cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21723767.v1
title: Supplementary Material for: Pitfall in the Surgical Management of a Shrunken Skin Defect after Neoadjuvant Chemotherapy for Locally Advanced Breast Cancer

description: A 53-year-old woman with a large, easy-bleeding, and ulcerated breast tumor visited our hospital due to severe anemia. Transfusion and Mohs’ chemosurgery gave the patient marked improvement of her local and general condition. After confirming the human epidermal growth factor receptor type 2 (HER2)-positive breast cancer with no distant metastasis, anti-HER2 agents-containing chemotherapy brought about clinical complete response of the locally advanced breast cancer with a shrunken but still large skin defect. We, therefore, treated the patient with mastectomy and axillary node dissection but failed to directly close the skin even after full skin undermining. We then tried to cover the skin defect using a latissimus dorsi flap, that is, horizontal spindle skin 12 × 6 cm in size, but again failed to fully cover the skin defect. We finally and ostensibly covered the skin defect through an additional skin incision to the recipient skin, but could not get complete wound healing. Pathological study showed a marked collagen fiber around the skin defect and faint viable cancer cells beneath the nipple. The patient required 3 months of wound management for complete wound healing, leading to the application of anti-HER2 agents without anticancer agent to the patient during that time as an adjuvant therapy. Regrowth of her hair once lost by the neoadjuvant chemotherapy (NAC) made the patient refuse the adjuvant anthracycline-containing chemotherapy after wound healing. The patient, therefore, received trastuzumab-emtansine for a year and has been well for 17 months postoperatively. Breast surgeons should note that a skin defect after favorable response to NAC is often surrounded by less stretchable skin due to chemotherapy-induced massive collagen fiber and requires careful preoperative planning for skin closure.
DOI: 10.6084/m9.figshare.7038434.v1
title: XVG files for quercetin

description: Arquivos XVG gerados pelo método de análise BAR do GROMACS
DOI: 10.6084/m9.figshare.9917171.v1
title: 10-year bird observation data from two routes in the state of Chihuahua, Mexico

description: Data from a 10-year period of bird observation from two routes in the state of Chihuahua. Six files are provided: a) spss: it contains species' count for the 10-year period, per year, per species; b) inv: contains the name of each species in English, Spanish and their scientific names, as well as the observation routes; c) tags: it has the Spanish, English and scientific names of all species in the form of tags; d) species, it contains sums in order to determine species' movements throught the routes of observation; e) la regina route: contatins latitudes and longitudes for each stop within La Regina route; f) santa monica route: contatins latitudes and longitudes for each stop within Santa Monica route.
DOI: 10.17632/9tg9dmsfhm
title: Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward specific metabolite. Seok et al.

description: Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux towards the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a new perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization. The original western blot image related to FigS3B demonstrates that CRP expression is reduced when its start codon is changed from ATG to TTG. The original western blot image related to FigS5A demonstrates that CRP mutation (T168P) changes the structure of CRP, causing difficulty of CRP detection by anti-CRP antibody. To solve this, synthetic 8-myc sequence is integrated downstream of the CRP and detected by anti-Myc antibody (the image related to FigS5D).
DOI: 10.6084/m9.figshare.28883525.v1
title: Supplementary Material for: GLPG2737, a CFTR Inhibitor, Prevents Cyst Growth in Preclinical Models of Autosomal Dominant Polycystic Kidney Disease

description: Introduction: Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder that is characterized by the development of fluid-filled kidney cysts, which often lead to kidney failure. The vasopressin receptor 2 antagonist, tolvaptan, is the only approved treatment that slows the progression of ADPKD. There is an unmet need for treatment options for patients with ADPKD because tolvaptan has limited efficacy and non-negligible side effects. In vitro and in vivo data suggest that inhibition of the cystic fibrosis transmembrane conductance regulator (CFTR) may be a suitable approach to treating ADPKD. Here, we assessed the capacity of GLPG2737, a CFTR inhibitor, to inhibit cyst growth in preclinical models of ADPKD. 

Methods: We investigated the ability of GLPG2737 to modulate CFTR activity in mouse kidney inner medullary collecting duct (mIMCD-3) epithelial cells by measuring chloride flux, and to prevent cyst growth in mIMCD-3 cells, cells from human ADPKD kidney donors, and metanephric organ cultures (MOCs). We assessed cyst volume, kidney weight or volume, and blood urea nitrogen (BUN) in two mouse ADPKD models (Pkd1 kidney-specific knockout mouse model; Pkd1RC/RC mouse model) that received GLPG2737, tolvaptan, or their combination. Statistical tests used for data analysis were based on the normality and variance of the data.

Results: GLPG2737 inhibited chloride flux in mIMCD-3 cells with an IC50 of 2.41 µM. In a 3D assay, GLPG2737 inhibited cyst growth in both wild-type (IC50 = 2.36 µM) and Pkd1 knockout (IC50 = 2.5 µM) mIMCD-3 cells. Preincubation of human ADPKD kidney cells with 10 µM of GLPG2737, 10 µM of tolvaptan, or their combination prevented forskolin-induced cyst growth by 40%, 29%, and 70%, respectively. Furthermore, 10 µM of GLPG2737 inhibited cyst growth in MOCs, decreasing the cyst area by 67% and the number of cysts per area by 46% after 6 days of culture. In both in vivo models, GLPG2737, tolvaptan, or their combination improved the projected cyst volume. In the Pkd1RC/RC model, GLPG2737 also improved the total kidney volume normalized to tibia length (LnTKV) and BUN, while tolvaptan improved the LnTKV and fibrosis but did not lower BUN at sacrifice. The combination reduced all parameters measured in the Pkd1RC/RC model, including cyclic adenosine monophosphate (cAMP) content in the kidneys.

Conclusions: Our findings in preclinical models provide evidence of the therapeutic potential of CFTR inhibition, and its possible combination with tolvaptan. The present work shows that targeting CFTR is a valid strategy to slow ADPKD progression.
DOI: 10.17632/8kgftsbf5k
title: Raw data from transcriptome sequencing of 12 colorectal cancer patients in Ruijin hospital (performed by Dr. Jing Sun))

description: The study was approved by the Ethical Committee of Ruijin Hospital with a clinical trial registration number NCT04714814. Among the prospective patient cohort collected, 12 CRC individuals for the High-throughput transcriptome analysis were strictly screened in our center, without any medical treatment before recruitment. Total RNA was isolated from the surgically discarded normal and tumor colorectal tissues of these 12 CRC individuals. Then, the cDNA library was constructed, and high-throughput sequencing was performed at Shanghai Jiao Tong University School of Medicine (Shanghai, China) using the HiSeq 4000 (Illumina, San Diego, CA). Raw data of the gene expression and clinical information about them is listed below.
DOI: 10.6084/m9.figshare.27886287.v1
title: Raw Data, PC scores, and secondary variables

description: The skull base serves as structural support for the brain and an important conduit for cranial nerves and vessels. Paraclival and parasellar features are particularly complex, as these sites represent the union of multiple bony elements with many neurovascular components. Although morphometric descriptions of these components are common, these methods have intrinsic limitations which make global assessment of these anatomical features and their relationships very challenging. Here we apply geometric morphometric (GM) techniques to address the problems associated with traditional morphometric strategies of evaluating skeletal and soft tissue components of the skull base. Our aims are to describe the geometry of relevant skull base features and assess the relationship between 3-D shape variables and more traditional craniometric variables. A Microscribe® i+ 3-D digitizer was used to register the location of 20 3-D skeletal and neural landmarks on the skull base of the middle and posterior cranial fossae on 80 anatomical body donors (mean age 83.0 ± 10.1 years). Linear measurements of neurocranial length, width, skull base length, and ulnar length (as a proxy for general body size) were collected with traditional methods. A principal component analysis (PCA) was applied to Procrustes aligned coordinates. The results of the PCA revealed 27 principal components (PCs). The first component accounted for 34.24% of the variation in the sample and was associated with changes in clival width with corresponding changes in sella turcica length. Shape changes associated with PC1 scores correlated with configuration size (centroid size) (R2=.532, p&lt;.001). Principal component 2 (12.85%) was associated with isolated changes in clival width driven primarily by the jugular tubercles. Results related to PC3 (11.10%) showed variation in skull base flattening. While PC2 and PC3 results were not correlated with size, they were correlated with neurocranial length and measurements of cranial width. In summary, we were able to determine the primary axes of 3-D morphological variation in the skull base features we assessed. Skull base size emerged as a principal driver of skull base shape. Variable anatomy of the jugular tubercle and its relationships to the jugular foramen and hypoglossal canal represented another key component to shape variation and should be considered in surgical approaches to the posterior fossa. Finally, our results support the idea that a wide range of non-pathological skull base flattening may exist in the population, as this shape axis was a major contributor to the variation seen in the sample.
DOI: 10.6084/m9.figshare.7473005.v1
title: Data from: Differential effects of forestry plantations on bird diversity: A global assessment

description: Original data from: Castaño-Villa, G.J., J.V. Estevez, G. Guevara, M. Bohada-Murillo and F.E. Fontúrbel (2019) Differential effects of forestry plantations on bird diversity: A global assessment. Forest Ecology and Management.<br>This entry contains three files:<br><br>(1) richness_data.csv - a CSV file containing the original data from species richness case studies included in the meta-analysis.<br>(2) abundance_data.csv - a CSV file containing the original data from bird abundance case studies included in the meta-analysis.<br>(3) references.txt - a numbered list (corresponding to the ref number in the richness and abundance data files) of the original data sources used.
DOI: 10.6084/m9.figshare.22323424.v1
title: BASALT demo files

description: This is a demo dataset to test BASALT code, where the content of the files are as follows: <br> Data.tar.gz - short read and long read raw sequence files and an OPERA-MS assembled contig file. Final_bestbinset.tar.gz - expected output of final bins. basalt.sh - script running this demo <br> Using a workstation Intel(R) Xeon(R) Gold 5218 CPU @ 2.30GHz with 32 cores, this demo dataset is expected to be finished within 6 h.
DOI: 10.6084/m9.figshare.28766405.v1
title: <b>Genotype data of "Identification and genome-wide association analysis of wheat FHB resistance genes</b><b>"</b>

description: Fusarium head blight (FHB) is one of the most devastating fungal diseases, leading to significant yield losses and deterioration of grain quality under severe conditions. In this study, a genome-wide association study was conducted with 448 wheat varieties (lines) using genotyping data generated by the 660K SNP array. Nine relatively stable FHB resistance loci were identified on chromosomes 1B, 1D, 2D, 3B, 5A, 5B, 7A and 7B, respectively. Each locus accounted for 3.9%-11.8% of the phenotypic variation, among these, QFhb.nwafu-1DL, QFhb.nwafu-7BS, and QFhb.nwafu-7BL are novel loci. Polymorphisms of flanking AQP marker AX-94527414 was developed for QFhb.nwafu-7BL, which could be useful for marker assisted selection of FHB resistance. Through correlation analysis of different traits, it was demonstrated that the correlation between the severity of FHB and SL, UIL and PH across the three environments was not significant, indicating that FHB resistance was independent of these traits. These results offer new resistance resources for FHB resistance breeding and insights for marker-assisted selection and gene cloning.
DOI: 10.6084/m9.figshare.8286230.v1
title: Raw count table

description: A count table of raw counts of genes with an ensemble id (~25k genes) for all tissues.
DOI: 10.6084/m9.figshare.c.3657098_d1.v1
title: Additional file 1: Table S1. of QTLs for stomatal and photosynthetic traits related to salinity tolerance in barley

description: List of candidate genes within 10Â cM around Bmac0209 on chromosome 3H of barley. (XLSX 37 kb)
DOI: 10.17632/75fs3vm5sg
title: Fate of organic carbon burial in modern sediment within Yangtze River Estuary

description: Detailed information for Corg, TN, C/N, SA, CF, and isotopes of δ13Corg and δ15N in surface sediments and sediment cores within Yangtze River Estuary (YRE); Detailed information for physico-chemical properties of bottom water and surface sediment from the river channel to the estuary
DOI: 10.17632/85b999zcdz
title: Raw data for "A heterotrimeric protein complex assembles the metazoan V-ATPase upon dissipation of proton gradients"

description: Deposited is all the raw sequencing and AlphaFold3 models as described in the methods section of the manuscript.
DOI: 10.17632/nmb24z6jrp
title: Large Grid of 1D X-ray Burst Models with MCMC Sample Chains

description: This dataset contains the primary data used in: "Multi-epoch X-ray burst modelling: MCMC with large grids of 1D simulations", Johnston et al. (2020).
In this work, we interpolated and sampled a grid of 3840 KEPLER burst models using Markov Chain Monte Carlo (MCMC) methods to produce posterior distributions for the system parameters of the "Clocked Burster", GS 1826-238.

Provided here is the full burst model grid and the raw MCMC sample chains.
More details on the files, and how to load them, are provided in README.md
DOI: 10.6084/m9.figshare.12792092.v2
title: profiles dark SFM

description: p { margin-bottom: 0.1in; line-height: 120% } oxygen concentration profiles were measured with a clark-type oxygen microsensor (tip diameter : 10 um, Unisense). Several profiles were taken in precise x,y positions of the biofilm, especially in the center of biofilm structures. Each x,y (labeled with an <i>id</i>) position was sampled in both light and dark, hence light park profiles are coupled by their position, which is reported in the metadata files. Light and dark profiles are coupled in the file "Tables/Ph-Res_profiles_data_all_coords.csv". The raw OCT scans are in "OCT raw scans/ profiles/", and relative DEMs are in "DEMs/profiling_*"
DOI: 10.6084/m9.figshare.26543542.v3
title: Bases de datos OLTP y OLAP sobre ventas en una cadena de tiendas

description: Conjunto de datos <b>generado </b>sobre ventas durante un período en una cadena de tiendas. Los precios de los productos presentan variabilidad temporal y dependen de cada establecimiento.La base de datos OLTP almacena las líneas de detalle de los tickets emitidos, junto con una tabla de productos proveniente del sistema de gestión de almacén.En la base de datos OLAP, los hechos están estructurados en dos niveles de granularidad: resumen diario y línea de ticket.Los datos se proporcionan en formato de respaldo de PostgreSQL (al restaurarlo, se genera un error indicando que el esquema "public" ya existe, pero la restauración se completa correctamente) y en formato CSV (comprimido en un archivo ZIP). La base de datos OLAP también se ofrece en formato PBIX para su uso en Power BI.
DOI: 10.17632/jywsy5zz96
title: Circulating hematopoietic stem/progenitor cell subsets contribute to human hematopoietic homeostasis

description: In physiological conditions, few circulating hematopoietic stem/progenitor cells (cHSPC) are present in the peripheral blood but their contribution to hematopoietic homeostasis in humans remain unsolved. By integrating advanced immunophenotyping, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), functional single-cell assays and integration site (IS) clonal tracking, we unveiled the phenotypic composition, the transcriptional features and the biological role of human cHSPC subpopulations in relationship to their bone marrow (BM) counterpart. We found that cHSPC progressively reduced in cell count over aging and are enriched for primitive, lymphoid and erythroid subpopulations, showing pre-activated transcriptional and functional state. Moreover, cHSPC have low expression of multiple BM-retention molecules, but maintain their homing potential after xenotransplantation. By generating a comprehensive Human Organ-Resident HSPC (HuOR) dataset based on scRNAseq data, we detected organ-specific seeding properties of the distinct trafficking HSPC subpopulations. Of note, circulating multi-lymphoid progenitors (MLP) are primed for seeding the thymus and actively contribute to T-cell production at steady state in patients treated with HSPC-gene therapy (GT). Human clonal tracking data from GT patients also showed that cHSPC connect distant BM niches and participate to steady-state hematopoietic production, with primitive cHSPC having the highest re-circulation capability to travel in and out the BM. Finally, in case of hematopoietic impairment, cHSPC composition reflects the BM-HSPC content and might represent a biomarker of the BM state for clinical and research purposes. Overall, our comprehensive work unveiled fundamental insights into the in vivo dynamics of human HSPC trafficking and its role in sustaining hematopoietic homeostasis.
DOI: 10.17632/snxkknzs52
title: Dataset: Graded calls of the smallest terrestrial mammal, the Etruscan shrew, living in a closed habitat

description: Dataset used in the analysis of the publication "Graded calls of the smallest terrestrial mammal, the Etruscan shrew, living in a closed habitat"
DOI: 10.6084/m9.figshare.1334232.v1
title: Highest Resolution in vivo Human Brain MRI Using Prospective Motion Correction: highest resolution ToF data

description: Full dataset (140 slices) of the highest resolution 3D ToF scan (shown in Fig. 8).
DOI: 10.6084/m9.figshare.16651822.v1
title: Figure5

description: Data needed to create figure 5: RNA-5c, clustering of cells using the SCA meta-genes. A) SCA using TFs tagets, B) SCA using miRNA targets, C) clusters to cell association for A, D) clusters to cell association for B.<br>Figure 5A:somewhere_in_your_computer/fig5_slim/RNA2500-5c/tf-matrix_summed/5/matrix_summed_Stability_Plot.pdf<br>Figure 5B:somewhere_in_your_computer/fig5_slim/RNA2500-5c/mirna-0denseSpace_summed/5/0denseSpace_summed_Stability_Plot.pdf<br>
DOI: 10.6084/m9.figshare.24994233.v1
title: fraud_oracle.csv

description: This study leverages advanced methods and algorithms to create an automated insurance fraud detection system, using real insurance fraud data. The system consists of four phases: data resampling (Over, Under, and hybrid), feature selection (Filtering, Wrapping, and Embedding), binary classification (Bagging and Boosting), and explanatory model analysis (Shapley Additive Explanations, Break-down plots, and variable-importance Measures). Results show that not all resampling techniques improve algorithm performance, but all feature selection methods do. Notably, the Boosting algorithm, incorporating the Neighborhood Cleaning Rule for resampling and Tree-based feature selection, excels in detecting insurance claim fraud.
DOI: 10.6084/m9.figshare.26355835.v1
title: Supplemental Table 2

description: Immunity
DOI: 10.17632/7sstcvnctk
title: The roles of mindfulness and spiritual intelligence in transformational leadership and its ethical dimensions
DOI: 10.6084/m9.figshare.19313885.v1
title: Thermal and Rheological Structure of Lithosphere beneath Northeast China

description: •3D_Vp_Model.txt: The 3-D Vp model of Ma et al. (2018) with format of [Longitude (deg) Latitude (deg) Depth (km) Velocity (km/s)].•3D_T_Model.txt: The obtained 3-D temperature model with format of [Longitude (deg) Latitude (deg) Depth (km) Temperature (K)].•3D_Strenth_Model.txt: The obtained 3-D rheological strength model with format of [Longitude (deg) Latitude (deg) Depth (km) Strength (MPa)].•ISC_Catalog_NEC.txt: The list of crustal earthquakes (Mb ≥ 4.0) in Northeast China during 1970 to 2020 with format of [Time (UTC) Latitude (deg) Longitude (deg) Depth (km) Magnitude]<br>
DOI: 10.6084/m9.figshare.25778349.v1
title: BinBcla

description: This is the dataset for binary code similarity detection.
DOI: 10.6084/m9.figshare.28195844.v1
title: <b>Table S2. </b>Cell count and proportions in the 23 monocyte clusters

description: This study assesses the state of circulating monocytes in diabetes, with or without delayed gastric emptying, using a Streptozotocin (STZ)-induced mouse model, CyTOF, and computational analysis. Our findings show two classical monocyte subsets to be altered in the setting of diabetes with delayed gastric emptying and possible role of monocyte trafficking via the Ccr2-Ccl2 axis. All experiments were conducted in compliance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. All protocols were authorized by the Mayo Clinic Institutional Animal Care and Use Committee (A561020). Madhusudan Grover has received research grants from Takeda and Alfasigma Pharmaceuticals, as well as advisory fee from Evoke and Ardelyx Pharmaceuticals. Ruixue Hou, Yogesh Bhattarai, and Jill Wykosky are employees and shareholders of Takeda. Richard Myers and Alan J. Burns were employees during the time that this study was conducted and shareholders of Takeda. The rest of the authors declare no competing interests.
DOI: 10.6084/m9.figshare.28705913.v2
title: Supplementary materials for Climate-land use interactions outweigh individual effects in driving amphibian biodiversity loss: A karst case study from Guizhou, China

description: Supplementary materials for Climate-land use interactions outweigh individual effects in driving amphibian biodiversity loss: A karst case study from Guizhou, China
DOI: 10.6084/m9.figshare.3502742.v1
title: USPC-IPC Correspondence

description: The USPC and IPC systems were harmonized using the concordance provided by ReedTech at http://patents.reedtech.com/classdata.php. In order to simplify the classification of patents, we compared all IPCs found in the OECD's database to the USPTO classes liked in ReedTech's concordance table and assigned them to the appropriate USPTO label. 2 columns, 183K lines, "|" delimited; the columns are:--USPC: the USPC--IPC: the IPCs that are found in our database that are equivalent to that USPC. If more than one IPC is equivalent, they are separated by a ",".<br>