cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28692086.v1
title: <b>Divergent hydrological responses to restoration between planted and natural forests basins in drylands</b>

description: Datasets, and FiguresData used in this study are collected from the following sources:The global forest management data used here are publicly available at https://doi.org/10.1126/science.1244693; The global forest cover change used here are publicly available at https://developers.google.com/earth-engine/datasets/catalog/NASA_MEASURES_GFCC_TC_v3.The actual evaporation products based on observation data used here are publicly available at https://essd.copernicus.org/articles/13/447/2021/#section6; The MODIS AET (MOD16A2) datasets used here are publicly available at https://developers.google.com/earth-engine/datasets/catalog/MODIS_061_MOD16A2GF.The climate variables from ERA5 and Terraclimate database used here are publicly available at https://developers.google.com/earth-engine/datasets/catalog/ECMWF_ERA5_MONTHLY and https://developers.google.com/earth-engine/datasets/catalog/IDAHO_EPSCOR_TERRACLIMATE; The runoff products in FLDAs used here are publicly available at https://developers.google.com/earth-engine/datasets/catalog/NASA_FLDAS_NOAH01_C_GL_M_V001.The basins boundary from HydroSHEDS Basins Level 7 used in here are publicly available at https://developers.google.com/earth-engine/datasets/catalog/WWF_HydroSHEDS_v1_Basins_hybas_7. The population from LandScan used in here are publicly available at https://landscan.ornl.gov/. The nightlight used in here are publicly available at https://doi.org/10.6084/m9.figshare.9828827.v5. The irrigation lands used in here are publicly available at https://doi.org/10.1016/j.advwatres.2021.103910. The observation datasets used in here are publicly available at https://doi.org/10.6084/m9.figshare.20069900.v1.More details and information about the data used in this study are shown in the Table. S2.
DOI: 10.17632/xznpb436jh
title: Colorado Benzene Point Sources 2008-2020

description: This dataset in shapefile format includes point sources emitting benzene in the state of Colorado as reported to the United States Environmental Protection Agency (EPA) National Emissions Inventory (NEI) from 2008-2020. Report years are 2008, 2011, 2014, 2017, and 2020. Benzene is a hazardous air pollutant (HAP) that is a constituent of petroleum products and emitted during extraction, production, and combustion activities. Benzene is classified as a known human carcinogen. This dataset can be used for estimating benzene exposure in the state of Colorado based on location and can serve as a template for creating similar datasets for point sources of benzene in other states. 

The EPA NEI compiles estimated emissions of Criteria Air Pollutants (CAP) and HAPs from point, nonpoint, on-road, nonroad, and fire sources every three years, starting with 2008. The point emissions data is derived from annual emissions estimates provided by each facility to each state, which then reports these amounts to the EPA. Point source emissions data of benzene were downloaded from publicly available US EPA NEI datasets [https://www.epa.gov/air-emissions-inventories/national-emissions-inventory-nei]. These comma-separated value (.csv) files contain reported benzene point emissions data (in pounds) from Colorado facilities in the calendar years 2008, 2011, 2014, 2017, and 2020. Facilities on tribal lands were not included in these state reports and are not included in this dataset.
DOI: 10.6084/m9.figshare.12213746.v1
title: Learning Controllers for Adaptive Spreading of Carbon Fiber Tows: Preprocessed Data

description: Part of the paper "Learning Controllers for Adaptive Spreading of Carbon Fiber Tows". Preprocessed data, recorded on a spreading system.<br><br><br>
DOI: 10.6084/m9.figshare.28677209.v1
title: Collagen.xlsxIntegrated Bioprinting of Trachea-Like Structures Based on Tissue-Specific bioink

description: database for artical uploaded :"Integrated Bioprinting of Trachea-Like Structures Based on Tissue-Specific bioink"
DOI: 10.6084/m9.figshare.5129140.v1
title: Supplementary Material for: Collagen Matrix Remodeling in Stented Pulmonary Arteries after Transapical Heart Valve Replacement

description: The use of valved stents for minimally invasive replacement of semilunar heart valves is expected to change the extracellular matrix and mechanical function of the native artery and may thus impair long-term functionality of the implant. Here we investigate the impact of the stent on matrix remodeling of the pulmonary artery in a sheep model, focusing on matrix composition and collagen (re)orientation of the host tissue. Ovine native pulmonary arteries were harvested 8 (n = 2), 16 (n = 4) and 24 (n = 2) weeks after transapical implantation of self-expandable stented heart valves. Second harmonic generation (SHG) microscopy was used to assess the collagen (re)orientation of fresh tissue samples. The collagen and elastin content was quantified using biochemical assays. SHG microscopy revealed regional differences in collagen organization in all explants. In the adventitial layer of the arterial wall far distal to the stent (considered as the control tissue), we observed wavy collagen fibers oriented in the circumferential direction. These circumferential fibers were more straightened in the adventitial layer located behind the stent. On the luminal side of the wall behind the stent, collagen fibers were aligned along the stent struts and randomly oriented between the struts. Immediately distal to the stent, however, fibers on both the luminal and the adventitial side of the wall were oriented in the axial direction, demonstrating the stent impact on the collagen structure of surrounding arterial tissues. Collagen orientation patterns did not change with implantation time, and biochemical analyses showed no changes in the trend of collagen and elastin content with implantation time or location of the vascular wall. We hypothesize that the collagen fibers on the adventitial side of the arterial wall and behind the stent straighten in response to the arterial stretch caused by oversizing of the stent. However, the collagen organization on the luminal side suggests that stent-induced remodeling is dominated by contact guidance.
DOI: 10.17632/9hgj757b46
title: Data and MEP expression for Resilient Modulus in Stabilized aggregate base

description: The programming file for MEP and the dataset for the resilient modulus in stabilized aggregate base are mepx_MR.xml and Multi Expression Programming Calculations, respectively. The Excel file has both input and output information. From column 1 to column 5, the inputs are WDC (wet-dry cycles), CSAFR (ratio of calcium oxide to silica, alumina, and iron oxide compounds in cementitious materials), DMR (ratio of maximum dry density to optimal moisture content), CP (confining pressure), DS (deviator stress), and in column 6, Mr (target resilient modulus parameter).  Col 7 has the MEP expression and the results of calculating the target Mr based on the information in cols 1–5. Col. 9 is the R-squared calculation between actual and MEP-outcomes. The training data for MEP is found in rows 2 through 494, and the testing data is found in rows 495 through 705. In columns 11 and 12, you can compare the published results of the Gene expression programming equation on the same dataset. In the Excel file, you can find the reference. But the results don't match up with the results in the article. A calculation error is possible.
DOI: 10.17632/kxyfdgsbc3
title: Airyscan confocal time-lapse data of cellulose synthase in developing protoxylem vessels of the Arabidopsis root.

description: These datasets are continuous time lapse of protoxylem vessels in roots of Arabidopsis thaliana. The aim is to study movement of cellulose synthase complexes (CSCs) during secondary wall formation.

Timecourse 1 is a three channel movie showing CFP-Microtubules (CFP:MBD), YFP-CSCs (YFP:CESA7) and mCherry-Actin (mCherry:fABD2). Frame interval is 6 s.
Timecourses 2, 3, 4 and 5 are single channel movies showing YFP-CSCs. Frame interval is 0.57s (timecourse 2) or 0.69s (timecourses 3, 4, 5).

All data before Airyscan software processing, containing signal from each of the sub-airy detectors, is provided in the .zip archives ("Airyscan_raw"). Extracted files are Zeiss .czi format and can be opened in Zeiss Zen confocal software.
Airyscan processed data is provided as .czi files ("Airyscan processed") and can be viewed in Zeiss ZEN software or ImageJ/Fiji BioFormats import tool. Multipage .tif files (see "steps to reproduce section") can be open natively by ImageJ/Fiji software.

For viewing fast dynamic processes the airyscan datasets are viewed without further processing. For viewing slower process (e.g. CSCs moving below the emerging secondary cell wall thickenings), the fast time-lapse data (timecourses2-5) are subjected to a running average (ImageJ/Fiji plugins "walking average" or "running Z projector") of x6.
DOI: 10.6084/m9.figshare.12890687.v1
title: Indels between soybean genome assemblies and IGA1008

description: Indels analyzed from MUMer between soybean genome assemblies and IGA1008
DOI: 10.6084/m9.figshare.26104864.v2
title: InfiBench Detail Evaluation Data

description: Detail evaluation data of the benchmark in https://infi-coder.github.io/infibench, across over 100 open-source and proprietary large language models on a diverse set of free-form software developing questions (https://huggingface.co/datasets/llylly001/InfiBench).
DOI: 10.6084/m9.figshare.27601239.v1
title: Phylogenomic and genome-based metrics analysis of <i>Candida</i> and related genera in the <i>Saccharomycotina</i>: Contributons to understand phylogenetic divergence

description: The yeast genus <i>Candida </i>includes several medically important and various biotechnologically important species of yeasts. This genus is highly polyphyletic and occurs in most lineages of <i>Saccharomycotina</i>. In the past two decades, more than half of the <i>Candida </i>species have been reassigned into existing or newly introduced genera, but the polyphyly of the genus remains. Various genera, i.e., <i>Kuraishia</i>, <i>Ogataea</i>, <i>Wickerhamiella </i>and <i>Wickerhamomyces</i>, became heterogeneous and polyphyletic with the transfer to those genera of species that were formerly classified in <i>Candida</i>. To fully resolve the polyphyletic feature of <i>Candida </i>and other genera in the <i>Saccharomycotina</i>, a robust phylogenomic analysis using 1 134 genomes of 1 128 species of <i>Saccharomycotina </i>was made. Several genome-based metrics parameters, i.e., the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP), the presence-absence patterns of orthologs (PAPO), and the relative evolutionary divergence (RED), were analyzed to address the phylogenetic relationship of all genera in the <i>Saccharomycotina</i> and to assess genome diversity at different taxon ranks, such as genus, family, order, and class. Fifty-five monophyletic clades and 31 single-species lineages that might be equivalent to genera were recognized based on the phylogenomic analysis, and AAI, PAPO, POCP, and RED genome-based approaches. In addition, the data suggests the presence of 24 new families, 11 new orders and four new classes. Formal taxonomic proposals based on these results will be made elsewhere.
DOI: 10.6084/m9.figshare.28677272.v1
title: CFT.mp4Integrated Bioprinting of Trachea-Like Structures Based on Tissue-Specific bioink

description: database for artical uploaded :"Integrated Bioprinting of Trachea-Like Structures Based on Tissue-Specific bioink"
DOI: 10.6084/m9.figshare.7564760.v1
title: Supplementary Material for: Mean Corpuscular Volume and Mortality in Incident Hemodialysis Patients

description: <b><i>Background/Aims:</i></b> Anemia is common in patients with advanced chronic kidney disease (CKD). A proportion of patients present with macrocytic anemia, manifested by elevated mean corpuscular volume (MCV), which has been associated with worse outcomes in CKD patients. However, it is unknown whether elevated MCV is associated with higher mortality risk in incident hemodialysis (HD) patients. <b><i>Methods:</i></b> This retrospective observational cohort study examined all-cause, cardiovascular, and infectious mortality associations with both baseline and time-varying MCV in 109,501 incident HD patients using Cox proportional hazards models with 3 levels of hierarchical multivariable adjustment. Odds ratios of high versus low baseline MCV were evaluated using logistic regression. <b><i>Results:</i></b> The mean age of patients was 65 ± 15 (standard deviation) years and the cohort was 44% female, 58% diabetic, and 31% African American. Higher MCV was associated with older age, female sex, non-Hispanic White race-ethnicity, alcohol consumption, and having a decreased albumin or protein intake. Patients with higher MCV levels (&gt; 98 fL) had a higher all-cause, cardiovascular, and infectious mortality risk in both baseline and time varying models, and across all levels of adjustment. In the fully adjusted models, compared to a reference of MCV 92–&lt; 94 fL, patients with a baseline MCV &gt; 100+ fL had a 28% higher risk of all-cause mortality (hazard ratio [HR] 1.28, 95% CI 1.22–1.34), 27% higher risk of cardiovascular mortality (HR 1.27, 95% CI 1.18–1.36), and 18% higher risk of infectious mortality (HR 1.18, 95% CI 1.02–1.38). Associations of higher MCV with these adverse outcomes persisted across all examined subgroups of clinical characteristics. <b><i>Conclusions:</i></b> Higher MCV was associated with higher all-cause, cardiovascular, and infectious mortality in HD patients. Further investigation is necessary to understand the underlying nature of the observed association.
DOI: 10.17632/46srpvw9xb
title: A compilation of human tri-allelic SNPs from 1000 Genomes

description: A complete list of tri-allelic SNP sites identified by the 1000 Genomes project (Phase III variant database) is provided, compiled as individual chromosome datasets. Data includes tetra-allelic SNPs and sites are listed in chromosome position order with all 1000 Genomes genotypes (2504 samples) plus summary heterozygosity estimates per SNP. No Y chromosome variants were collected.
DOI: 10.6084/m9.figshare.2063184.v1
title: S1 File

description: Amplification of 16S rDNA was carried out by polymerase chain reaction (PCR) using a thermal cycler (Mycycler, BioRad). The PCR was carried out with approximately 100 ng of pure genomic DNA. The forward primer PA (AGA GTT TGA TCC TGG CTC AG) and the reverse primer PH (AAG GAG GTG ATC CAG CCG CA), were used for amplification of nearly entire gene. The amplification reactions were performed in a 50 μl volume, by mixing 2 µl of template DNA with 2 μl of each primer, 0.66 μl of (3u/µl) <i>Taq</i> polymerase (Genei, India), 1 μl dNTPs (10 μM each dATP, dCTP, dTTP and dGTP) (Genei, India), PCR buffer (10X) 5 μl and 37.34 μl MQ water for each reaction mixture. PCR amplified DNA was purified by HiYield PCR DNA mini kit from Real Biotech Corporation (RBC, India) through gel excision method. Purified DNA was sequenced by Amnion Biosciences Pvt. Ltd, India.
DOI: 10.17632/559kb329p2
title: AhKin: A modular and efficient code for the Doppler shift attenuation method

description: We present a set of programs for measuring lifetimes tau of nuclear states by the Doppler shift attenuation method (DSAM). The algorithms are based on the analysis of a probabilistic model of the processes occurring during a DSAM experiment. This analysis allows us to formulate the calculation of the theoretical lineshape as the application of an integral transform that converts the probability density of the cascade time (the time elapsed from nucleus creation to state decay) into the probability density of the (scaled) photon energy in the laboratory reference frame. The kernel of this integral transform, which encapsulates information related to the processes of nuclei stopping and photon detection, is independent of the state decay process, and hence needs not be recalculated on every trial of a candidate tau-value, allowing for fast computation of theoretical lineshapes. Further efficiency is gained by using algorithms that approximate continuous random variables by suitably chosen discrete ones. These codes were used to measure the lifetimes and sidefeeding times of the excited states of the normally deformed bands of 83Y (Rodríguez, et al. 2019) finding for all states good agreement between the experimental lineshape and the best-fitting theoretical one.
DOI: 10.6084/m9.figshare.24051111.v1
title: Data and R codes for Meng et al. Scale-dependent changes in ecosystem temporal stability over six decades ofsuccession

description: Data and R codes for Meng et al. Scale-dependent changes in ecosystem temporal stability over six decades of succession
DOI: 10.6084/m9.figshare.25033913.v1
title: Python code and Excel data for statistical and machine learning models developed to investigate the efficiency of nutrient recovery by struvite precipitation.

description: The Python code consists of five machine-learning methods to evaluate the efficiency of nutrient recovery by struvite precipitation. These methods include Multiple Linear Regression (MLR), Polynomial Regression (PLR), K-Nearest Neighbors (KNN), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost). Input data for the Python code used to model phosphate and ammonium recovery is provided in the Excel files. The inventory data embedded within the Python code represents the digestate of various organic feedstocks.
DOI: 10.6084/m9.figshare.6539675.v1
title: VoxEL

description: This dataset has manual annotations with respect to Wikipedia over the same text written in five languages: German (de), English (en), Spanish (es), French (fr) and Italian (it). The dataset is composed of 15 annotated news articles (in each of the 5 languages; 75 articles in total) where there is the same number of sentences in each language, as well as the same set of annotations for each corresponding sentence in the different languages. Each language has a total of 94 sentences across the 15 articles.<br>We propose two annotated versions of the dataset: a strict version that only annotates persons, organizations and places (per, for example, traditional NER/MUC definitions of an entity), and a relaxed version that includes a larger number of annotations (e.g., capturing entity mentions such as “inflation” that have a corresponding Wikipedia article). Both the relaxed and the strict versions have the same text in the same languages. The strict version has 204 annotations per language, while the relaxed version has 674 annotations per language.<br>If you use VoxEL in a research work, we would ask you to reference the following paper that describes the dataset in detail:Henry Rosales-Méndez, Aidan Hogan, Barbara Poblete. "VoxEL: A Benchmark Dataset for Multilingual Entity Linking". International Semantic Web Conference (ISWC), Monterey, United States, 2018. [http://aidanhogan.com/docs/voxel-entity-linking.pdf]
DOI: 10.17632/6g6pxwjj48
title: ADAM-Sense: Anxiety-Displaying Activities Recognition by Motion Sensors

description: There are some behaviors which anxiety patients perform unknowingly which become their habit, for example, nail biting, knuckles cracking etc. However, it is not guaranteed that if someone does one or more of these activities, they are anxious. But it is usually the case that people do some physical repetitive actions when they are anxious, and they are not aware of their actions. Such behaviors become their habits and can be used as an indicative of their anxiety status. We have collected some of these common behaviors which are usually performed by individuals when they are in anxiety. This is not an exhaustive list of such behaviors but can be used as the starting point to identify the presence of anxiety. These behaviors are physical actions so that we can capture them through motion sensors.
DOI: 10.6084/m9.figshare.12102348.v1
title: THE FREQUENCY AND DISTRIBUTION OF SISTER CHROMATID EXCHANGES (SCES) IN THE INDIVIDUAL CHROMOSOMES OF HUMAN KA¬RYOTYPE

description: The difference in the number of SCEs found per cell in 50 mitoses of control subjects when evaluated from photomicrographs or karyotypes is small but sig­nificant (p&lt; 0.01). Therefore, the data described have been obtained from karyo­types only. The mean value of 9.5 SCEs per mitosis found in the control group was in no way significantly different from mean values of the other groups, i.e. those consisting of pathological karyotypes and lymphoblastoid cell lines (p &gt;0.05). High frequency of SCEs (20%) was found in the centromeric region of chro­mosomes after the 2nd and 3rd divisions in BUdR medium (6).<i></i> The distribution of SCEs both observed and expected on the basis of the rela­tive length of chromosomal groups in the karyotype with results of χ2 test is shown in Table II. The changes were similar in all observed groups. The only exception were B group chromosomes of the lymphoblastoid ceil lines, where the number of breakpoints increased significantly (p&lt;0.01). In this particular chromosomal group the breakpoints leading to exchanges were distributed pro­portionally along the whole length of all chromosomes. Significant difference was found not only as against the expected number of SCEs but also as against the control group. The increased number of breakpoints on the long chromosomes was naturally matched by their decrease in small chromosomes (5).<i></i> We preferred to evaluate the non-banded chromosomes (G-banding considerably interferes with the accuracy of SCE calculation), the regions of break points are only roughly delineated. Even so it is clear that some regions are more often involved in SCEs than others. This is the case especially with regions 1q1, 3q2, 4q2, 8c and 16c. SCEs seem to be preferentially located on G-negative bands, as mentioned also by Morad , Jonasson and Lindsten (3)
DOI: 10.6084/m9.figshare.5129743.v1
title: Supplementary Material for: Downregulation of SIRT4 Expression Is Associated with Poor Prognosis in Esophageal Squamous Cell Carcinoma

description: <b><i>Objective:</i></b> SIRT4, a mitochondria-localized sirtuin, represses glutamine metabolism by inhibiting glutamate dehydrogenase (GDH). The current study aimed to evaluate the clinical and biological significance of SIRT4 in esophageal squamous cell carcinoma (ESCC). <b><i>Methods:</i></b> The study comprised 172 patients with surgically resected ESCC in two independent cohorts. <i>SIRT4</i> mRNA expression was analyzed in Cohort 1 (n = 79) and SIRT4 protein expression in Cohort 2 (n = 93). The association of SIRT4 expression with clinicopathological parameters and prognosis was assessed. Furthermore, the biological role of SIRT4 in ESCC cell lines was examined. <b><i>Results:</i></b> SIRT4 expression was not correlated with any clinicopathological parameters in both cohorts. In Cohort 1, low-<i>SIRT4</i>-expression cases had poorer overall survival than high-<i>SIRT4</i>-expression cases (p = 0.016). In Cohort 2, SIRT4-negative cases had poorer overall survival and disease-free survival than SIRT4-positive cases (p = 0.011 and 0.0026). Multivariate analysis revealed that SIRT4 expression was an independent prognostic factor for overall survival (HR = 2.06, p = 0.038). The rate of distant recurrence was significantly higher in SIRT4-negative cases than in SIRT4-positive cases (39.4 vs. 7.4%; p = 0.0023). In vitro, <i>SIRT4</i> knockdown significantly increased GDH activity and promoted cell proliferation and migration. <b><i>Conclusion:</i></b> SIRT4 is a potential prognostic biomarker in ESCC.
DOI: 10.6084/m9.figshare.6476426.v2
title: Supplementary material for Fibres of Failure

description: Supplementary material for the paper Fibres of Failure.
DOI: 10.6084/m9.figshare.7672223.v1
title: Additional file 10: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S8. Performance of error correction methods on correcting bases at heterozygous positions. (XLSX 15 kb)