cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24648756.v1
title: Supplementary Material for: LAG3 and TIGIT Expression on Tumor Infiltrating Lymphocytes in Cutaneous Melanoma.

description: Background: Melanoma is widely recognized to be an immunogenic tumor that often contains tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment (TME).During cancer progression, expression of ligands that bind immune checkpoint (IC) proteins, such as PD1, expressed on the surface of TILs, hinder them from exerting their antitumor functions. TILs consist of a heterogenous group of immune cells and their presence is associated with an improved overall survival (OS) in melanoma patients. Introduction of IC inhibitors has revolutionized management and prognosis of advanced melanoma. Unfortunately, the response rates have continued to be limited, resulting in growing interest in characterizing novel IC proteins, and developing combination therapy that includes inhibitors against multiple IC proteins. Methods: In a regional cohort of 166 patients diagnosed with cutaneous superficial spreading melanoma (SSM) with different degree of TILs, we investigated the tumor-immune associated gene expression profile using NanoString Technology. We used multiplex immunofluorescence (mIF) staining in a subset of tumors (N=7), combining IC proteins TIGIT and LAG3 with a melanoma cell marker (SOX10) and immune cell markers (CD8 (cytotoxic T cells), CD4 (T helper cells), FOXP3 (regulatory T cells/Tregs), PAX5 (B cells), and CD56 (NK/NKT cells)) and IC protein PD1. Results: We found upregulation of 91 differentially expressed genes, including IC proteins, LAG3 and TIGIT in melanomas with brisk TILs compared to tumors where TILs were absent. mIF staining revealed LAG3 and TIGIT expression in the majority of CD8+ T cells. Only few Tregs and CD4+ T cells expressed LAG3, whereas majority of them expressed TIGIT. LAG3 and TIGIT were expressed in a small fraction of the NK/NKT cells and lacked in the B cells. The majority of PD1+ cells co-localized with LAG3 and TIGIT. Conclusion: We report a variable expression of LAG3 and TIGIT on TILs subtypes and a coeval occurrence with PD1. This knowledge places LAG3 and TIGIT in spatial and cellular context in melanoma. The data suggest that targeting multiple IC proteins might help to overcome the current challenges with IC therapies.
DOI: 10.17632/zp9fghcbgm
title: wavelet-creation

description: We present a novel technique for the calculation of the coefficients required for a Wavelet Multiresolution Analysis (WMA). When a WMA is performed, a mother wavelet is used as a decomposition base to find how the scales and translations of the wavelet best describe the signal. The result of decomposition is a matrix containing the weight for each scale and time instant. To perform the decomposition, a filter bank composed with a low pass filter build with the scaling coefficients and a high pass filter build with the wavelet coefficients it is used. By reconstructing using a selected subset of the scales, we can use the WMA to reduce noise. Our proposal focuses on finding the scaling and wavelet coefficients that best describe a given function by solving an optimization problem with nonlinear restrictions. As an example of the proposed model, we create a new wavelet using as a function the base of communication between neurons, the Spike. With the calculated coefficients, we use the WMA to demonstrate the reduction of noise from a set of brain signals related to visual stimuli.
DOI: 10.6084/m9.figshare.22105040.v1
title: Raw data for Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity

description: Includes raw quantifications of GFP fluorescence, smFISH RNA puncta number, dauer assays, AFD morphology, thermotaxis behavior, and calcium imaging. For GFP fluorescence and smFISH puncta number, each value is from one neuron. For dauer and thermotaxis behavior assays, each value is from one assay. For AFD morphology and calcium imaging, each value is from one animal. RNA-Seq data and code for Figures 1 and S1 are separately available at GEO (GSE222226).
DOI: 10.6084/m9.figshare.3381517.v1
title: Templates for Automated Fiber Quantification from Diffusion MRI data

description: These templates are used to segment human white matter into the major tracks, as described in Yeatman et al. 2012 (Yeatman JD, Dougherty RF, Myall NJ, Wandell BA, Feldman HM (2012) Tract Profiles of White Matter Properties: Automating Fiber-Tract Quantification. PLoS ONE 7(11): e49790. doi:10.1371/journal.pone.0049790). Briefly, The regions of interest (ROIs) in these templates are defined in locations that isolate the central portion of the track where the fibers are coherently bundled together and before they begin diverging towards cortex. Each waypoint ROI was drawn on a group-average DTI data set in MNI space based on the anatomical prescriptions defined in Wakana et al (Wakana S, Caprihan A, Panzenboeck MM, Fallon JH, Perry M, et al. (2007) Reproducibility of quantitative tractography methods applied to cerebral white matter. Neuroimage 36: 630–644. doi: 10.1016/j.neuroimage.2007.02.049).<br>
DOI: 10.6084/m9.figshare.20281914.v1
title: Supplementary Material for: A novel ANK1 mutation in a neonatal hereditary spherocytosis case: Diagnostic challenges and familial genetic analysis

description: Hereditary spherocytosis (HS) is a congenital disease in which erythrocyte membranes are abnormal, with ANK1 defects as the main cause. The diagnosis of neonatal HS is difficult due to poor phenotypic specificity. Therefore, a detailed inquiry into family history may be helpful for diagnosis. Here, we describe a familial case of HS caused by a novel mutation in ANK1. The proband is a premature infant of Chinese Han ethnicity, characterized by progressive aggravation of anemia and jaundice. The disease was caused by a frameshift mutation (c.3392delT/p.Leu1131Argfs*15) of ANK1 that was identified by genetic testing. In vitro functional experiments showed that this variant may seriously affect the protein expression, and further expanded the mutation spectrum of ANK1-HS. In this case, we emphasize the diagnostic value of early-intervention genetic testing for neonatal hemolytic anemia with a family history.
DOI: 10.6084/m9.figshare.22225930.v1
title: SFA_CLCD_CHINA

description: The dataset presents the Secondary forest age (sfa) from CLCD in china. The sfa_clcd_china was driven from the continuous China Land Cover Dataset (CLCD). The age of the dataset ranged from 0 to 30. The 15 profiles were included in the dataset in tiff format. The more description referenced from the paper “Mapping of secondary forest age in China using stacked generalization and Landsat time series”.
DOI: 10.6084/m9.figshare.28827293.v1
title: <b>Aurian Number</b>.pdf

description: An Aurian Number is a positive integer in which the result of subtracting all its digits from right to left (starting from the last digit and subtracting each previous one) is equal to the difference between the sum and product of its digits. Let a number N have digits: N = d1 d2 d3 ... dk Step 1 – Subtractive Reduction: Subtract = dk - d(k-1) - d(k-2) - ... - d1 Step 2 – Sum and Product of Digits: Sum = d1 + d2 + ... + dk Product = d1 × d2 × ... × dk Aurian Condition: If Subtract == (Sum - Product), then the number is called an Aurian Number.10.6084/m9.figshare.28827293
DOI: 10.15468/dl.d4g3ru
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Holtbyrnia innesi (Fowler, 1934)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((37.8208 19.3058,37.7519 19.8496,35.9648 19.8496,35.9648 10.8496,44.9648 10.8496,44.9648 11.0757,44.5079 10.8984,44.021 11.3535,43.8449 12.4869,43.4392 13.1773,42.7805 13.6576,42.3014 14.2854,41.9925 14.3935,41.4722 15.0272,40.477 15.6908,40.2575 16.0951,39.9024 16.3482,38.9748 18.3342,37.8208 19.3058))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013442-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.23799789.v1
title: Data for Mitochondrial Genome Diversity across the Subphylum Saccharomycotina

description: Underlying data for "Mitochondrial Genome Diversity across the Subphylum Saccharomycotina"
DOI: 10.15468/dl.afzkzm
title: Occurrence Download

description: A dataset containing 1446 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Taxus L."
 ]
}

 The dataset includes 1446 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013441-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.21463092.v1
title: Replication Package

description: Replication package related to the paper "Estimating Causal effects of Multi-valued Treatments accounting for Network Interference: Immigration policies and crime rates"
DOI: 10.17632/wkn4w66cwc
title: ANALYSIS OF THE UNDERLYING FACTORS AFFECTING BIM-LCA INTEGRATION IN THE CONSTRUCTION INDUSTRY: A FACTOR ANALYSIS APPROACH

description: The integration of Building Information Modelling (BIM) and Life Cycle Assessment (LCA) is an effective means of achieving sustainability in the built environment. This study evaluates the barriers to BIM-LCA integration in the GCI from the perspective of construction professionals. Interpretivism and postpositivist guided the epistemological development of pertinent theory that was analytically tested using primary quantitative data. A comprehensive literature review was first conducted to identify and examine the barriers related to BIM-LCA integration. Data on the barriers to BIM-LCA integration was solicited using structured survey questionnaires that were administered to 216 Ghanaian construction professionals. Data was then analysed using factor analysis. Findings revealed three clusters of barriers viz.: 1) organisational barriers; 2) technical complexity; and 3) knowledge and education. The paper concludes with future research direction which could examine how artificial intelligence and machine learning could improve BIM-LCA integration in building designs. The research delineated provides the first novel and insightful knowledge on the barriers to BIM-LCA adoption in Ghana. Practical recommendations for overcoming these barriers are also proposed, e.g., developing standardised procedures and protocols, increasing awareness and education, and integrating BIM-LCA into project management systems.
DOI: 10.6084/m9.figshare.16802509.v1
title: Cherry blossoms

description: Historical Series of Phenological data for Cherry Tree Flowering at Kyoto City.
DOI: 10.6084/m9.figshare.26993332.v1
title: Carlsbad Cavern metaviromes

description: High confidence viral contigs from co-assembly of metaviromes from four Carlsbad Cavern pools.
DOI: 10.6084/m9.figshare.5241442.v1
title: Erratum: Imaging Cutaneous T-Cell Lymphoma with Optical Coherence Tomography

description: <b><i>Aim:</i></b> To investigate the presentation of a patch-stage cutaneous T-cell lymphoma (CTCL) using optical coherence tomography (OCT). <b><i>Methods:</i></b> A patient with a patch caused by CTCL was photographed digitally, OCT-scanned and biopsied. A normal skin area adjacent to the patch was OCT-scanned for comparison, but not biopsied. The OCT image and the histological image were compared. <b><i>Results:</i></b> The OCT images illustrated a thickened and hyperreflective stratum corneum. OCT also demonstrated several elongated hyporeflective structures in the dermis. The largest structure was measured to have a width of 0.13 mm. A good immediate correlation was found between histology and OCT imaging of the sample. <b><i>Conclusion:</i></b> The aetiology of the elongated structures is thought to be lymphomatous infiltrates. Similar findings have been described in ocular lymphoma and may therefore be an important characteristic of cutaneous lymphoma. It may further be speculated that the differences in OCT images may reflect the biological behaviour of the infiltrate. This observation therefore suggests that OCT imaging may be a relevant tool for the in vivo investigation of mycosis fungoides and other CTCLs, but in order to verify these observed patterns in OCT imaging, further investigations will be required.
DOI: 10.17632/7snjbpv4y5
title: Extrusion of Shrimp Shell - Polylactic Acid Composites: Dataset for the Impact of Surfactants on Morphology and Thermal Properties

description: Shrimp shell waste obtained from Louisiana Gulf shrimp (Litopenaeus setiferus) was heat-treated at varying temperatures and ground into a powder by ball-milling. The powder was used with and without surface treatment with maleic anhydride or stearic acid to form shrimp shell - polylactic acid (PLA) composite granules by solution processing and mechanical grinding. These granules were used as feedstock for the extrusion of composite filaments. The dataset shows the thermal properties of the shrimp shells and the presence of covalent bonding for surface treatment with maleic anhydride. The thermal properties of the composite granules and the influence of the use of surfactants on the morphology, density, and die swell of the extruded filaments are also collected to assess their use as a manufacturing material. The database is organized into five folders. The folder "Filament Weight and Diameter" contains .xlsx files containing the weight and diameter of five specimens of the extruded filaments for each surface treatment. "FTIR" contains an .xlsx file with data for the FTIR spectra of shrimp shells with and without surface treatment with maleic anhydride. Optical images in .tiff format of the ball-milled shrimp powder at 10x, 20x, and 40x magnification are found in the folder "Optical Microscopy". "Photos" contains digital photos in .tiff format for the dried shrimp, ball-milled shrimp, and extruded filament for each surface treatment. Lastly, the folder "TGA-DSC" contains TGA and DSC data for the raw shrimp shells and the composite granules.
DOI: 10.6084/m9.figshare.29063117.v1
title: Sorghum virgatum genome annotation

description: Sorghum virgatum genome annotation
DOI: 10.17632/hmxj6m7p93
title: Condition Assessment Dataset

description: Dataset for structural condition assessment of residential buildings in Botswana
DOI: 10.17632/jgbkkbmvsm
title: Gender and grades differences in emotional intelligence

description: This data set contains data of the study and instrument
DOI: 10.6084/m9.figshare.14869656.v1
title: Legumes Csv

description: Legume consumption by type.<br>Columns:id,pure_name,pure_portion,total<br>
DOI: 10.6084/m9.figshare.26095444.v2
title: Interconnecting fragmented forests: small and mobile birds are cornerstones in the plant-frugivore meta-network

description: The datasets and R codes for the sumbitted manuscript titled '<b>Interconnecting fragmented forests: small and mobile birds are cornerstones in the plant-frugivore meta-network</b>'.
DOI: 10.6084/m9.figshare.28741640.v1
title: Electronic structure calculations of HADHA and SOX9

description: This dataset consists of two parts:<b>Part 1</b>: In previous experiments, we found that acetylation at the K728 site of HADHA may affect its enzymatic activity. To further elucidate this finding from a structural perspective, we performed molecular docking simulations of the wild-type HADHA, the K728R mutant, and the HADHA K728ac mutant with their catalytic substrates, β-hydroxybutyryl-CoA. We calculated the Solvent Accessible Surface Area (SASA) and binding energies for all three forms of HADHA.<b>Part 2</b>: In earlier experiments, we discovered that the phosphorylation of six sites (T25, T87, S98, S136, T138, and T193) on the SOX9 protein could influence its interaction with the E3 ligase TRIM9, potentially affecting its ubiquitination and subsequent degradation. Therefore, we conducted molecular docking simulations to study the interactions between both the phosphorylated and non-phosphorylated forms of SOX9 and TRIM9.
DOI: 10.17632/xbm6zykgd6
title: Rescue of fragile X syndrome by CRISPR activation of the ribosome associated quality control factor ASCC3

description: Original blots and Mass spectrometry data
DOI: 10.6084/m9.figshare.23269757.v1
title: Cycle threshold values of qPCR data for genes in the liver and skin of animals that were exposed to both control and simulated shift conditions.

description: CT values of qPCR data for genes in the liver and skin from animals exposed after control and simulating shift conditions.
DOI: 10.6084/m9.figshare.27641136.v5
title: Paper data of "<b>Linking leaf dark respiration to leaf traits and reflectance spectroscopy across diverse forest types"</b> in <i>New Phytologist</i>

description: Leaf dark respiration (Rdark) is an important but minimally quantified component of carbon cycling in forest ecosystems. In terrestrial biosphere models, it is typically simulated through leaf traits such as maximum carboxylation capacity (Vcmax), leaf mass per unit area (LMA), nitrogen and phosphorus concentrations. However, the effectiveness of these relationships between different forest types still needs to be thoroughly evaluated. We collected canopy leaves of three typical temperate (mountain Changbai, 42°23' N, 128°05' E), subtropical (mountain GT, 29°15' N, 118°07' E) and tropical (Xishuangbanna, 21°37' N, 101°34' E) forests in China through the Chinese Academy of Sciences canopy tower crane observation network. Rdark and Vcmax were measured using a portable photosynthesis measurement system, leaf reflectance spectra were measured using a portable ground spectrometer, and leaf morphology and biochemical traits were measured using conventional laboratory methods. We found that leaf magnesium and calcium concentrations are more important in explaining cross site Rdark than commonly used traits such as LMA, nitrogen and phosphorus concentrations, but the univariate trait Rdark relationship remains weak (r2 ≤ 0.15) and varies depending on the forest. Although the multivariate relationship of leaf traits improves model performance, leaf spectroscopy outperforms trait Rdark relationship, accurately predicting cross site Rdark (r2=0.65) and identifying factors that lead to Rdark variation. Our research findings reveal some new traits with greater cross site scalability, challenging the use of empirical trait Rdark relationships in process models, and emphasizing the potential of leaf spectroscopy as a promising alternative method for estimating Rdark, ultimately improving the modeling of terrestrial plant respiration processes.
DOI: 10.6084/m9.figshare.6923354.v1
title: Supplementary Material for: The RNA-Binding Protein PCBP1 Functions as a Tumor Suppressor in Prostate Cancer by Inhibiting Mitogen Activated Protein Kinase 1

description: <b><i>Background/Aims:</i></b> Poly r(C) binding protein (PCBP) 1 or heterogeneous ribonucleoprotein (hnRNP) E1 is a RNA binding protein functional in multiple biological processes. In prostate cancer (PCa), PCBP1 loss was shown to be involved with increased stemness in PCacells; however, the underlying mechanism remains unclear. <b><i>Method:</i></b> The role of PCBP1 in prostate tumor formationwas determined by xenograft assays. Immunoprecipitationand mass spectrometry were performed to find the pathways altered after PCBP1 knockdown. Cell proliferation, migration, invasion, and soft agar colony formationassays and xenograft assays were used to determine the role of target protein pathogenesis regulation and formation of PCa. QRT-PCR was performedto quantify relative mRNA expression. <b><i>Results:</i></b> The expression of mitogen activated protein kinase 1 (MAPK1) or extracellular signal regulated kinase 2 (ERK2) was increased following PCBP1 loss. Attenuation of MAPK1 inhibited <i>in vitro</i> and <i>in vivo</i> tumorigenicity and metastasis in PCa cell line, PC3. Overexpression of MAPK1 in the PC3 cells increased the tumorigenicity and metastasis. Analysis of PCBP1 and MAPK1 mRNA levels in 25 PCa patients compared to tumor-adjacent normal tissue confirmed an inverse correlation between PCBP1 and MAPK1 expression. <b><i>Conclusions:</i></b> PCBP1 can act as a suppressor of tumor in prostate epithelial cells by inhibiting MAPK1 expression.
DOI: 10.6084/m9.figshare.c.3833362_d3.v1
title: Additional file 3 of Common and phylogenetically widespread coding for peptides by bacterial small RNAs

description: Mass spectrometry results. (XLSX 21 kb)
DOI: 10.17632/c556368bd3
title: Dataset for the calculation of renewable electricity generation and gross electricity consumption of municipalities in Germany in 2019

description: This is a dataset of comma-separated data files collected from open sources to calculate renewable electricity generation and gross electricity consumption at the municipal level in Germany in 2019. All sources and the structure of the data files are specified in the data descriptor.
DOI: 10.6084/m9.figshare.16946032.v2
title: the modified IEEE-33 bus system

description: IEEE 33-bus system parameters of the distribution network refers to matpower. All codes are implemented on MATLAB. In "system data.txt", words explanation is show as follow: curvePd is unit value curve of power load.
DOI: 10.6084/m9.figshare.26830264.v1
title: Arf family GTPases are present in Asgard archaea

description: The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. We report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with an endomembrane system evolving early in eukaryogenesis.Here we provided source data for phylogenetic analyses. For each analysis, four files are provided:*_unaligned.fasta - unaligned protein sequences, in some cases trimmed to the GTPase domain*_alignment.fasta - multiple sequence alignment (details about programs are provided in Supplementary information and Supplementary Table 5)*_trimmed_alignment.fasta - trimmed multiple sequence alignment, input for phylogenetic analysis (details about programs and settings are provided in Supplementary information and Supplementary Table 5)*_newick tree.treefile - phylogenetic tree in the Newick formatPreprint is available at bioRxiv: https://doi.org/10.1101/2024.02.28.582541
DOI: 10.17608/k6.auckland.5207887.v1
title: The Index of Multiple Deprivation (IMD)

description: A fileset containing excel spreadsheets allowing researchers to map area-deprivation using the IMD.<br><br>