cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24192336.v1
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.5066/p9ppbsh5
title: Active Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) projects vector data

description: Shapefile contains project boundaries for active Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) projects as of December 2022.
DOI: 10.6084/m9.figshare.24192261
title: <b>Tree species diversity increases soil microbial carbon use efficiency in a subtropical forest</b>

description: Plant communities strongly influence soil microbial communities and, in turn, soil carbon (C) cycling. Microbial carbon use efficiency (CUE) is an important parameter for predicting soil C accumulation, yet how plant and soil microbial community traits influence microbial CUE remains poorly understood. Here, we determined how soil microbial CUE is influenced by plant and soil microbial community traits, by studying a natural gradient of plant species diversity in a subtropical forest. Our results showed that microbial CUE increased with increasing tree species diversity, suggesting a correlation between plant community traits and soil C storage. The specific soil properties that explained the greatest variation in microbial CUE were associated with microbial communities (biomass, enzyme activities and the ratio of oligotrophic to copiotrophic taxa); there were weaker correlations with plant-input properties, soil chemistry and soil organic C quality and its mineral protection. Overall, high microbial CUE was associated with soil properties correlated with increased tree species diversity: higher substrate availability (simple SOM chemical structures and weak mineral organic associations) and high microbial growth rates despite increased community dominance by oligotrophic strategists. Our results point to a mechanism by which increased tree species diversity may increase the forest C sink by affecting carbon-use with the soil microbial community.
DOI: 10.5517/ccdc.csd.cc2d5bwt
title: CCDC 2209676: Experimental Crystal Structure Determination

description: Related Article: Sergey A. Dobrynin, Mark M. Gulman, Denis A. Morozov, Irina F. Zhurko, Andrey I. Taratayko, Yulia S. Sotnikova, Yurii I. Glazachev, Yuri V. Gatilov, Igor A. Kirilyuk|2022|Molecules|27|7626|doi:10.3390/molecules27217626
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24192318
title: mentoring_data.xlsx

description: <b>The mechanisms of the impact of mentoring relationship on protégés' work attitudes: Evidence from meta-analysis</b>
DOI: 10.6084/m9.figshare.24192318.v1
title: mentoring_data.xlsx

description: <b>The mechanisms of the impact of mentoring relationship on protégés' work attitudes: Evidence from meta-analysis</b>
DOI: 10.6084/m9.figshare.24192366
title: Data

description: Manuscript data
DOI: 10.6084/m9.figshare.24192366.v1
title: Data

description: Manuscript data
DOI: 10.5066/p96hvjsl
title: New Source Rock Data for the Niobrara and Sage Breaks intervals of the lower Cody Shale in the Wyoming part of the Bighorn Basin

description: In 2019 the U.S. Geological Survey (USGS) quantitively assessed the potential for undiscovered, technically recoverable continuous (unconventional) oil and gas resources in the Niobrara interval of the Cody Shale in the Bighorn Basin Province (Finn and others, 2019). Leading up to the assessment, in 2017, the USGS collected samples from the Niobrara and underlying Sage Breaks intervals (Finn, 2019) to better characterize the source rock potential of the Niobrara interval. Eighty-two samples from 31 wells were collected from the well cuttings collection stored at the USGS Core Research Center in Lakewood, Colorado. The selected wells are located near the outcrop belt along the shallow margins of the basin to obtain samples that were not subjected to the effects of deep burial and subsequent organic carbon loss due to thermal maturation as described by Daly and Edman (1987) (fig. 1). Sixty samples are from the Niobrara interval, and 22 from the Sage Breaks interval (fig. 2).
DOI: 10.5281/zenodo.8377177
title: amphiuma_means_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8377176
title: amphiuma_means_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5517/ccdc.csd.cc201gbw
title: CCDC 1848447: Experimental Crystal Structure Determination

description: Related Article: Tadashi Kawamoto, Kohei Kurata, Takehiko Mori|2018|J.Phys.Soc.Jpn.|87|083703|doi:10.7566/JPSJ.87.083703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8377221
title: eurycea_guttolineata_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8377220
title: eurycea_guttolineata_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.15128/r1t148fh184
title: Making molecules by mergoassociation: two atoms in adjacent non spherical optical traps [dataset]

description: This work was supported by the U.K. Engineering and Physical Sciences Research Council (EPSRC) Grant Nos. EP/P01058X/1, EP/T518001/1, EP/W00299X/1, and EP/V011677/1.
description: Mergoassociation of two ultracold atoms to form a weakly bound molecule can occur when two optical traps that each contain a single atom are merged. Molecule formation occurs at an avoided crossing between a molecular state and the lowest motional state of the atom pair. We develop the theory of mergoassociation for pairs of nonidentical nonspherical traps. We develop a coupled- channel approach for the relative motion of the two atoms and present results for pairs of cylindrically symmetrical traps as a function of their anisotropy. We focus on the strength of the avoided crossing responsible for mergoassociation. We also develop an approximate method that gives insight into the dependence of the crossing strength on aspect ratio.
description: BOUND and MOLSCAT programs for solving coupled channel scattering and bound state problems.
DOI: 10.5284/1113242
title: Charles French Geoarchaeological and Micromorphological Reports and Bibliography

description: This dataset includes the geoarchaeological, micromorphological, and molluscan reports made by Charles French in over 45 years of involvement in excavation and research projects both in the UK and internationally. Over half of the UK the sites and projects included in the archive are located in Cambridgeshire, with the remainder located in other parts of Britain, but especially in southern and eastern England, Yorkshire and Orkney, as well as the Channel Islands. Internationally, the main areas where sites and projects are located are: Chile, Peru, southwestern USA, Europe (France, Spain, Portugal, Italy, Sardinia, Sicily, Hungary), the Balkans, East Africa, India and Kazakhstan.
DOI: 10.25380/iastate.23837100
title: Topographic Scans of Breech Face Impressions on Cartridge Case Primers

description: This repository contains topographic scans of breech face impressions on the surface of 2,625 fired cartridge case primers. We obtained these cartridge cases from the Defense Forensic Science Center (DFSC) Ames Lab I study. We provide this data set as a benchmark to develop and validate cartridge case processing and comparison algorithms.Topographic images of the cartridge case surfaces were taken using the Cadre Forensic (TM) TopMatch-3D High Capacity scanner at a resolution of approximately 1.8 micrometers ("microns") per pixel. Each image is digitally represented as a 2D array called a "surface matrix" containing the relative depth values of the cartridge case surface. Each surface matrix is saved along with metadata concerning the parameters under which the image was taken (including size, resolution, author, and others) to the x3p (XML 3D Surface Profile) file format. Additionally, each image is accompanied with a second 2D array of the same size called a "mask" representing manual annotations on the image. These manual annotations are intended to identify a region of the cartridge case surface containing "breech face impressions," which, analogous to a fingerprint, can be used to identify the firearm from which the cartridge case was fired.Apart from the original, full resolution topographic images, versions of each image undergoing various pre-processing steps are also included in the "sample_400_balanced," "sample_400"balanced_afterAutoPreproc_masks," and "sample_400_balanced_preprocessed" folders. These pre-processing steps are intended to isolate and emphasize the breech face impressions in the image. For example, manual annotations saved in the x3p mask are used to extract the breech face impression region away from the rest of the image. The "code/" folder contains an executable script written in the R programming language called "preProcess-scans.R" that fully reproduces the pre-processed scans. The "validation" folder contains results and reproducible code from applying a cartridge case comparison algorithm called the Congruent Matching Cells method. Additionally, the folder contains results from comparing NIST Standard Reference Material #2461 cartridge cases. These validations were performed to ensure that the scanning and processing procedures resulted in scans that accurately represent the original cartridge case surfaces.
DOI: 10.25380/iastate.23837100.v1
title: Topographic Scans of Breech Face Impressions on Cartridge Case Primers

description: This repository contains topographic scans of breech face impressions on the surface of 2,625 fired cartridge case primers. We obtained these cartridge cases from the Defense Forensic Science Center (DFSC) Ames Lab I study. We provide this data set as a benchmark to develop and validate cartridge case processing and comparison algorithms.Topographic images of the cartridge case surfaces were taken using the Cadre Forensic (TM) TopMatch-3D High Capacity scanner at a resolution of approximately 1.8 micrometers ("microns") per pixel. Each image is digitally represented as a 2D array called a "surface matrix" containing the relative depth values of the cartridge case surface. Each surface matrix is saved along with metadata concerning the parameters under which the image was taken (including size, resolution, author, and others) to the x3p (XML 3D Surface Profile) file format. Additionally, each image is accompanied with a second 2D array of the same size called a "mask" representing manual annotations on the image. These manual annotations are intended to identify a region of the cartridge case surface containing "breech face impressions," which, analogous to a fingerprint, can be used to identify the firearm from which the cartridge case was fired.Apart from the original, full resolution topographic images, versions of each image undergoing various pre-processing steps are also included in the "sample_400_balanced," "sample_400"balanced_afterAutoPreproc_masks," and "sample_400_balanced_preprocessed" folders. These pre-processing steps are intended to isolate and emphasize the breech face impressions in the image. For example, manual annotations saved in the x3p mask are used to extract the breech face impression region away from the rest of the image. The "code/" folder contains an executable script written in the R programming language called "preProcess-scans.R" that fully reproduces the pre-processed scans. The "validation" folder contains results and reproducible code from applying a cartridge case comparison algorithm called the Congruent Matching Cells method. Additionally, the folder contains results from comparing NIST Standard Reference Material #2461 cartridge cases. These validations were performed to ensure that the scanning and processing procedures resulted in scans that accurately represent the original cartridge case surfaces.
DOI: 10.3217/wt2bh-20214
title: Arcing in Li-Ion Batteries: Supplementary Information

description: Raw data and the videos of the experiment which is described in the submitted publication with the title 'Arcing in Li-Ion Batteries' in the journal Batteries (ISSN 2313-0105).
DOI: 10.5281/zenodo.8377272
title: mionectes_olivaceus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8377271
title: mionectes_olivaceus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23930172
title: Data base of YKL-40 serum levels are predicted by inflammatory state, age and diagnosis of idiopathic inflammatory myopathies

description: Clinical, immunological and demographical features of our study group
DOI: 10.6084/m9.figshare.23930172.v2
title: Data base of YKL-40 serum levels are predicted by inflammatory state, age and diagnosis of idiopathic inflammatory myopathies

description: Clinical, immunological and demographical features of our study group
DOI: 10.6084/m9.figshare.23930172.v3
title: Data base of YKL-40 serum levels are predicted by inflammatory state, age and diagnosis of idiopathic inflammatory myopathies

description: Clinical, immunological and demographical features of our study group
DOI: 10.5517/ccdc.csd.cc2fcxc3
title: CCDC 2245775: Experimental Crystal Structure Determination

description: Related Article: Shichong Wang, Huayan Xu, Ruoyu Zhang, Siyu Zhang, Yun Chai, Bingchuan Yang, Jingjing Zhao, Yuanqing Xu, Pan Li|2023|Org.Lett.|25|6746|doi:10.1021/acs.orglett.3c02653
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21705956
title: Methodological precision of in situ and in vitro algal density measurements in the model cnidarian, Exaiptasia diaphana

description: The objective of this study was to evaluate the precision of <i>in vitro</i> and <i>in situ</i> algal density measurement protocols using light, fluorescent, and confocal microscopy and an automated cell counter. <i>In situ</i> algal density was quantified as algal area fraction (%) using confocal images of tentacle clippings mounted on two types of slides. <i>In vitro</i> algal density of holobiont homogenate was quantified as algal cells/µl of holobiont homogenate using an automated cell counter and a hemocytometer viewed using light and fluorescent microscopy. Triplicate measurements of each method for ten anemones were collected and the coefficient of variation was calculated and compared across the ten anemones within each method.
DOI: 10.6084/m9.figshare.21705956.v1
title: Methodological precision of in situ and in vitro algal density measurements in the model cnidarian, Exaiptasia diaphana

description: The objective of this study was to evaluate the precision of <i>in vitro</i> and <i>in situ</i> algal density measurement protocols using light, fluorescent, and confocal microscopy and an automated cell counter. <i>In situ</i> algal density was quantified as algal area fraction (%) using confocal images of tentacle clippings mounted on two types of slides. <i>In vitro</i> algal density of holobiont homogenate was quantified as algal cells/µl of holobiont homogenate using an automated cell counter and a hemocytometer viewed using light and fluorescent microscopy. Triplicate measurements of each method for ten anemones were collected and the coefficient of variation was calculated and compared across the ten anemones within each method.
DOI: 10.6084/m9.figshare.5007974
title: Genetic fingerprinting of Exaiptasia pallida anemones by AFLP

description: R codeJaccard indices
DOI: 10.6084/m9.figshare.5007974.v1
title: Genetic fingerprinting of Exaiptasia pallida anemones by AFLP

description: R codeJaccard indices
DOI: 10.5281/zenodo.8377327
title: mitrocomella_polydiademata_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8377326
title: mitrocomella_polydiademata_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.21227/ezyb-tc34
title: COCO-MMR

description: Multimodal reasoning is a critical component in the pursuit of artificial intelligence systems that exhibit human-like intelligence, especially when tackling complex tasks. While the chain-of-thought (CoT) technique has gained considerable attention, the existing ScienceQA dataset, which focuses on multimodal scientific questions and explanations from elementary and high school textbooks, lacks a comprehensive evaluation of diverse approaches. To address this gap, we present COCO Multi-Modal Reasoning(COCO-MMR) dataset, a novel dataset that encompasses an extensive collection of open-ended questions, rationales, and answers derived from the large object dataset COCO. Unlike previous datasets that rely on multiple-choice questions, our dataset pioneers the use of open-ended questions in the context of multimodal CoT, introducing a more challenging problem that effectively assesses the reasoning capability of CoT models. Through comprehensive evaluations and detailed analyses, we provide valuable insights and propose innovative techniques, including multi-hop cross-modal attention and sentence-level contrastive learning, to enhance the image and text encoders. Extensive experiments demonstrate the efficacy of the proposed dataset and techniques, offering novel perspectives for advancing multimodal reasoning.  The data and code are available at \href{https://github.com/weijingxuan/COCO-MMR}{https://github.com/weijingxuan/COCO-MMR}.
DOI: 10.6073/pasta/27475c9b14b7f7d175e75ba3b4e2c13b
title: ASM01 Soil water content measured by neutron probe at Konza Prairie

description: Data set contains measurements of soil moisture (%volume) at various depths (25-200 cm) in deep (lowland) soils collected on LTER grazed and ungrazed watersheds burned at 1-, 4-, and 20-year intervals. Soil moisture measured by the neutron probe method.
DOI: 10.5281/zenodo.8367289
title: Dataset for the study "Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics in Legionella pneumophila serogroup 1 isolates from Portugal"

description: Dataset for the study "Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics in <em>Legionella pneumophila</em> serogroup 1 isolates from Portugal"
DOI: 10.5281/zenodo.8367288
title: Dataset for the study "Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics in Legionella pneumophila serogroup 1 isolates from Portugal"

description: Dataset for the study "Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics in <em>Legionella pneumophila</em> serogroup 1 isolates from Portugal"
DOI: 10.5281/zenodo.8377349
title: monocelis_spectator_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8377348
title: monocelis_spectator_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5517/ccdc.csd.cc2fkvsn
title: CCDC 2251492: Experimental Crystal Structure Determination

description: Related Article: Hua Zhang, Rong-Chuan Su, Yu-Li Qin, Xiao-Juan Wang, Dan Chen, Xiao-Rong Liu, Yu-Xin Jiang, Peng Zhao|2023|RSC Advances|13|26581|doi:10.1039/D3RA03193D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8377141
title: Data for "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface"

description: Code and data for a project looking at how bioturbation by two benthic invertebrate taxa influence oxygen and nutrient dynamics a coastal freshwater wetland along Lake Erie, located in Ohio, USA. Article is titled "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface" and is published in Wetlands.
DOI: 10.5281/zenodo.8377140
title: Data for "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface"

description: Code and data for a project looking at how bioturbation by two benthic invertebrate taxa influence oxygen and nutrient dynamics a coastal freshwater wetland along Lake Erie, located in Ohio, USA. Article is titled "Invertebrate Activities in Wetland Sediments Influence Oxygen and Nutrient Dynamics at the Sediment-Water Interface" and is published in Wetlands.