cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9922727
title: Dataset for: Population-specific modelling of between/within-subject flow variability in the carotid arteries of the elderly

description: Computational fluid dynamics models are increasingly proposed for assisting the diagnosis and management of vascular diseases. Ideally, patient-specific flow measurements are used to impose flow boundary conditions. When patient specific flow measurements are unavailable, mean values of flow measurements across small cohorts are used as normative values. In reality, both the between-subjects and within-subject flow variabilities are large. Consequently, neither one-shot flow measurements nor mean values across a cohort are truly indicative of the flow regime in a given person. We develop models for both the between-subjects and within-subject variability of internal carotid flow. A log-linear mixed effects model is combined with a Gaussian process to model the between-subjects flow variability, while a lumped parameter model of cerebral autoregulation is used to model the within-subject flow variability in response to heart rate and blood pressure changes. The model parameters are identified from carotid ultrasound measurements in a cohort of 103 elderly volunteers. We use the models to study intracranial aneurysm flow in 54 subjects under rest and exercise and conclude that OSI, a common wall shear stress -derived quantity in vascular CFD studies, may be too sensitive to flow fluctuations to be a reliable biomarker.
DOI: 10.6084/m9.figshare.9922754.v1
title: Data deposition for "Historical change of El Niño properties shed light on future changes of extreme El Niño"

description: SSTA composite: SSTA_4type_copmposite.ncU1000 composite: U1000_4type_copmposite.ncH20 composite: H20_4type_copmposite.ncU1000(NCEP) and SSTA trend(running mean):background_runningmean.ncheat budget analysis:TempA_monthly.nc;TempA_monthly.nc;WA_monthly.ncCMIP5 data for eight models:CMIP5_SBW_data.xlsxdecadal change of ocean temperature:decadalchange_oceantemp.ncRelatinship betwen the mean-state zonal SSTA gradient and WP SSTA During El Nino onset:the mean-state zonal SSTA gradient.xlsx
DOI: 10.1184/r1/9922697
title: CESAW Project Data Fact sheets

description: This is data from projects within the scope of the CESAW research project. The data contains detailed logs of software project development at the task level. All project effort, defects, and size have been recorded for each individual task performed. There are 35 projects within this data set. <br> The project objective was to measure the cost and benefits of applying Static analysis to development.
DOI: 10.6084/m9.figshare.9922709
title: Dataset for: A finite element approach for gastrointestinal tissue mechanics

description: The biomechanical properties of gastrointestinal (GI) tissue play a significant role in the normal functioning of the organ. GI soft tissues exhibit a highly nonlinear rate- and time-dependent stress-strain behaviour. In recent years, many constitutive relations have been proposed to characterise these properties. However, a constitutive relation is not sufficient to analyse the biomechanics at the organ level with complex loading and boundary conditions. Hence, for a refined mechanical analysis, a finite element (FE) implementation of the constitutive relation is needed. Here, we propose a FE implementation of a finite nonlinear hyper-viscoelastic model suitable for soft biological tissues. The FE model has been validated at first by comparing its results with the analytical solutions of a standard linear solid, and then it has been used to recreate experimental observations performed on tissue strips obtained from different animals. We have also proposed a method, in this work, to construct a residually stressed FE model so that the consequences of residual stresses on GI mechanics can be examined. Our FE formulation was able to capture the nonlinear soft tissue properties and also demonstrated that the addition of residual stresses reduces stress concentrations as well as the stress gradient in the GI wall.
DOI: 10.6084/m9.figshare.9922727.v1
title: Dataset for: Population-specific modelling of between/within-subject flow variability in the carotid arteries of the elderly

description: Computational fluid dynamics models are increasingly proposed for assisting the diagnosis and management of vascular diseases. Ideally, patient-specific flow measurements are used to impose flow boundary conditions. When patient specific flow measurements are unavailable, mean values of flow measurements across small cohorts are used as normative values. In reality, both the between-subjects and within-subject flow variabilities are large. Consequently, neither one-shot flow measurements nor mean values across a cohort are truly indicative of the flow regime in a given person. We develop models for both the between-subjects and within-subject variability of internal carotid flow. A log-linear mixed effects model is combined with a Gaussian process to model the between-subjects flow variability, while a lumped parameter model of cerebral autoregulation is used to model the within-subject flow variability in response to heart rate and blood pressure changes. The model parameters are identified from carotid ultrasound measurements in a cohort of 103 elderly volunteers. We use the models to study intracranial aneurysm flow in 54 subjects under rest and exercise and conclude that OSI, a common wall shear stress -derived quantity in vascular CFD studies, may be too sensitive to flow fluctuations to be a reliable biomarker.
DOI: 10.1184/r1/9922697.v1
title: CESAW Project Data Fact sheets

description: This is data from projects within the scope of the CESAW research project. The data contains detailed logs of software project development at the task level. All project effort, defects, and size have been recorded for each individual task performed. There are 35 projects within this data set. <br> The project objective was to measure the cost and benefits of applying Static analysis to development.
DOI: 10.6084/m9.figshare.9922709.v1
title: Dataset for: A finite element approach for gastrointestinal tissue mechanics

description: The biomechanical properties of gastrointestinal (GI) tissue play a significant role in the normal functioning of the organ. GI soft tissues exhibit a highly nonlinear rate- and time-dependent stress-strain behaviour. In recent years, many constitutive relations have been proposed to characterise these properties. However, a constitutive relation is not sufficient to analyse the biomechanics at the organ level with complex loading and boundary conditions. Hence, for a refined mechanical analysis, a finite element (FE) implementation of the constitutive relation is needed. Here, we propose a FE implementation of a finite nonlinear hyper-viscoelastic model suitable for soft biological tissues. The FE model has been validated at first by comparing its results with the analytical solutions of a standard linear solid, and then it has been used to recreate experimental observations performed on tissue strips obtained from different animals. We have also proposed a method, in this work, to construct a residually stressed FE model so that the consequences of residual stresses on GI mechanics can be examined. Our FE formulation was able to capture the nonlinear soft tissue properties and also demonstrated that the addition of residual stresses reduces stress concentrations as well as the stress gradient in the GI wall.
DOI: 10.6084/m9.figshare.9922577
title: Dataset for: The Spatially-Conscious Machine Learning Model

description: Successfully predicting gentrification could have many social and commercial applications; however, real estate sales are difficult to predict because they belong to a chaotic system comprised of intrinsic and extrinsic characteristics, perceived value, and market speculation. Using New York City real estate as our subject, we combine modern techniques of data science and machine learning with traditional spatial analysis to create robust real estate prediction models for both classification and regression tasks. We compare several cutting edge machine learning algorithms across spatial, semi-spatial and non-spatial feature engineering techniques, and we empirically show that spatially-conscious machine learning models outperform non-spatial models when married with advanced prediction techniques such as random forests, generalized linear models, gradient boosting machines, and artificial neural networks.
DOI: 10.6084/m9.figshare.9922538
title: Current Lophotrochozoan Genomes

description: Current list of published lophotrochozoan genomes.
DOI: 10.6084/m9.figshare.9922478
title: The Geometry of Masking

description: Code and sample code for "The Geometry of Coding in Neural Populations"
DOI: 10.6084/m9.figshare.9922577.v1
title: Dataset for: The Spatially-Conscious Machine Learning Model

description: Successfully predicting gentrification could have many social and commercial applications; however, real estate sales are difficult to predict because they belong to a chaotic system comprised of intrinsic and extrinsic characteristics, perceived value, and market speculation. Using New York City real estate as our subject, we combine modern techniques of data science and machine learning with traditional spatial analysis to create robust real estate prediction models for both classification and regression tasks. We compare several cutting edge machine learning algorithms across spatial, semi-spatial and non-spatial feature engineering techniques, and we empirically show that spatially-conscious machine learning models outperform non-spatial models when married with advanced prediction techniques such as random forests, generalized linear models, gradient boosting machines, and artificial neural networks.
DOI: 10.6084/m9.figshare.9922478.v1
title: The Geometry of Masking

description: Code and sample code for "The Geometry of Coding in Neural Populations"
DOI: 10.6084/m9.figshare.9922304
title: Supplementary material.pdf

description: Raw data
DOI: 10.6084/m9.figshare.9922283
title: Cumulative human impact estimated for 33 species

description: This data set contains GIS maps of cumulative human impacts of 35 species including two data-deficient species.
DOI: 10.6084/m9.figshare.9922292
title: Supplementary data: Microglial cell-derived interleukin-6 influences behavior and inflammatory response in the brain following traumatic brain injury

description: Supplementary data for the article: <b>Microglia-derived IL-6 influences behavior and inflammatory response in the brain following traumatic brain injury</b><br><br>We include the high quality PDF for Figure 4, Figure S1 and S2, the supplementary table S1 (Microarray analysis table including the list of all analyzed genes [and separated for the 5 sections described in the manuscript], expression values, fold change and statistical significance) and S2 (Gene ontology enrichment analysis data).<br>
DOI: 10.6084/m9.figshare.9922304.v1
title: Supplementary material.pdf

description: Raw data
DOI: 10.6084/m9.figshare.9922274
title: Mobile_and_Stationary_Anemometer_Wind-SoutheasternSK_May2017_v2.csv

description: A .csv file containing mobile and stationary anemometer measurements sampled along a square route with 12.8 km perimeter in Southeastern Saskatchewan, Canada. Mobile anemometer measurements of wind speed and wind direction were sampled at 1 Hz on public roads using a RM Young 86004 ultrasonic anemometer mounted on a 1.2 m tall mast above the cap of a 2016 Toyota Tacoma. The anemometer was positioned 0.5 m from the longitudinal axis of the truck on the driver’s side, and 0.3 m behind the start of the truck’s cap. Stationary anemometer measurements were collected using Decagon Device DS-2 sonic anemometers mounted at a height of 3 m above the ground. Measurements of time, wind speed, maximum gust, and direction were recorded with a Decagon Device Em50 datalogger in one minute intervals at the same time the mobile anemometer measurements were sampled. The GPS Coordinates of the Stationary Anemometers are Station 1 : N 49°26.678 W 103°49.350; Station 2: N 49°27.881 W 103°49.040; Station 3: N 49°27.762 W 103°46.664; Station 4: N 49°26.122 W 103°46.890. All sample times have been converted to Central Standard Time (CST). Wind speed and wind gust measurements are in km/h, and wind direction measurements are in degrees. This dataset is the same as Mobile_and_Stationary_Anemometer_Wind-SoutheasternSK_May2017 with specified units.
DOI: 10.6084/m9.figshare.9922283.v1
title: Cumulative human impact estimated for 33 species

description: This data set contains GIS maps of cumulative human impacts of 35 species including two data-deficient species.
DOI: 10.6084/m9.figshare.9922247
title: Database.xlsx

description: Dataset of papers about beta lactam resistance in Latin America from 2014 to Febraury 2019<br>
DOI: 10.6084/m9.figshare.9922247.v1
title: Database.xlsx

description: Dataset of papers about beta lactam resistance in Latin America from 2014 to Febraury 2019<br>
DOI: 10.6084/m9.figshare.9920234
title: Altitude and its inverse association with abdominal obesity in an Andean country

description: This is the dataset for the study entitle: "Altitude and its inverse association with abdominal obesity in an Andean country" sent for publication to the journal F1000Research
DOI: 10.6084/m9.figshare.9920111
title: Subject-specific whole-brain decoding accuracy maps (normalized and smoothed)

description: Whole-brain decoding accuracy map of each participant. The value at each voxel displays how well choice can be predicted from the local activity pattern surrounded that voxel. <br>
DOI: 10.6084/m9.figshare.9920135
title: Code and data supplement from Inferring the dynamics of rising radical right-wing party support using Gaussian processes

description: Python code and data files necessary to reproduce the results in this paper. Please see read_me.txt for further details.
DOI: 10.6084/m9.figshare.9920135.v1
title: Code and data supplement from Inferring the dynamics of rising radical right-wing party support using Gaussian processes

description: Python code and data files necessary to reproduce the results in this paper. Please see read_me.txt for further details.
DOI: 10.6084/m9.figshare.9920084
title: Data

description: Dataset
DOI: 10.6084/m9.figshare.9920111.v2
title: Subject-specific whole-brain decoding accuracy maps (normalized and smoothed)

description: Whole-brain decoding accuracy map of each participant. The value at each voxel displays how well choice can be predicted from the local activity pattern surrounded that voxel. <br>
DOI: 10.6084/m9.figshare.9920084.v1
title: Data

description: Dataset
DOI: 10.6084/m9.figshare.9920111.v1
title: Main analysis: subject-specific whole-brain decoding accuracy maps (normalized and smoothed)

description: Whole-brain decodind accuracy map of each participant. The value at each voxel displays how well choice can be predicted from the local activity pattern surrounded that voxel. <br>
DOI: 10.6084/m9.figshare.9919994
title: DYNACROSS_190927.zip.007

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 7.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9920033
title: EnergyFluxes_JGR_2019.xlsx

description: A Bowen ratio was established in a horizontal flow wetland (seasonally frozen) and energy and water fluxes data were collected from July 2013 to April 2019 in Jiuzhaigou, a subalpine river valley that located in the transition zone between the Tibetan Plateau and the Sichuan Basin<b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.9919994.v1
title: DYNACROSS_190927.zip.007

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 7.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9920033.v1
title: EnergyFluxes_JGR_2019.xlsx

description: A Bowen ratio was established in a horizontal flow wetland (seasonally frozen) and energy and water fluxes data were collected from July 2013 to April 2019 in Jiuzhaigou, a subalpine river valley that located in the transition zone between the Tibetan Plateau and the Sichuan Basin<b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.9919985
title: DYNACROSS_190927.zip.005

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 5.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9919988
title: DYNACROSS_190927.zip.006

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 6.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9919943
title: DYNACROSS_190927.zip.004

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 4.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9919988.v1
title: DYNACROSS_190927.zip.006

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 6.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9919928
title: Terminal digit preference: a source of measurement error in breast cancer diameter reporting

description: <b>Objectives:</b> Women diagnosed with breast cancer are offered treatment and therapy based on tumor characteristics, including tumor diameter. There is scarce knowledge whether tumor diameter is accurately reported, or whether it is unconsciously rounded to the nearest half-centimeter (terminal digit preference). This study aimed to assess the precision (number of digits) of breast cancer tumor diameters and whether they are affected by terminal digit preference. Furthermore, we aimed to assess the agreement between mammographic and histopathologic tumor diameter measurements. <b>Material and Methods:</b> This national registry study included reported mammographic and registered histopathologic tumor diameter information from the Cancer Registry of Norway for invasive breast cancers diagnosed during 2012–2016. Terminal digit preference was assessed using histograms. Agreement between mammographic and histopathologic measurements was assessed using the intraclass correlation coefficient (ICC) and Bland-Altman plots. <b>Results:</b> Mammographic, histopathologic, or both tumor measurements were available for 7792, 13,541 and 6865 cases, respectively. All mammographic and 97.2% of histopathologic tumor diameters were recorded using whole mm. Terminal digits of zero or five were observed among 38.7% and 34.8% of mammographic and histopathologic measurements, respectively. There was moderate agreement between the two measurement methods (ICC = 0.52, 95% CI: 0.50–0.53). On average, mammographic measurements were 1.26 mm larger (95% limits of agreement: −22.29–24.73) than histopathologic measurements. This difference increased with increasing tumor size. <b>Conclusion:</b> Terminal digit preference was evident among breast cancer tumor diameters in this nationwide study. Further studies are needed to investigate the potential extent of under-staging and under-treatment resulting from this measurement error.
DOI: 10.6084/m9.figshare.9919943.v1
title: DYNACROSS_190927.zip.004

description: Cleaned up docking Benchmark 5 starting structures (plus CAPRI target T131) and SwarmDock docking results, in PDB format, altogether with CAPRI assessment values (IRMSD, LRMSD, FNAT, FNONNAT, quality). Zip part 4.<br>Reference:M. Torchala, T. Gerguri, R.R.A. Chaleil, P. Gordon, F. Russell, M. Keshani, P.A. Bates, 'Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock', Proteins: Structure, Function, and Bioinformatics (2019).
DOI: 10.6084/m9.figshare.9919928.v1
title: Terminal digit preference: a source of measurement error in breast cancer diameter reporting

description: <b>Objectives:</b> Women diagnosed with breast cancer are offered treatment and therapy based on tumor characteristics, including tumor diameter. There is scarce knowledge whether tumor diameter is accurately reported, or whether it is unconsciously rounded to the nearest half-centimeter (terminal digit preference). This study aimed to assess the precision (number of digits) of breast cancer tumor diameters and whether they are affected by terminal digit preference. Furthermore, we aimed to assess the agreement between mammographic and histopathologic tumor diameter measurements. <b>Material and Methods:</b> This national registry study included reported mammographic and registered histopathologic tumor diameter information from the Cancer Registry of Norway for invasive breast cancers diagnosed during 2012–2016. Terminal digit preference was assessed using histograms. Agreement between mammographic and histopathologic measurements was assessed using the intraclass correlation coefficient (ICC) and Bland-Altman plots. <b>Results:</b> Mammographic, histopathologic, or both tumor measurements were available for 7792, 13,541 and 6865 cases, respectively. All mammographic and 97.2% of histopathologic tumor diameters were recorded using whole mm. Terminal digits of zero or five were observed among 38.7% and 34.8% of mammographic and histopathologic measurements, respectively. There was moderate agreement between the two measurement methods (ICC = 0.52, 95% CI: 0.50–0.53). On average, mammographic measurements were 1.26 mm larger (95% limits of agreement: −22.29–24.73) than histopathologic measurements. This difference increased with increasing tumor size. <b>Conclusion:</b> Terminal digit preference was evident among breast cancer tumor diameters in this nationwide study. Further studies are needed to investigate the potential extent of under-staging and under-treatment resulting from this measurement error.