cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13203385.v1
title: Additional file 2 of Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

description: Additional file 2: Table S2. An overview of all enriched KEGG pathways associated with atom % 13C (ALC) and atom % 15N (ALN) in the liver.
DOI: 10.6084/m9.figshare.13203382.v1
title: Additional file 1 of Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

description: Additional file 1: Table S1. An overview of all trait-associated genes (TAG) with atom % 13C (ALC) and atom % 15N (ALN) in the liver.
DOI: 10.6084/m9.figshare.12671432.v1
title: Additional file 2 of The prognosis of hepatoid adenocarcinoma of the stomach: a propensity score-based analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.14251918
title: Additional file 18 of The effect of calorie intake, fasting, and dietary composition on metabolic health and gut microbiota in mice

description: Additional file 18. The dynamics of the 6 co-abundance groups in high-fat-diet mice.
DOI: 10.15131/shef.data.5863443
title: Data for paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis"

description: This deposit contains data for reproducing the results reported in the paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis".<br>The folder "Repeatability Study" contains two sub folders:1. "Fitting3x3" with data relative to three subjects (P1,P2,P3). For each subject, the foot bone geometries are in "Geometries"; the surfaces used for fitting and the output of fitting are in "Fitting results", where nine repetitions are available (3x3operators).NB1: the surface called talonavicular.stl was selected onto the proximal surface of the navicular bone instead of the distal talus surface as described in the paper methodology. This choice was dictated by the impossibility of selecting correctly the talar surface on some of the segmented geometries, due to poor quality. However, testing the two approaches on a subset of subjects, proved equivalent results when building the joint axis from one or the other surface. NB2: the file Fitted_geometries.txt contains a list of points output from the fitting in Matlab and useful to build the joint reference systems. The point X_cylinder is only randomly assigned at this stage and needs to be relocated in NMSBuilder environment according to the instructions desctibed in the modelling Guide.2. "RepeatabilityKinematicsP3" containing "Inputdata" for the subject with worst repeatability results with trc files for a standing and a walking trial; "OpemsimModels3x3" with nine repetitions (3x3operators) of the opensim model of that subject.<br>The folder "Models for analysis" contains forty sub folders, relative to the two limbs of the twenty enrolled subjects. Each folder contains the opensim model of the foot and ankle and a sub folder with the full lower limb model, geometries, trc data, and results of IK simulations in opernsim.<br>
DOI: 10.15131/shef.data.5863443.v3
title: Data for paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis"

description: This deposit contains data for reproducing the results reported in the paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis".<br>The folder "Repeatability Study" contains two sub folders:1. "Fitting3x3" with data relative to three subjects (P1,P2,P3). For each subject, the foot bone geometries are in "Geometries"; the surfaces used for fitting and the output of fitting are in "Fitting results", where nine repetitions are available (3x3operators).NB1: the surface called talonavicular.stl was selected onto the proximal surface of the navicular bone instead of the distal talus surface as described in the paper methodology. This choice was dictated by the impossibility of selecting correctly the talar surface on some of the segmented geometries, due to poor quality. However, testing the two approaches on a subset of subjects, proved equivalent results when building the joint axis from one or the other surface. NB2: the file Fitted_geometries.txt contains a list of points output from the fitting in Matlab and useful to build the joint reference systems. The point X_cylinder is only randomly assigned at this stage and needs to be relocated in NMSBuilder environment according to the instructions desctibed in the modelling Guide.2. "RepeatabilityKinematicsP3" containing "Inputdata" for the subject with worst repeatability results with trc files for a standing and a walking trial; "OpemsimModels3x3" with nine repetitions (3x3operators) of the opensim model of that subject.<br>The folder "Models for analysis" contains forty sub folders, relative to the two limbs of the twenty enrolled subjects. Each folder contains the opensim model of the foot and ankle and a sub folder with the full lower limb model, geometries, trc data, and results of IK simulations in opernsim.<br>
DOI: 10.6084/m9.figshare.11106239.v2
title: Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model

description: Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLIF) pharmacophore and docking was utilised for screening the CDK2 inhibitors. The evaluation of the validation set indicated that this method can be used to screen large chemical databases because it has a high hit-rate and enrichment factor (80.1% and 332.83 respectively). Six compounds were screened out from NCI, Enamine and Pubchem database. After molecular dynamics and binding free energy calculation, two compounds had great potential as novel CDK2 inhibitors and they also showed selective inhibition against CDK2 in the kinase activity assay.
DOI: 10.6084/m9.figshare.13203385
title: Additional file 2 of Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

description: Additional file 2: Table S2. An overview of all enriched KEGG pathways associated with atom % 13C (ALC) and atom % 15N (ALN) in the liver.
DOI: 10.6084/m9.figshare.12671432
title: Additional file 2 of The prognosis of hepatoid adenocarcinoma of the stomach: a propensity score-based analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.13203351.v1
title: Additional file 9 of RICE ACYL-COA-BINDING PROTEIN6 Affects Acyl-CoA Homeostasis and Growth in Rice

description: Additional file 9. Dataset S1-S10.
DOI: 10.17882/57288
title: Arctic Western Eurasian Basin: IAOOS 23 and IAOOS 24 ocean CTD-DO, CDOM and nitrate profiles in 2017

description: The two platforms IAOOS 23 and IAOOS 24 were deployed within 600 m from each other at the North Pole from the Russia-operated Barneo ice camp on April 12, 2017. They followed a meandering trajectory, reaching as far as 30°E in the Nansen Basin, before turning back to the western Fram Strait. On both IAOOS 23 and 24, the ocean profiler was a PROVOR SPI (from French manufacturer NKE) equipped with a Seabird SBE41 CTD (Conductivity, Temperature, Depth) and a dissolved oxygen (DO) Aandera 4330 optode. For the first time, the profiler on IAOOS 23 also carried biogeochemical sensors. It featured a bio-optics sensor suite and a submersible ultraviolet nitrate analyzer (SUNA, Satlantic-Seabird Inc.). The bio-optics sensor suite (called Pack Rem A) combines a three-optical-sensor instrument (ECO Triplet, WET Labs Inc.) and a multispectral radiometer (OCR-504, Satlantic Inc.). The present dataset is composed of CTD-DO data from IAOOS 23 and 24, corrected from the thermal lag and the sensor lag, despiked and interpolated vertically every 0.5 m. It also comprises nitrate concentrations from the SUNA and CDOM fluorescence from the WETLabs ECO sensor on IAOOS 23. Other biogeochemical data will be added to this dataset. The profilers were set to perform two upward profiles a day from 250 m (IAOOS 23) and 350 m (IAOOS 24) upward starting at approximately 6 am and 6 pm. They provided a unique 8-month long dataset, gathering a total of 793 profiles of the temperature, salinity and oxygen (upper 350m) and 427 profiles of CDOM and nitrates concentrations (upper 250m).
DOI: 10.17882/59183
title: Arctic Western Eurasian Basin: IAOOS 23 physical and biogeochemical profiles in 2017

description: In April 2017, two Ice Atmosphere Arctic Ocean Observing System platforms (IAOOS 23 and IAOOS 24) were deployed near the North Pole. Over the next 8 months, they meandered southwards with the ice in the Transpolar Drift, collecting measurements in the upper 250 m of Amundsen Basin, Nansen Basin and Fram Strait. The ocean profilers are PROVOR SPI (from French manufacturer NKE), which includes a Seabird SBE41 CTD (Conductivity, Temperature, Depth) and a dissolved oxygen (DO) Aandera 4330 optode. IAOOS 23 also featured a bio-optics sensor suite and a submersible ultraviolet nitrate analyzer (SUNA, Satlantic-Seabird Inc.). The bio-optics sensor suite (called Pack Rem A) combines a three-optical-sensor instrument (ECO Triplet, WET Labs Inc.) and a multispectral radiometer (OCR-504, Satlantic Inc.). The present dataset is composed of chlorophyll-a fluorescence, backscatter, irradiances (at 412, 490 and 555 nm), photosynthetically active radiation (PAR), nitrate and colored-dissolved organic matter data from the IAOOS 23 platform, as well as composites of absolute salinity, conservative temperature and apparent oxygen utilization data from both profilers. The profilers were set to perform two upward profiles a day from 250 m starting at approximately 6 am and 6 pm. In this dataset, chlorophyll-a, PAR and irradiances were corrected with a shift to set dark values to zero. Nitrate was interpolated vertically every 5 m, and all other parameters were interpolated vertically every 0.5 m.
DOI: 10.18112/openneuro.ds004952.v1.0.1
title: Novel Reading
DOI: 10.15131/shef.data.5863422.v2
title: Data for paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling"

description: This folder contains data and material used in the paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling".A complementary figshare is available with Matlab code.<br> The content of this figshare is:1. PDF document with guidelines: "Step-by-step_modelling_guide.pdf" contains step-by-step operations for building subject-specific anatomical model of the lower-limb from gait data and MR Images.<br><br>2. Modelling_materiala. Modelling Folder Structure: this folder structure helps in the organisation of the modelling data and files and is required to correctly use the Matlab scripts. Reference to the structure and how to populate it can be find in in the "Step-by-step_modelling_guide.pdf".<br>b. NMSBuilder model structure template: this template is used in NMSBuilder to build the subject-specific anatomical model of the lower-limb according to the pipeline described in "Step-by-step_modelling_guide.pdf".c. NMSBuilder dictionaries: these dictionaries can be imported in NMSBuilder to perform virtual palpation of anatomical landmarks and visible gait markers. A description of the anatomical landmarks is also available as excel file.d. Muscle attachments atlas: this in contained in the folder "NMSBuilder_gait2392_muscle_attachments (mm)" where muscle attachments and their 3d coordinates (derived from the Opensim model gait2392) are listed within the respective body segment as txt files.<br>3. Simulations results (see README.txt): this folder contains the results published in the paper. It is organised in subfolders depending on the different approach to calculate musculotendon parameters, with the same identifiers as in the paper. For each approach, twenty-two folders contain each patient's OpenSim model (vtp files for geometries are not included due to sharing policies) and a Mat_summary with the results of the dynamic simulations run in OpenSim (as .mat files).
DOI: 10.15131/shef.data.5863422
title: Data for paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling"

description: This folder contains data and material used in the paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling".A complementary figshare is available with Matlab code.<br> The content of this figshare is:1. PDF document with guidelines: "Step-by-step_modelling_guide.pdf" contains step-by-step operations for building subject-specific anatomical model of the lower-limb from gait data and MR Images.<br><br>2. Modelling_materiala. Modelling Folder Structure: this folder structure helps in the organisation of the modelling data and files and is required to correctly use the Matlab scripts. Reference to the structure and how to populate it can be find in in the "Step-by-step_modelling_guide.pdf".<br>b. NMSBuilder model structure template: this template is used in NMSBuilder to build the subject-specific anatomical model of the lower-limb according to the pipeline described in "Step-by-step_modelling_guide.pdf".c. NMSBuilder dictionaries: these dictionaries can be imported in NMSBuilder to perform virtual palpation of anatomical landmarks and visible gait markers. A description of the anatomical landmarks is also available as excel file.d. Muscle attachments atlas: this in contained in the folder "NMSBuilder_gait2392_muscle_attachments (mm)" where muscle attachments and their 3d coordinates (derived from the Opensim model gait2392) are listed within the respective body segment as txt files.<br>3. Simulations results (see README.txt): this folder contains the results published in the paper. It is organised in subfolders depending on the different approach to calculate musculotendon parameters, with the same identifiers as in the paper. For each approach, twenty-two folders contain each patient's OpenSim model (vtp files for geometries are not included due to sharing policies) and a Mat_summary with the results of the dynamic simulations run in OpenSim (as .mat files).
DOI: 10.15131/shef.data.5863422.v1
title: Data for paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling"

description: This folder contains data and material used in the paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling".A complementary figshare is available with Matlab code.<br> The content of this figshare is:1. PDF document with guidelines: "Step-by-step_modelling_guide.pdf" contains step-by-step operations for building subject-specific anatomical model of the lower-limb from gait data and MR Images.<br><br>2. Modelling_materiala. Modelling Folder Structure: this folder structure helps in the organisation of the modelling data and files and is required to correctly use the Matlab scripts. Reference to the structure and how to populate it can be find in in the "Step-by-step_modelling_guide.pdf".<br>b. NMSBuilder model structure template: this template is used in NMSBuilder to build the subject-specific anatomical model of the lower-limb according to the pipeline described in "Step-by-step_modelling_guide.pdf".c. NMSBuilder dictionaries: these dictionaries can be imported in NMSBuilder to perform virtual palpation of anatomical landmarks and visible gait markers. A description of the anatomical landmarks is also available as excel file.d. Muscle attachments atlas: this in contained in the folder "NMSBuilder_gait2392_muscle_attachments (mm)" where muscle attachments and their 3d coordinates (derived from the Opensim model gait2392) are listed within the respective body segment as txt files.<br>3. Simulations results (see README.txt): this folder contains the results published in the paper. It is organised in subfolders depending on the different approach to calculate musculotendon parameters, with the same identifiers as in the paper. For each approach, twenty-two folders contain each patient's OpenSim model (vtp files for geometries are not included due to sharing policies) and a Mat_summary with the results of the dynamic simulations run in OpenSim (as .mat files).
DOI: 10.15131/shef.data.5863443.v2
title: Data for paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis"

description: This deposit contains data for reproducing the results reported in the paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis".<br>The folder "Repeatability Study" contains two sub folders:1. "Fitting3x3" with data relative to three subjects (P1,P2,P3). For each subject, the foot bone geometries are in "Geometries", the surfaces used for fitting and the output of fitting are in "Fitting results", where nine repetitions are available (3x3operators).2. "RepeatabilityKinematicsP3" containing "Inputdata" for the subject with worst repeatability results with c3d and trc files for a standing and a walking trial; "OpemsimModels3x3" with nine repetitions (3x3operators) of the opensim model of that subject.<br>The folder "Models for analysis" contains forty sub folders, relative to the two limbs of the twenty enrolled subjects. Each folder contains the opensim model of the foot and ankle and a sub folder with the full lower limb model, geometries, trc data, and results of IK simulations in opernsim.<br>
DOI: 10.5066/p9ne2acv
title: Density and magnetic susceptibility measurements on Precambrian rocks in the Iron Mountain-Menominee region, Michigan-Wisconsin

description: The U.S. Geological Survey (USGS) collected rock physical property measurements to help understand causative sources of gravity and magnetic survey anomalies in the Iron Mountain-Menominee region, Michigan-Wisconsin. A total of 2,356 measurements of magnetic susceptibility and density from 152 locations have been conducted on Precambrian rocks. The measurements aid in interpretation of newly acquired ground-based gravity and airborne magnetic data that are helping to understand concealed Precambrian geology and potential mineral resources. Multiple measurements were made at each location and sample lithology units were derived from existing USGS geologic maps noted in the supplemental information section of the metadata file. However, if no formal unit name exists, the rock lithology determined in the field were recorded. For outcrop measurements, sample locations were determined using handheld Global Position System units. Measurements from drill core samples at the State of Michigan public core facility in Harvey are also presented. For these measurements, the drill hole name, depth, and lithologic unit are provided.
DOI: 10.6084/m9.figshare.6387722.v1
title: Construction of pSPI12-cured <i>Salmonella enterica</i> serovar Pullorum and identification of IpaJ as an immune response modulator

description: In <i>Salmonella</i>, plasmids participate in many pathways involved in virulence, metabolism, and antibiotic resistance. To investigate the function of the <i>ipaJ</i> gene in a multi-copy plasmid pSPI12 prevalent in <i>Salmonella enterica</i> serovar Pullorum (<i>S</i>. Pullorum), we established a method to eliminate the plasmid and constructed the plasmid-cured bacteria C79-13-ΔpSPI12 by using the suicide vector pDM4. Briefly, a 500 bp fragment <i>ipaJU</i> from pSPI12 was cloned into pDM4 and transformed into <i>S.</i> Pullorum C79-13 by conjugative transfer. After homologous recombination, the suicide vector was inserted into pSPI12 to produce pSPI12-pDM4-<i>ipaJU</i>. Induction of the expression of the <i>sacB</i> gene in the suicide vector killed the bacteria harbouring plasmid, while the progeny losing the plasmid survived in the plate with sucrose. The plasmid-cured strain showed extremely decreased ability to infect chicken macrophage HD11 cells and LMH hepatic epithelial cells compared to wild type strain and complementary strain carrying <i>ipaJ</i>. Additionally, IFN-<i>γ</i> mRNA levels were up-regulated in HD11 cells or chicken spleens infected by plasmid-cured strain, but no difference was detected in IL-4 among the three strains. Transforming <i>ipaJ</i> into <i>S.</i> Enteritidis also decreased expression of proinflammatory cytokines in infected macrophages or chicken spleens compared to wild type strain. These results suggest that the <i>ipaJ</i> gene in pSPI12 is involved in <i>S.</i> Pullorum infection and that IpaJ protein modulates immune response.
DOI: 10.6084/m9.figshare.5863527.v1
title: Landfill leachate treatment by coagulation/flocculation combined with microelectrolysis-Fenton processes

description: Landfill leachate was pretreated by chemical flocculation with polyaluminum chloride (PAC) as a flocculant, and subsequently purified by the microelectrolysis-Fenton (MEF) process. Response surface methodology was employed to optimize the MEF process, and the optimal conditions were initial pH 3.20, H<sub>2</sub>O<sub>2</sub> concentration 3.57 g/L, and Fe-C dosage 104.52 g/L. The PAC coagulation combined with MEF processes obtained a superior decontamination performance, and the predicted chemical oxygen demand (COD) and humic acids (HA) removal were respectively 90.27% and 93.79%. The strong fluorescence peak at 425 nm and the trapping experiment showed that ⋅OH was generated during MEF, which had a strong oxidation ability to degrade organic recalcitrant pollutants. The ultraviolet–visible spectra and three-dimensional excitation–emission matrices spectra (3D-EEMs) indicated that PAC coagulation could preferentially remove protein-like substances, while the MEF process was effective in destructing organic recalcitrant pollutants, especially humic-like and fulvic-like substances.
DOI: 10.6084/m9.figshare.14252002
title: Additional file 2 of Reorganization of the 3D chromatin architecture of rice genomes during heat stress

description: Additional file 2: Table S1. Statistics Hi-C sequencing. Table S3. Statistics RNA-seq. Table S4. List of differentially expressed genes upon HS treatments in Nip. Table S5. List of differentially expressed genes upon HS treatments in 93-11.
DOI: 10.6084/m9.figshare.14252002.v1
title: Additional file 2 of Reorganization of the 3D chromatin architecture of rice genomes during heat stress

description: Additional file 2: Table S1. Statistics Hi-C sequencing. Table S3. Statistics RNA-seq. Table S4. List of differentially expressed genes upon HS treatments in Nip. Table S5. List of differentially expressed genes upon HS treatments in 93-11.
DOI: 10.6084/m9.figshare.14252005
title: Additional file 3 of Reorganization of the 3D chromatin architecture of rice genomes during heat stress

description: Additional file 3: Table S2 List of TADs identified in normal and HS conditions in Nip and 93-11, respectively.