cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24080436.v1
title: Supplementary Material for: Objective response and progression free survival contribute to prolong overall survival in atezolizumab plus bevacizumab treatment for unresectable hepatocellular carcinoma.

description: Introduction: Atezolizumab plus bevacizumab (Atez/Bev) is a standard treatment for unresectable hepatocellular carcinoma (HCC) due to its good anti-tumor and survival prolongation effects. Post-progression survival (PPS) has been reported to be a great contributor in the treatment with tyrosine kinase inhibitors for unrecetable HCC. This study aimed to clarify the significance of progression-free survival (PFS) or PPS of Atez/Bev treatment for HCC. Methods: We analyzed the correlations of PFS and PPS with overall survival (OS) in studies of HCC patients treated with Atez/Bev and evaluated the contribution to OS in Atez/Bev treatment with patients at our institutions as clinical practice. Results: Analysis of 18 studies involving 2,937 patients treated with Atez/Bev found that PPS had a stronger correlation with OS (R2=0.872, p&lt;0.001) than did PFS (R2=0.605, p=0.001). Analysis of 80 patients with unresectable HCC treated with Atez/Bev found that presence of anti-tumor responses during Atez/Bev was the most significant contributor to OS, and post-progression treatment after Atez/Bev also significantly contribute to OS. Conclusion: The presence of anti-tumor response with tumor shrinkage during Atez/Bev treatment contributes to good OS through its durable response. Atez/Bev treatment could be considered as first-line treatment for unresectable HCC. However, there is a need for optimal biomarkers for good-anti-tumor response.
DOI: 10.6084/m9.figshare.25975273.v2
title: Data_final.csv

description: This folder contains the data.
DOI: 10.6084/m9.figshare.7883378.v1
title: gVCF_HG01058

description: 1000 Genomes gVCF mapped to hs37d5 for HG01058. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.20134208.v2
title: Baltic - North Sea

description: This record contains 6 datasets used in "Benthic Alkalinity fluxes from coastal sediments of the Baltic and North Seas: Comparing approaches and identifying knowledge gaps" published at Biogeosciences. Data were gathered during two cruises in the North Sea: HE541 (Sept 2019) MSM50a (Jan 2016), and two in the Baltic Sea: EMB111 (Aug-Sept 2015) and EMB238 (May 2020). Results from MSM50 and EMB111 are published by Lipka et al. (2018) and Gogina et al. (2018). https://figshare.com/account/home# 1) CombinedData_for_PROFILE_PW.xlsx 2) flux_summary.csv 3) NSea_Baltic_sediment.xlsx 4) PROFILE_prod_irr_summary.csv 5) Ra_based_fluxes.csv 6) HE541_RaFlux_summary.xlsx <br> 1) Input parameters and concentrations used to inform the PROFILE models. All concentrations are in units of mM. 2) Modelled sediment-water fluxes, as averages across all cores sampled at each site. Units are µmol cm-2 hr-1 <strong>flux_top:</strong> PROFILE output sediment-water flux <strong>flux_incubation</strong>: sediment-water flux calculated by combining Ra-224 derived porewater flushing rates from ex-situ incubations with surficial porewater concentration measurements. <strong>flux_budget</strong>: sediment-water flux determined from Ra-224 decay balance combined with surficial porewater concentrations <strong>flux_Br</strong>: sediment-water flux determined by combining Br- derived irrigation rates from ex-situ core incubations with surficial porewater concentrations 3) Combined dataset with separate tabs containing: a) metadata for the sites at which samples were collected b) porewater concentrations for metals, TA, DIC (units mM), and 13C-DIC (permil) c) nutrient concentrations in porewater (µM) d) sediment-water flux results from HE541 cruise, including Br-derived irrigation rates and O2 fluxes 4) PROFILE output of production and irrigation, integrated over the length of the core (µmol cm-3 hr-1). 5) Table containing computed water fluxes (irrigation rates) and sediment-water fluxes derived from ex-situ incubations (flux_incubation and flux_Br) as well as Ra-224 budget (flux_budget). Units are L m-2 d-1 for irrigation rates and µmol m-2 hr-1 for sediment-water fluxes. 6) Calculations of irrigation rates from Ra-224 measurements in surface water (column G), pore water (column L), and ex-situ incubations (columns M and N). <br> Lipka, M., Woelfel, J., Gogina, M., Kallmeyer, J., Liu, B., Morys, C., Forster, S. and Böttcher, M. E.: Solute reservoirs reflect variability of early diagenetic processes in temperate brackish surface sediments, Front. Mar. Sci., 9(NOV), 1–20, doi:10.3389/fmars.2018.00413, 2018. Gogina, M., Lipka, M., Woelfel, J., Liu, B., Morys, C., Böttcher, M. E. and Zettler, M. L.: In Search of a Field-Based Relationship Between Benthic Macrofauna and Biogeochemistry in a Modern Brackish Coastal Sea, Front. Mar. Sci., 5(DEC), 1–18, doi:10.3389/fmars.2018.00489, 2018.
DOI: 10.26180/20399376.v1
title: List with the published papers

description: This is an overview of the published papers in the top ten journals from 2000 through 2021, per year and per journal.
DOI: 10.6084/m9.figshare.5048059.v1
title: Harari D data.xlsm

description: A program consisting of Participatory Ergonomics, Workplace Exercise and Physical Therapy was conducted for 22 months with 88 workers of a hearing aid company. The outcomes were complaints of musculoskeletal disorders and absenteeism measured by the Nordic Musculoskeletal Questionnaire. Outcomes were analyzed for 1) all eligible participants of the study, 2) only workers with MSDs at baseline, and 3) only workers without MSDs at baseline. We also measured workers’ perceptions about the intervention by using a Likert-based questionnaire addressing muscle pain, absenteeism, wellbeing/productivity at work and life habits.
DOI: 10.6084/m9.figshare.14529372.v1
title: D'Ario_et_al_2021_image_analysis_scripts

description: This dataset contains scripts and supporting files for image analysis as described in the manuscript "Cell size controlled in plants using DNA content as an internal scale", by D'Ario et al., 2021.<br>Full instructions on installation and use of the scripts are found in the file "Image_processing_instructions". Source images, landmark files and metadata should be downloaded into the folder "processed_images" using the DOIs provided in the manuscript's Supplementary Table S2, also available here: dx.doi.org/10.6084/m9.figshare.14529351
DOI: 10.6084/m9.figshare.4479734.v2
title: 8.5 m Ammonite tool mark (trace fossil of shell drag)

description: An 8.5 m Ammonite Trace. From Lomax et al 2017, PLOS ONE.<br>Contains model (*.obj), material (*.mtl), texture (*.jpg), and complete photoset used to generate the model (*.zip).<br>
DOI: 10.6084/m9.figshare.16592429.v1
title: Supplementary Material for: Vacuum Therapy and Internal Drainage as the First-Line Endoscopic Treatment for Post-Bariatric Leaks: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> Several endoscopic methods can be employed to manage post-bariatric leaks. However, endoluminal vacuum therapy (EVT) and endoscopic internal drainage (EID) are relatively new methods, and studies regarding these methods are scarce. We performed a systematic review of the literature and a meta-analysis to evaluate the efficacy of EVT and EID. <b><i>Methods:</i></b> Databases were searched for eligible studies. The clinical success of leak closure was the primary outcome of interest. A proportional meta-analysis was performed for pooling the primary outcome using a fixed-effects model. A meta-analysis or descriptive analysis of other outcomes was performed based on the data availability. <b><i>Results:</i></b> Data from 3 EVT and 10 EID studies (<i>n</i> = 279) were used for evidence synthesis. The leak closure rates (95% confidence interval [CI]) of EVT and EID were 85.2% (75.1%–95.4%) and 91.6% (88.1%–95.2%), respectively. The corresponding mean treatment durations (95% CI) were 28 (2.4–53.6) and 78.4 (50.1–106.7) days, respectively. However, data about other outcomes were extremely limited; thus, a pooled analysis could not be performed. <b><i>Conclusions:</i></b> Both EVT and EID were effective when used as the first-line treatment for post-bariatric leaks. However, larger studies must be conducted to compare the efficacy of the 2 interventions.
DOI: 10.6084/m9.figshare.26348983.v1
title: Vretenovy_lis_simulation

description: FEM simulation check for the genetic algorithm design methodology<br><br>
DOI: 10.6084/m9.figshare.16438977.v1
title: Statistical Analysis Methods

description: All statistics were done in R Studio
DOI: 10.6084/m9.figshare.12480620.v1
title: feature database for MODNet

description: This file contains the database consisting of most materials from the MaterialsProject with a large set of corresponding ML features.<br>This file should first be unzipped, and the .pkl is then used for the featurization function in MODNet. (https://github.com/ppdebreuck/modnet)
DOI: 10.6084/m9.figshare.25688718.v4
title: Hierarchical Deep Learning Framework for Automated Marine Vegetation and Fauna Analysis Using ROV Video Data

description: Experimental data for the paper "Hierarchical Deep Learning Framework for Automated Marine Vegetation and Fauna Analysis Using ROV Video Data."This dataset supports the study "Hierarchical Deep Learning Framework for Automated Marine Vegetation and Fauna Analysis Using ROV Video Data" by providing resources essential for reproducing and validating the research findings.Dataset Contents and Structure:<br><b>Hierarchical Model Weights:</b> - `.pth` files containing trained weights for all alpha regularization values used in hierarchical classification models.<b>MaskRCNN-Segmented Objects</b>: - `.jpg` files representing segmented objects detected by the MaskRCNN model. - Accompanied by `maskrcnn-segmented-objects-dataset.parquet`, which includes metadata and classifications: - <b>Columns</b>:masked_image: Path to the segmented image file.confidence: Confidence score for the prediction.predicted_species: Predicted species label.species: True species label.<b>MaskRCNN Weights</b>: - Trained MaskRCNN model weights, including hierarchical CNN models integrated with MaskRCNN in the processing pipeline.<b>Pre-Trained Models</b>:.pt files for all object detectors trained on the Esefjorden Marine Vegetation Segmentation Dataset (EMVSD) in YOLO txt format.<b>Segmented Object Outputs</b>: - Segmentation outputs and datasets for the following models: - RT-DETR: - Segmented objects: `rtdetr-segmented-objects/` - Dataset: `rtdetr-segmented-objects-dataset.parquet` - <b>YOLO-SAG</b>: - Segmented objects: `yolosag-segmented-objects/` - Dataset: `yolosag-segmented-objects-dataset.parquet` - <b>YOLOv11</b>: - Segmented objects: `yolov11-segmented-objects/` - Dataset: `yolov11-segmented-objects-dataset.parquet` - <b>YOLOv8</b>: - Segmented objects: `yolov8-segmented-objects/` - Dataset: `yolov8-segmented-objects-dataset.parquet` - <b>YOLOv9</b>: - Segmented objects: `yolov9-segmented-objects/` - Dataset: `yolov9-segmented-objects-dataset.parquet`<b>Usage Instructions</b>:1. Download and extract the dataset.2. Utilize the Python scripts provided in the associated GitHub repository for evaluation and inference: https://github.com/Ci2Lab/FjordVision<b>Reproducibility</b>:The dataset includes pre-trained weights, segmentation outputs, and experimental results to facilitate reproducibility. The `.parquet` files and segmented object directories follow a standardized format to ensure consistency.<b>Licensing</b>:This dataset is released under the CC-BY 4.0 license, permitting reuse with proper attribution.<b>Related Materials</b>:- GitHub Repository: https://github.com/Ci2Lab/FjordVision
DOI: 10.6084/m9.figshare.15028470.v1
title: Supporting Data: Repeated dietary shifts in elapid snakes (Squamata: Elapidae) revealed by ancestral state reconstruction

description: Data for:<br>Maritz, B, Barends, JM, Mohammed, R, Maritz, RM, and GJ Alexander. Repeated dietary shifts in elapid snakes (Squamata: Elapidae) revealed by ancestral state reconstruction.<i> [In Press]</i><br>elapid_phylo.nex–Phylogeny of elapid species used in all analyses<br>elapid_diet.csv–Presence/absence (0/1) of prey used for all analyses–'mtl' maximum total body length (mm)<br>reduced_tree.csv–Tips to be included for Figure 1<br><br>Associated R code10.6084/m9.figshare.15028449
DOI: 10.6084/m9.figshare.2009742.v1
title: Adult_Giraffe_Arteries_OUVC-10513

description: Cranial arteries of the adult giraffe, OUVC-10513
DOI: 10.6084/m9.figshare.27977172.v1
title: ChatGPT Data EN (DeepL)

description: Input and output data from long-term learning in mathematical statistics using ChatGPT, translated by DeepL.
DOI: 10.6084/m9.figshare.23501508.v1
title: fig2e_and_4f.pzfx

description: Quantitative data of cytokines were performed using qRT-PCR in the manuscript. Visualization and statistical analysis were performed using Graphpad prism 9.0, and the results were saved in pzfx format. <br> <br>
DOI: 10.6084/m9.figshare.7528418.v1
title: Carabus uenoi protein BLAST results

description: Results of BLAST search of C.uenoi gene sets against subsets of Refseq protein database (D.melanogaster and T.castaneum subsets).
DOI: 10.6084/m9.figshare.16866961.v3
title: velocity.xlsx

description: Data used in Fig_6
DOI: 10.6084/m9.figshare.10116158.v1
title: Force-sharing within the triceps surae: an Achilles heel in Achilles tendinopathy

description: We compared the distribution of force among the three heads of the triceps surae between 21 participants with Achilles tendinopathy and 21, case-wise paired, asymptomatic controls. <br>Ultrasonography was used to measure muscle volume, fascicle length, pennation angle and subtendon length at rest. Muscle activation was estimated using surface electromyography during maximal and submaximal isometric plantarflexion tasks. The product of normalized activation, physiological cross-sectional area (PCSA), and the cosine of the pennation angle was considered as an index of individual muscle force. Displacement of the distal myotendinous junction of each muscle was measured during the submaximal contractions. <br>All processed data are made available here.<br>
DOI: 10.6084/m9.figshare.25352899.v1
title: Comparison of tools to support healthy young citrus plantings in a region with endemic huanglongbing, <i>C</i>Las, and Asian citrus psyllid (<i>Diaphorina citri</i>)

description: Datasets accompanying the identically titled publication with the following abstract: <br>The Florida citrus industry has been devastated by huanglongbing (HLB), a fatal citrus disease vectored by the Asian citrus psyllid (ACP). Current management relies primarily on insecticides to reduce vector populations. Growers are interested in options for protecting new plantings including individual protective covers (IPCs), reflective mulch ground cover, and red-dyed kaolin particle films. We tested the efficacy of these tools in reducing ACP densities on young citrus trees against a grower standard control. We also quantified the effects of these treatments on other citrus pests, including citrus leafminer, spider mites, and citrus rust mites, as well as on the incidence and severity of plant pathogens, including huanglongbing and its associated pathogen (<i>Candidatus</i> Liberibacter asiaticus), citrus canker, greasy spot, sooty mold, and melanose. Among these treatments, the IPCs successfully excluded ACP, with no covered trees infected with HLB after two years. Trees in this treatment also showed the lowest densities of citrus leafminer infestation and citrus canker incidence. However, trees under IPCs were susceptible to other issues including sooty mold and spider mites, suggesting that there are trade-offs with using this tool. Trees in the reflective mulch and kaolin treatments did not have reduced infestation of key citrus pests and pathogens compared to the grower standard for key citrus pests and pathogens. Although IPCs are not a silver bullet for all citrus ailments, we show that they are a promising tool for protecting young citrus trees from ACP and HLB.
DOI: 10.6084/m9.figshare.11777784.v1
title: Velocity and attenuation of P wave in sands

description: Phase velocity and quality factor of P wave in unconsolidatedToyoura sands and compressed glass beads.
DOI: 10.6084/m9.figshare.11803998.v1
title: condensed_traits_GTDB v1.1.0

description: The condensed_traits.csv dataset is the first data product from the data merger workflow. It include species and strains, and the raw are in their clean, but raw, form.
DOI: 10.6084/m9.figshare.21670880.v1
title: dataset_ncomms_22_25688.xlsx

description: This dataset is obtained for a photonic blind source separation research, which is submitted to Nature Communications (titled "Broadband physical layer cognitive radio with an integrated photonic processor for blind source separation").
DOI: 10.6084/m9.figshare.15261906.v4
title: Supplemental Information S10: Simple muscle twitch LabChart data file

description: LabChart data file of simple muscle twitch experiment. The file can be opened using LabChart reader provided freely by ADInstruments, Australia at: https://www.adinstruments.com/products/labchart-reader.
DOI: 10.6084/m9.figshare.28559276.v1
title: Nepal Living Standard Survey Data -IV

description: This data file contains survey data of Nepal named "Nepal Living Standard Survey Data -IV" and it is in stata format
DOI: 10.6084/m9.figshare.8281730.v1
title: Skeleton analysis 8209 GP 1

description: Skeleton analysis 8209 GP 1 2019 paper
DOI: 10.4121/uuid:1b214a8f-f59c-460f-8eb9-3ef8db5e85ee
title: Dutch adults (DINED - anthropometric database)

description: The most recent version of the DINED-series was based on two sources. The first is the Geron-project 1993-1998 of the TU Delft Ergonomics group (see also the Geron 1998 table), which provides the basic body dimensions. Second source is the Caesar-project from TNO Human Factors Soesterberg, which provides the circumferences. (2004)
DOI: 10.6084/m9.figshare.6609581.v1
title: Supplementary Material for: How Should We Define Postnatal Growth Restriction in Preterm Infants?

description: <b><i>Background:</i></b> Postnatal growth restriction is very common among preterm infants. Growth restriction might be associated with neurodevelopment impairment. The definition of postnatal growth restriction varies among studies. It has often been based on statistical parameters, but we lack biological data to support this definition. <b><i>Objectives:</i></b> The aim here was to study the association between neurodevelopment and postnatal growth restriction defined applying 2 different strategies. <b><i>Methods:</i></b> Bayley Scales of Infant Development-II was performed at 2 years corrected age in 168 preterm infants. Postnatal growth restriction was defined as a weight <i>z</i>-score at 36 weeks z-scores from birth to 36 weeks postmenstrual age). <b><i>Results:</i></b> Weight <i>z</i>-scores fell in almost all patients (98.8%), and 44.1% had <i>z</i>-scores <i></i> After adjusting for gestational age and small for gestational age at birth, every 1-point fall in weight <i>z</i>-score was associated with a 5.6 point (95% CI 1.7 to 9.4) decrease in the Mental Developmental Index. A weight <i>z</i>-score <i>Conclusion:</i> A fall in the weight <i>z</i>-score from birth to 36 weeks is a more rational definition of postnatal growth restriction, and it could predict neurodevelopment.
DOI: 10.6084/m9.figshare.24968958.v2
title: <b>Secondary production and biomass in mussel assemblages relate to species richness and stream size but not life history</b>

description: Increases in species richness with habitat area (species-area relationship, or SAR) and increases in ecosystem function with species richness (biodiversity-ecosystem functioning, or BEF) are among the most widely studied ecological patterns. Incorporating functional trait analysis into assemblage datasets may help clarify interpretations of SAR and BEF relationships in natural ecological systems. For example, life history theory can be used to make predictions about what species are most important in generating ecosystem function given a certain set of environmental conditions. We used a quantitative assemblage data set for freshwater mussels at 9 sites in western Alabama, USA to test for SAR and BEF relationships. At each site we calculated species richness, mussel assemblage density, and two fundamental metrics of ecosystem function: biomass and secondary production. We also tested whether the proportional biomass and production contributions from species belonging to each of three life history strategies—<i>opportunistic strategists</i> adapted to unstable or frequently disturbed habitats, <i>periodic strategists</i> adapted to habitats subject to predictable large-scale disturbances, and <i>equilibrium strategists</i> adapted to stable habitats—varied longitudinally with stream drainage area, a proxy for habitat area. Species richness increased with stream size (SAR), and both biomass and production increased with species richness (BEF) and mussel density. There were few longitudinal changes in the proportional contributions of the different life history strategy classifications that we used, but the invasive clam <i>Corbicula fluminea</i> contributed proportionally more biomass and production at sites that had smaller drainage areas. This study provides further evidence for a clear longitudinal SAR in stream-dwelling taxa. It also suggests apparent BEF relationships for biomass and secondary production in natural assemblages but underscores the importance of assemblage density in BEF studies that use observational field data. Variation in proportional biomass and production contributions by different life history strategies was likely limited by the size of the environmental gradient (stream size) in our study, as contributions were uniformly high for species with life history traits better adapted to stable and productive habitats such as mid-sized to large rivers with low or predictable hydrologic disturbance frequencies. This highlights the need to understand how organisms’ functional traits govern their relationships to the environment at different scales.
DOI: 10.6084/m9.figshare.25106123.v2
title: Oceanic Anoxic Event 2 triggered by Kerguelen Plateau volcanism - datasets

description: Large Igneous Provinces (LIPs) are associated with global warming and carbon cycle perturbations during Oceanic Anoxic Event 2 (OAE2, ~94 Ma) and the Mid-Cenomanian Event (MCE, ~96.5 Ma). However, there is still no consensus on the role volcanism played as a trigger, or its source – previously ascribed to the Caribbean LIP or High Arctic LIP. Here, we use Mentelle Basin sedimentary mercury (Hg) concentrations to determine the timing of volcanism, and neodymium (Nd) and strontium (Sr) isotopes for sedimentary provenance. High Hg concentrations compared to Northern Hemisphere records, and a shift to radiogenic Nd isotopes, indicates Kerguelen volcanic activity and plateau uplift occurred in the lead up to and within OAE2. Whilst we find limited evidence that a volcanic event caused the MCE, pulsed Hg spikes before and during OAE2 imply volcanic emissions were key in driving climate and carbon cycle changes and triggering OAE2.  The data here are from the following paper: Oceanic Anoxic Event 2 triggered by Kerguelen Plateau volcanism