cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25493/z60a-bgy
title: fMRI data of early visual cortex while viewing 24 occluded scenes

description: This dataset is from the 24-scene occlusion project, in which subjects viewed 24 partially occluded scenes. The data consists of 3T fMRI data from 18 subjects recorded at 3 mm isotropic resolution, and anatomical at 1 mm isotropic resolution. These data were compared to behaviorally-collected line drawings of the occluded portions of scenes, which are also included in this data release. Here human fMRI data were recorded while presenting partially occluded visual scenes. Visual occlusion allows to experimentally control sensory input to subregions of visual cortex while internal models continue to influence activity in these regions. Since the observed activity is dependent on internal models, but not on sensory input, there was the opportunity to map visual features conveyed by the brain’s internal models. The results show that activity related to internal models in early visual cortex are more related to scene-specific features than to categorical or depth features. It is further demonstrated that behavioral line drawings provide a good description of internal model structure representing scene-specific features.
DOI: 10.6084/m9.figshare.17197811
title: Lipidomics raw data for KirBac

description: Raw data for the lipidomics analysis of KirBac<br>
DOI: 10.6084/m9.figshare.17197811.v1
title: Lipidomics raw data for KirBac

description: Raw data for the lipidomics analysis of KirBac<br>
DOI: 10.6073/pasta/0c4b4621e89bef54ec8906f5228627b8
title: Density and cover of winter annual plants in three harvester ant habitats at the Jornada Basin LTER site, 1987

description: This dataset contains plant cover and density data collected in three harvester ant (Pogonomyrmex rugosus) nesting habitats at the Jornada Basin LTER site in 1987. The purpose of this investigation was to answer three general questions: 1. How does the modification of soil properties and the ratios of resources (e.g., water-N) by ants alter species assemblages of winter annual plants at the edge of the ant nests? 2. How does the "spring cleaning", clipping, predation or herbivory by ants affect success of the winter annual plants at the edge of ant nests? 3. Are there significant differences in the floristic assemblage and belowground standing crop (root biomass) between the edge of ant nest and the surrounding unaffected soils? Variables included in the dataset include density and cover of all winter annual plants measured at regular intervals between January and May of 1987. Density is expressed as the number of individuals of a species per square meter. The cover of each species was calculated as the area covered by a perpendicular (not vertical) projection of its aerial parts onto the ground surface and expressed in covered area (cm squared) per square meter. This study was completed in 1987.
DOI: 10.6073/pasta/7ccd11a0513cfcb98684ffb4be166842
title: Soil nutrients sampled in and around harvester ant nests in three habitats at the Jornada Basin LTER site, 1987

description: This dataset contains soil nutrient content measurements from harvester ant nests and reference soils in three nesting habitats at the Jornada Basin LTER site in 1987. The purpose of this investigation was to answer three general questions: 1. How does the modification of soil properties and the ratios of resources (e.g., water-N) by ants alter species assemblages of winter annual plants at the edge of the ant nests? 2. How does the "spring cleaning", clipping, predation or herbivory by ants affect success of the winter annual plants at the edge of ant nests? 3. Are there significant differences in the floristic assemblage and belowground standing crop (root biomass) between the edge of ant nest and the surrounding unaffected soils? Five ant nests and paired (non-nest) reference soils were sampled in three study locations. This dataset contains chemical analyses for the soil samples collected for each of the three sites, including total nitrogen, (ammonium, nitrate), inorganic phosphorus, and exchangeable cations (K+, Na+, Ca2+ and Mg2+). Also included is below ground biomass from five ant nests for each of the three sites. This study was completed in 1987.
DOI: 10.5281/zenodo.4562382
title: Fixed Inducing Points Online Bayesian Calibration for Computer Models with an Application to a Scale-Resolving CFD Simulation

description: Abstract This paper proposes a novel fixed inducing points online Bayesian calibration (FIPO-BC) algorithm to efficiently learn the model parameters using a benchmark database. The standard Bayesian calibration (STD-BC) algorithm provides a statistical method to calibrate the parameters of computationally expensive models. However, the STD-BC algorithm does not scale well with regard to the number of data points and also it lacks an online learning capability. The proposed FIPO-BC algorithm greatly improves the computational efficiency of the algorithm and, in addition, enables online calibration to be performed by executing the calibration on a set of predefined inducing points. To demonstrate the procedure of the FIPO-BC algorithm, two tests are performed, finding the optimal value and exploring the posterior distribution of 1) the parameter in a simple function, and 2) the high-wave number damping factor in a scale-resolving turbulence model (scale adaptive simulation shear-stress transport model/SAS-SST). The results (such as the calibrated model parameter and its posterior distribution) of FIPO-BC with different inducing points are compared to those of STD-BC. It is found that FIPO-BC and STD-BC can provide very similar results, once the predefined set of inducing points in FIPO-BC is sufficiently fine. Given that fewer datapoints are needed in the proposed FIPO-BC algorithm, compared to the STD-BC algorithm, it will be a more computational efficient algorithm. In our demonstration test cases, the proposed FIPO-BC algorithm is at least ten times faster than the STD-BC algorithm. Meanwhile, the online feature of the FIPO-BC allows continuous updating of the calibration outputs and potentially reduces the workload on generating the database.
DOI: 10.5281/zenodo.4562381
title: Fixed Inducing Points Online Bayesian Calibration for Computer Models with an Application to a Scale-Resolving CFD Simulation

description: Abstract This paper proposes a novel fixed inducing points online Bayesian calibration (FIPO-BC) algorithm to efficiently learn the model parameters using a benchmark database. The standard Bayesian calibration (STD-BC) algorithm provides a statistical method to calibrate the parameters of computationally expensive models. However, the STD-BC algorithm does not scale well with regard to the number of data points and also it lacks an online learning capability. The proposed FIPO-BC algorithm greatly improves the computational efficiency of the algorithm and, in addition, enables online calibration to be performed by executing the calibration on a set of predefined inducing points. To demonstrate the procedure of the FIPO-BC algorithm, two tests are performed, finding the optimal value and exploring the posterior distribution of 1) the parameter in a simple function, and 2) the high-wave number damping factor in a scale-resolving turbulence model (scale adaptive simulation shear-stress transport model/SAS-SST). The results (such as the calibrated model parameter and its posterior distribution) of FIPO-BC with different inducing points are compared to those of STD-BC. It is found that FIPO-BC and STD-BC can provide very similar results, once the predefined set of inducing points in FIPO-BC is sufficiently fine. Given that fewer datapoints are needed in the proposed FIPO-BC algorithm, compared to the STD-BC algorithm, it will be a more computational efficient algorithm. In our demonstration test cases, the proposed FIPO-BC algorithm is at least ten times faster than the STD-BC algorithm. Meanwhile, the online feature of the FIPO-BC allows continuous updating of the calibration outputs and potentially reduces the workload on generating the database.
DOI: 10.6073/pasta/e2de12a62e48e01a3b1df5c99c41f51e
title: Soil organic matter content sampled in and around harvester ant nests in three habitats at the Jornada Basin LTER site, 1987

description: This dataset contains soil organic matter content measurements from harvester ant nests and reference soils in three nesting habitats at the Jornada Basin LTER site in 1987. The purpose of this investigation was to answer three general questions: 1. How does the modification of soil properties and the ratios of resources (e.g., water-N) by ants alter species assemblages of winter annual plants at the edge of the ant nests? 2. How does the "spring cleaning", clipping, predation or herbivory by ants affect success of the winter annual plants at the edge of ant nests? 3. Are there significant differences in the floristic assemblage and belowground standing crop (root biomass) between the edge of ant nest and the surrounding unaffected soils? Five ant nests and paired (non-nest) reference soils were sampled in three study locations. This dataset contains percent (%) organic matter content measured by mass-loss on combustion in a muffle furnace. This study was completed in 1987.
DOI: 10.6073/pasta/0a74dbd170b464f5f44afadd6b747163
title: Gravimetric soil water content sampled in and around harvester ant nests in three habitats at the Jornada Basin LTER site, 1987

description: This dataset contains gravimetric soil water content measurements from harvester ant nests and reference soils in three nesting habitats at the Jornada Basin LTER site in 1987. The purpose of this investigation was to answer three general questions: 1. How does the modification of soil properties and the ratios of resources (e.g., water-N) by ants alter species assemblages of winter annual plants at the edge of the ant nests? 2. How does the "spring cleaning", clipping, predation or herbivory by ants affect success of the winter annual plants at the edge of ant nests? 3. Are there significant differences in the floristic assemblage and belowground standing crop (root biomass) between the edge of ant nest and the surrounding unaffected soils? Five ant nests and paired (non-nest) reference soils were sampled in three study locations on a monthly schedule from January to May 1987. This dataset contains percent (%) soil water content in these samples determined using the gravimetric method. This study was completed in 1987.
DOI: 10.5281/zenodo.4719614
title: Quantification of the uncertainty within a SAS-SST simulation caused by the unknown high-wavenumber damping factor

description: This paper aims to quantify the uncertainty in the SAS-SST simulation of a prism bluff-body flow due to varying the higher-wavenumber damping factor (). Instead of performing the uncertainty quantification on the CFD simulation directly, a surrogate modelling approach is adopted. The mesh sensitivity is first studied and the numerical error due to the mesh is approximated accordingly. The Gaussian processes/Kriging method is used to generate surrogate models for quantities of interest (QoIs). The suitability of the surrogate models is assessed using the leave-one-out cross-validation tests (LOO-CV). The stochastic tests are then performed using the cross-validated surrogate models to quantify the uncertainty of QoIs by varying Cs. Four prior probability density functions (such as U(0,1), N(0.5, 0.1^2), Beta (2,2) and Beta (5,1.5)) of Cs are considered. It is demonstrated in this study that the uncertainty of a predicted QoI due to varying Cs is regionally dependent. The flow statistics in the near wake of the prism body are subject to larger variance due to the uncertainty in Cs. The influence of Cs rapidly decays as the location moves downstream. The response of different QoIs to the changing Cs varies greatly. Therefore, the calibration of Cs only using observations of one variable may bias the results. Last but not least, it is important to consider different sources of uncertainties within the numerical model when scrutinising a turbulence model, as ignoring the contributions to the total error may lead to biased conclusions.
DOI: 10.5281/zenodo.4719581
title: Quantification of the uncertainty within a SAS-SST simulation caused by the unknown high-wavenumber damping factor

description: This paper aims to quantify the uncertainty in the SAS-SST simulation of a prism bluff-body flow due to varying the higher-wavenumber damping factor (). Instead of performing the uncertainty quantification on the CFD simulation directly, a surrogate modelling approach is adopted. The mesh sensitivity is first studied and the numerical error due to the mesh is approximated accordingly. The Gaussian processes/Kriging method is used to generate surrogate models for quantities of interest (QoIs). The suitability of the surrogate models is assessed using the leave-one-out cross-validation tests (LOO-CV). The stochastic tests are then performed using the cross-validated surrogate models to quantify the uncertainty of QoIs by varying Cs. Four prior probability density functions (such as U(0,1), N(0.5, 0.1^2), Beta (2,2) and Beta (5,1.5)) of Cs are considered. It is demonstrated in this study that the uncertainty of a predicted QoI due to varying Cs is regionally dependent. The flow statistics in the near wake of the prism body are subject to larger variance due to the uncertainty in Cs. The influence of Cs rapidly decays as the location moves downstream. The response of different QoIs to the changing Cs varies greatly. Therefore, the calibration of Cs only using observations of one variable may bias the results. Last but not least, it is important to consider different sources of uncertainties within the numerical model when scrutinising a turbulence model, as ignoring the contributions to the total error may lead to biased conclusions.
DOI: 10.6073/pasta/66c32b5cad9bb29e23658635bfed35f7
title: Plant community responses to removal of functional groups and species along vegetation transects at the Jornada Basin LTER site, 1997-2002

description: This data package contains vegetative cover data of plots that have had various plant functional groups or species experimentally removed at the Jornada Basin LTER site in southern New Mexico, USA. This data was collected in an effort to distinguish the differential effects of plant community biomass, plant community functional groups, and biodiversity within functional groups on plant community function. To make these distinctions, treatments were established by the selective removal of plant species or functional groups within experimental plots. There are eight treatments: control (C, no removals); four functional group removal treatments (PG, perennial grass removed; S, shrubs removed; SSh, subshrubs removed; Succ, succulents removed), and three species richness manipulation treatments. Richness manipulations included a simplified treatment (Simp), where only the single most abundant species of each growth form is preserved and all other species in the growth form are removed, a reduced‐Larrea treatment (rL), where the Larrea is assumed to be the dominant and is removed while minority components remain, and a reduced-Prosopsis treatment (rP), where Prosopis rather than Larrea is removed as the shrub dominant. Following treatments, vegetative data was collected by sampling each plot along three transects twice a year (Spring and Fall) for 5 years from 1997-2002 (no data collected in 1998). This data set consists of the date of collection, plot number, treatment type, transect number, quadrat number, species codes, two diameters, height, condition, count, record IDs, and error codes. This study is complete.
DOI: 10.6073/pasta/9ce9a7139153fa22636bdfef63c4cdb8
title: The effects of changing vegetative composition on the abundance, species diversity and activity of birds at the Jornada Basin LTER site, 1997

description: This data package contains bird abundance data collected in plots that have had various plant functional groups or species experimentally removed at the Jornada Basin LTER site in southern New Mexico, USA. This data was collected in an effort to distinguish the differential effects of plant community biomass, plant community functional groups, and biodiversity within functional groups on plant community function, including effects on animals. To make these distinctions, treatments were established by the selective removal of plant species or functional groups within experimental plots. There are eight treatments: control (C, no removals); four functional group removal treatments (PG, perennial grass removed; S, shrubs removed; SSh, subshrubs removed; Succ, succulents removed), and three species richness manipulation treatments. Richness manipulations included a simplified treatment (Simp), where only the single most abundant species of each growth form is preserved and all other species in the growth form are removed, a reduced‐Larrea treatment (rL), where the Larrea is assumed to be the dominant and is removed while minority components remain, and a reduced-Prosopsis treatment (rP), where Prosopis rather than Larrea is removed as the shrub dominant. Following treatments, bird abundance and habitat preference data was collected in 1997. This data set consists of plot number, treatment type, and time of bird presence by taxa and by habitat and behavior. This study is complete.
DOI: 10.5281/zenodo.5717329
title: Data for: Reconfigurable asymmetric protein assemblies through implicit negative design

description: Supplementary Information for <strong>Reconfigurable asymmetric protein assemblies through implicit negative design: </strong>design scripts, design models and sequence information Authors:<strong> Danny D. Sahtoe*, Florian Praetorius*, </strong>Alexis Courbet, Yang Hsia, Basile I.M. Wicky, Natasha I. Edman, Lauren M. Miller, Bart J. R. Timmermans, Justin Decarreau, Hana M. Morris, Alex Kang, Asim K. Bera, David Baker <strong>* These authors contributed equally</strong> Correspondence to: dabaker@uw.edu
DOI: 10.5281/zenodo.5781391
title: Data and output files for the paper, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome"

description: The above files contain the output of the model, which we call MDSINE2, developed in the paper titled, "<em>Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome</em>" (See https://github.com/gerberlab/MDSINE2_Paper for implementation details). More specifically, forward_sims.tgz contains the output of forward simulations in .npy format; mixed_prior_fixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for fixed topology; mixed_prior_unfixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for unfixed topology; other_files contains information on eigenvalues and cycles, results for Phylogenetic Neighborhood Analysis, Keystoneness Analysis and the output in .npy format for comparator methods; ASV_OTU_aggregate_and_plylogeneteic trees contains the plots of trajectories (relative abundance) of OTUS and their constituent ASVs, and of phylogenetic trees.
description: The files can be used to produce the figures in the paper without having to run the full model.
DOI: 10.5281/zenodo.5717328
title: Data for: Reconfigurable asymmetric protein assemblies through implicit negative design

description: Supplementary Information for <strong>Reconfigurable asymmetric protein assemblies through implicit negative design: </strong>design scripts, design models and sequence information Authors:<strong> Danny D. Sahtoe*, Florian Praetorius*, </strong>Alexis Courbet, Yang Hsia, Basile I.M. Wicky, Natasha I. Edman, Lauren M. Miller, Bart J. R. Timmermans, Justin Decarreau, Hana M. Morris, Alex Kang, Asim K. Bera, David Baker <strong>* These authors contributed equally</strong> Correspondence to: dabaker@uw.edu
DOI: 10.5517/ccdc.csd.cc1pjq20
title: CCDC 1565192: Experimental Crystal Structure Determination

description: Related Article: Zeki Kartal, Onur Şahin|2021|J.Mol.Struct.|1252|132088|doi:10.1016/j.molstruc.2021.132088
DOI: 10.5517/ccdc.csd.cc28m3lm
title: CCDC 2103740: Experimental Crystal Structure Determination

description: Related Article: Alexander Schmer, Dhanushi Welideniya, Tatjana Terschüren, Gregor Schnakenburg, Jörg Daniels, Antonio Bauza, Antonio Frontera, Rainer Streubel|2021|Dalton Trans.|50|17892|doi:10.1039/D1DT03350F
DOI: 10.5517/ccdc.csd.cc2556cy
title: CCDC 2000999: Experimental Crystal Structure Determination

description: Related Article: Alexander Schmer, Dhanushi Welideniya, Tatjana Terschüren, Gregor Schnakenburg, Jörg Daniels, Antonio Bauza, Antonio Frontera, Rainer Streubel|2021|Dalton Trans.|50|17892|doi:10.1039/D1DT03350F
DOI: 10.21223/fm3imx/ullydp
title: 01_meta_raw_data.tab

description: :unav
DOI: 10.21223/fm3imx/t321sv
title: 05_TripleS - SPIA Pilot - Mozambique - English - June 27 2021 Clean.pdf

description: :unav
DOI: 10.21223/fm3imx/uo2m6u
title: 02_meta_raw_data_stata.tab

description: :unav
DOI: 10.21223/fm3imx/3tyi3h
title: 03_tripleS_pilot_questionnaire.xlsx

description: :unav
DOI: 10.21223/fm3imx/1dhpc3
title: 04_TripleS - SPIA Pilot - Mozambique - English - June 27 2021 Clean Translated into Portuguese2981 NA.docx

description: :unav
DOI: 10.5281/zenodo.5781790
title: Inferring size-based functional responses from the physical properties of the medium

description: Databases used to test the model described in the article "Inferring size-based functional responses from the physical properties of the medium", Frontiers in Ecology and Evolution. Please read the "Readme.pdf" file for detailed information. This file explains all the variables and provides full references for the data in each of the datasets. "Portalier_et_al_2021_Species_Speeds.csv" provides species speeds according to body size for numerous species in aquatic systems. "Portalier_et_al_2021_Predator_Prey_Interactions.csv" provides attack rates, capture probabilities and handling times for numerous predator-prey interactions in aquatic systems.
description: Matlab code used to run the model deposited in the Zenodo Repository: 10.5281/zenodo.5781805.
DOI: 10.5281/zenodo.5781789
title: Inferring size-based functional responses from the physical properties of the medium

description: Databases used to test the model described in the article "Inferring size-based functional responses from the physical properties of the medium", Frontiers in Ecology and Evolution. Please read the "Readme.pdf" file for detailed information. This file explains all the variables and provides full references for the data in each of the datasets. "Portalier_et_al_2021_Species_Speeds.csv" provides species speeds according to body size for numerous species in aquatic systems. "Portalier_et_al_2021_Predator_Prey_Interactions.csv" provides attack rates, capture probabilities and handling times for numerous predator-prey interactions in aquatic systems.
description: Matlab code used to run the model deposited in the Zenodo Repository: 10.5281/zenodo.5781805.
DOI: 10.5519/qd.8fv6wcxn
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4991086 records)
DOI: 10.5281/zenodo.5781816
title: INICIB- URP. DATASET GASTRIC CANCER HOSPITAL MARIA AUXILIADORA, LIMA , PERU , 2018-2020

description: DATASET GASTRIC CANCER HOSPITAL MARIA AUXILIADORA, LIMA , PERU , 2018-2020
DOI: 10.5281/zenodo.5781815
title: INICIB- URP. DATASET GASTRIC CANCER HOSPITAL MARIA AUXILIADORA, LIMA , PERU , 2018-2020

description: DATASET GASTRIC CANCER HOSPITAL MARIA AUXILIADORA, LIMA , PERU , 2018-2020
DOI: 10.6084/m9.figshare.17197925
title: Lung myeloid cell interferon response correlates with clearance of SARS-CoV-2

description: This is the dataset for representative confocal figures in this article.
DOI: 10.6084/m9.figshare.17197925.v1
title: Lung myeloid cell interferon response correlates with clearance of SARS-CoV-2

description: This is the dataset for representative confocal figures in this article.