and common voles) and is stored in csv. format. The readme file contains the explanation for abbreviations used in the raw data, a short description of used methods and statistical analysis, and explanation of abbreviations used in the data file.
DOI: 10.6084/m9.figshare.13492158.v1
title: ALL_tsp.tgz

description: This is a data set often used to test combinatorial optimization problems and traveling salesman problems。
DOI: 10.6084/m9.figshare.23160137.v4
title: Oxygen and carbon isotopes, Mg/Ca ratios and depth of thermocline data for the last 160 kyr in the eastern Indian Ocean

description: Oxygen and carbon isotopes, Mg/Ca ratios and depth of thermocline data for the last 160 kyr from two cores in the eastern Indian Ocean
DOI: 10.6084/m9.figshare.21407250.v1
title: Transferability of cathodal tDCS effects from the primary motor to the dorsolateral prefrontal cortex: a multimodal TMS-EEG study

description: cathodal tDCS, TMS-EEG, MEP, computational modeling
DOI: 10.6084/m9.figshare.3518543.v1
title: Appendix C. Ecological response functions.

description: Ecological response functions.
DOI: 10.5522/04/29114606.v1
title: Processed XAFS data for Co-containing MOF materials before and after pyrolysis from the article entitled 'The Second Life of Cobalt MOF: Alternating Magnetic Field Assisted ThermoElectrocatalysis in Cobalt MOF-derived Nanoparticles for Oxygen Evolution Reaction'

description: Magnetic Field Assisted ThermoElectrocatalysis for the Oxygen Evolution Reaction (OER) has been achieved for Co-containing Metal Organic Frameworks before and after pyrolysis. The data provided concern the X-ray Absorption data recorded on the samples before and after pyrolysis, confirming in the latter, the formation of Co nanoparticles. <br>
DOI: 10.6084/m9.figshare.10265993.v1
title: Dataset: Decoding of the other´s focus of attention by a temporal cortex module

description: The dataset contains electrophysilogical data recorded from the two monkeys used in "Decoding of the other's focus of attention by a temporal cortex module" by Hamidreza Ramezanpour and Peter Thier. <br>For more information please contact thier@uni-tuebinegn.de or hamidreza.ramezanpour@uni-tuebingen.de
DOI: 10.6084/m9.figshare.1138671.v1
title: Raw data: Body weight

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.22015970.v1
title: A remote-sensing assessment of oak forest recovery after postfire restoration - Dataset

description: The analysis is based on a dataset of post-fire restoration interventions conducted on deciduous oak forests in Portugal between 2017 and 2018. The dataset includes data on 1314 restored sites and on 1699 control sites. We used a Generalized Additive Mixed Model (GAMM) to analyse how vegetation indices such as NDVI and MSAVI changed over time as a function of post-fire restoration and topography and climate variables.
DOI: 10.6084/m9.figshare.24139461.v1
title: Supplementary RAW data for "The complete assembly of human LAT1-4F2hc complex provides insights into its regulation, function and localisation"

description: ZIP archive containing raw mass spectrometry data
DOI: 10.6084/m9.figshare.28050083.v2
title: The attached file contains Gene expression data, pre-processed histopathological images and metadata for breast cancer patients.

description: The attached file contains Gene expression data, pre-processed histopathological images and metadata for 100 patients.
DOI: 10.6084/m9.figshare.28785422.v1
title: Load profiles of three types of consumers

description: The file contains three load profiles of three different customers, that were used as case study in the paper "Generation of Realistic Synthetic Load Profile based on the Markov Chains Theory: Methodology and Case Studies":Load profile of a domestic house in Ruse, Bulgaria;Load profile of a printing house in Varna, Bulgaria;Load profile of a pig house near Silistra, Bulgaria.
DOI: 10.17632/ch52rydwjh
title: SARS-CoV-2_S1

description: SARS-CoV-2 S1 protein causes brain inflammation by reducing intracerebral acetylcholine production
DOI: 10.17632/t59v47sshp
title: SAFmaps - Palm oil

description: Developed in the context of SAFmaps containing the georeferenced database and a case study report on SAF production based on the HEFA-SPK / palm oil pathway. SAFmaps is a database platform with information on the potential of promising feedstock for the production of Sustainable Aviation Fuels (SAF) in Brazil. SAFmaps includes a database of different feedstocks, background information and assessment results.
DOI: 10.6084/m9.figshare.15090486.v1
title: Supplementary Material for: Body Adiposity Index Is Predictive of Weight Loss after Roux-en-Y Gastric Bypass

description: <b><i>Background/Aims:</i></b> Roux-en-Y gastric bypass (RYGB) is one of the most effective therapies for morbid obesity, yet some patients who have taken the surgery still undergo insufficient weight loss. Visceral adiposity index (VAI), lipid accumulation product (LAP), body adiposity index (BAI), and cardiometabolic index (CMI) have been regarded as clinical indicators of adiposity phenotypes that associated closely with obesity-related metabolic diseases. However, no studies have evaluated the relationship between these indexes and weight loss after bariatric surgery. In this prospective study, we aimed to evaluate whether VAI, LAP, BAI, and CMI would predict postoperative weight loss outcomes after RYGB. <b><i>Methods:</i></b> This study included 38 men and 67 women who have undergone RYGB between January 2017 and May 2018 and recorded their %TWL (percent of total weight loss), �MIL (percent of excess body mass index loss), %EWL (percent of excess weight loss), anthropometric indices, and biochemical parameters before and 12 months after the surgery. In addition, VAI, LAP, BAI, and CMI were measured with anthropometric measures or lipid profiles using related equations and analyzed with metabolic characteristics. <b><i>Results:</i></b> Subjects with lower BAI (&lt;32.54 in men and 37.39 in women) displayed higher �MIL and %EWL 12 months after surgery. BAI was independently associated with %EWL 12 months after surgery in both men and women (both <i>p</i> &lt; 0.05). The area under the receiver operating characteristic curve for BAI was significantly higher (0.773 in men and 0.818 in women) than VAI, LAP, and CMI. <b><i>Conclusions:</i></b> BAI serves as a reliable surrogate marker of the weight loss outcome after RYGB. The predictivity of adiposity indexes in beneficial outcomes after weight loss therapies is of important referential value for the implementation and optimization of individualized and refined weight loss treatments for obese patients.
DOI: 10.6084/m9.figshare.1538646.v1
title: Algae Data Base

description: This database is supplementary material of the article "Update of the Brazilian floristic list of Algae and Cyanobacteria" published in the Journal Rodriguésia in 2015 (DOI: 10.1590 / 2175-7860201566408). <strong>Attention! In this database the genus <em>Characium </em>A.Braun is under Charophyceae. However, it should be considered as belonging to Chlorophyceae. </strong>
DOI: 10.6084/m9.figshare.23529204.v1
title: SD_FIGs

description: Source Data of "Detection of low-frequency mutations in clinical samples by increasing mutation abundance via the excision of wild-type sequences".
DOI: 10.6084/m9.figshare.24975339.v1
title: Supplementary Materieal: Acquired Treatment Resistance in a Patient with Metastatic PD-L1-Positive Breast Cancer and Germline BRCA1 Mutation

description:  Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer associated with higher rates of relapse and mortality compared to other subtypes. Chemotherapy has been a mainstream treatment approach for TNBC due to the lack of therapeutic targets. Recent advances have led to the introduction of novel agents against specific patients with programmed death-ligand 1 (PD-L1)-positive TNBC who harbor germline <em>BRCA</em> mutations. However, some patients who respond to PD-L1 or poly (ADP-ribose) polymerase PARP inhibitors often develop resistance. Additionally, treatment strategies are more complicated for patients with PD-L1-positive TNBC and germline <em>BRCA</em> mutations. Here, we report a patient with metastatic PD-L1-positive TNBC who harbored a germline <em>BRCA1</em> mutation. The patient sequentially received combination treatment regimens, including PD-L1 inhibitors with chemotherapy and the PARP inhibitor olaparib, acquiring resistance to the treatments in a couple of months. Further investigations are warranted to elucidate the mechanisms underlying resistance to PD-L1 antibodies and PARP inhibitors to improve treatment outcomes while preventing emergence of treatment resistance in patients with TNBC.
DOI: 10.6084/m9.figshare.25263637.v1
title: Changes in monsoon precipitation in East Asia under a 2°C interglacial warming scenario

description: Paleoclimate data of the 180 modern soils from the Chinese Loess Plateau and Paleoclimate data of the Caotan section over the past 800ka
DOI: 10.6084/m9.figshare.27289461.v1
title: Digital Media Literacy and Algorithmic Content Curation (Survey Responses)

description: This research was conducted to study the Digital Media Literacy Levels of undergraduate students enrolled in a media studies major within the National Capital Region of India - Delhi NCR. Along with the DML levels, the study seeks to find its impact on OTT content consumption of youth as well their awareness on algorithmically curated content recommendations. The results of the survey were put into the Chi-square test in order to find the relationship between variables. DML levels of the users were identified using Composite score method technique.
DOI: 10.17632/8rgzhgmgc5
title: FOXA1 Forms Biomolecular Condensates that unpack Condensed Chromatin to Function as a Pioneer Factor

description: Eukaryotic DNA is packaged into chromatin in the nucleus, which restricts the binding of transcription factors (TFs) to the target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of how FOXA1 recruits to and unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes both to its properties to form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that FOXA1 is recruited to and unpacks the condensed chromatin by its IDRs to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states by its IDRs.
DOI: 10.6084/m9.figshare.1149953.v1
title: network of American football games between Division IA colleges during regular season Fall 2000

description: The file football.gml contains the network of American football games<br>between Division IA colleges during regular season Fall 2000, as compiled<br>by M. Girvan and M. Newman. The nodes have values that indicate to which<br>conferences they belong. The values are as follows: 0 = Atlantic Coast<br>1 = Big East<br>2 = Big Ten<br>3 = Big Twelve<br>4 = Conference USA<br>5 = Independents<br>6 = Mid-American<br>7 = Mountain West<br>8 = Pacific Ten<br>9 = Southeastern<br>10 = Sun Belt<br>11 = Western Athletic If you make use of these data, please cite M. Girvan and M. E. J. Newman,<br>Community structure in social and biological networks,<br>Proc. Natl. Acad. Sci. USA 99, 7821-7826 (2002).
DOI: 10.6084/m9.figshare.13525883.v1
title: PCB-28 on duckweeds.

description: Dataset for PCB-28 on duckweeds.
DOI: 10.6084/m9.figshare.20372613.v1
title: Rep_1 plasmids

description: List of plasmids encoding a Rep_1 replication initiation protein, their accession number and meta data.
DOI: 10.6084/m9.figshare.28241969.v1
title: <b>Euchiloglanis kishinouyei Genome sequencing and assembly</b>

description: We have generated the first telomere-to-telomere genome of Euchiloglanis kishinouyei, a species of the Sisoridae family, with a genome size of 886.74 Mb.The consensus quality assessment yielded a quality score of 46.96, and the BUSCO evaluation indicated a completeness of over 98.5%, demonstrating the high quality of our genome assembly. Additionally, we identified 45.59% (404.23 Mb) of the genome as repetitive elements and predicted 24,403 protein-coding genes, of which 94.37% were annotated.
DOI: 10.6084/m9.figshare.29091176.v2
title: Social Perception Data

description: Social media data of 50 IFSs, and their pois.
DOI: 10.6084/m9.figshare.1005016.v2
title: Haq sea level curve

description: Digitisation of the Haq (http://www.sciencemag.org/content/235/4793/1156) sea level curve derived from the data supplied by the supplementary information in Miller et al 2005 (Science 310, 1293 DOI: 10.1126/science.1116412).
DOI: 10.17632/nfz7nncmcb
title: Cutaneous manifestations of misuse of androgenic anabolic steroids: A retrospective cohort study

description: Online Supplement.