cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3709900
title: Chameleon KVM cloud traces (2020-09-04)

description: This cloud trace contains Nova compute events for the OpenStack KVM cloud on the Chameleon testbed since it was built in 2015. Several text fields have been anonymized to hide user information. This is the last set of traces for the KVM cloud built in 2015 in a file "chameleon_legacy_kvm_tacc_2020_02_03.zip". Chameleon deprecated the legacy KVM site in February 2020 and future versions of this deposition will not include this historical trace data. This trace contains data from 2015-09-17T15:37:05.000Z until 2020-02-03T06:23:40.000Z. The epoch time for timestamps is 2015-09-06T00:00:00. It follows version 0.3 of the cloud trace format. You can find more information and trace datasets at Science Clouds.
description: Please contact the data owner for using this data for any research purpose prior to release and acknowledge the source of the data in any published material based on it.
description: {"references": ["Keahey, Kate, et al. \"Chameleon: a scalable production testbed for computer science research.\" Contemporary High Performance Computing. CRC Press, 2019. 123-148."]}
DOI: 10.6084/m9.figshare.1434045.v1
title: Villin folding contact maps

description: Training and test sets ~1M, 595-element binary valued contact maps for Villin folding trajectories Produced for C-alpha contacts below 8AA. ASCII-encoded, one line per contact map.
DOI: 10.6084/m9.figshare.1434041
title: Discerning enhanced dislocation plasticity in hydrogen-charged <i>α</i>-iron nano-crystals

description: Novel atomistic simulations of <i>α</i>-iron nano-crystals starting with pre-existing dislocation networks have been performed to identify the effect of high hydrogen concentrations on enhanced dislocation plasticity. Hydrogen is shown to decrease the dislocations free-surface nucleation stress, as well as increase the flow strength of crystals. The dislocation density is observed to increase in the presence of hydrogen due to dislocation pinning and enhanced dislocation self-multiplications. Hydrogen also changes the deformation morphology from discrete slip planes in hydrogen-free crystals to a homogeneous deformation in H-charged crystals due to the enhanced dislocations self-multiplication.
DOI: 10.6084/m9.figshare.1434037
title: CAESAR_ConditionSeverity_Public_wSNOMED.xlsx

description: We present a method for classifying severity at the phenotype-level that uses the Systemized Nomenclature of Medicine – Clinical Terms. Our method is called the Classification Approach for Extracting Severity Automatically from Electronic Health Records (CAESAR). CAESAR combines multiple severity measures – number of comorbidities, medications, procedures, cost and treatment time, and a proportional index term. Using a random forest algorithm and these severity measures as input, CAESAR differentiates between severe and mild phenotypes (sensitivity = 91.67, specificity = 77.78) when compared to a manually evaluated gold standard (k=0.716). CAESAR enables researchers to measure phenotype severity from EHRs to identify phenotypes that are important for comparative effectiveness research.
DOI: 10.6084/m9.figshare.1434040
title: Elevational distribution and species diversity of freshwater Ostracoda (Crustacea) in Çankırı region (Turkey)

description: We investigated how the richness and ecological characteristics of non-marine ostracod species varied across nine 100-m elevation bands (from 549 to 1457 m) in the Çankırı region. We collected a total of 37 taxa (25 living and 12 sub-recent) from 114 of 130 aquatic sites sampled during September of 2011; 34 of the taxa were new records for the region. Eight widely distributed ‘cosmopolitan’ species (<i>Candona neglecta</i>, <i>Cypridopsis vidua</i>, <i>Heterocypris incongruens</i>, <i>Ilyocypris bradyi</i>, <i>Limnocythere inopinata</i>, <i>Potamocypris villosa</i>, <i>Prionocypris zenkeri</i>, and <i>Psychrodromus olivaceus</i>) were found more frequently than other species. The first two axes of canonical correspondence analyses (CCA) explained 73.2% of the correlation between 11 species and 5 environmental variables. Of which, electrical conductivity (<i>F</i> = 3.99, <i>p</i> = 0.028) and altitude (<i>F</i> = 2.69, <i>p</i> = 0.004) were the most explanatory (<i>p</i> &lt; 0.05) variables for species. Optimum altitude and water temperature values of the cosmopolitan species were relatively higher than the other species. Significant regression models (<i>p</i> &lt; 0.01, <i>r</i><sup>2</sup> = 0.81) indicate that the frequency of occurrence was affected by changes in numbers of samplings sites from 549 to 1457 m. When highest numbers of species (15 spp.) were found at the range of 1231–1332 m, numbers of asexual species (10 spp.) were twice of the sexual species (5 spp.) with no statistical difference between numbers of swimming (7 spp.) and non-swimming (8 spp.) species. Results were discussed based on the ecological conditions that individual species prefer.
DOI: 10.6084/m9.figshare.1434040.v1
title: Elevational distribution and species diversity of freshwater Ostracoda (Crustacea) in Çankırı region (Turkey)

description: We investigated how the richness and ecological characteristics of non-marine ostracod species varied across nine 100-m elevation bands (from 549 to 1457 m) in the Çankırı region. We collected a total of 37 taxa (25 living and 12 sub-recent) from 114 of 130 aquatic sites sampled during September of 2011; 34 of the taxa were new records for the region. Eight widely distributed ‘cosmopolitan’ species (<i>Candona neglecta</i>, <i>Cypridopsis vidua</i>, <i>Heterocypris incongruens</i>, <i>Ilyocypris bradyi</i>, <i>Limnocythere inopinata</i>, <i>Potamocypris villosa</i>, <i>Prionocypris zenkeri</i>, and <i>Psychrodromus olivaceus</i>) were found more frequently than other species. The first two axes of canonical correspondence analyses (CCA) explained 73.2% of the correlation between 11 species and 5 environmental variables. Of which, electrical conductivity (<i>F</i> = 3.99, <i>p</i> = 0.028) and altitude (<i>F</i> = 2.69, <i>p</i> = 0.004) were the most explanatory (<i>p</i> &lt; 0.05) variables for species. Optimum altitude and water temperature values of the cosmopolitan species were relatively higher than the other species. Significant regression models (<i>p</i> &lt; 0.01, <i>r</i><sup>2</sup> = 0.81) indicate that the frequency of occurrence was affected by changes in numbers of samplings sites from 549 to 1457 m. When highest numbers of species (15 spp.) were found at the range of 1231–1332 m, numbers of asexual species (10 spp.) were twice of the sexual species (5 spp.) with no statistical difference between numbers of swimming (7 spp.) and non-swimming (8 spp.) species. Results were discussed based on the ecological conditions that individual species prefer.
DOI: 10.6084/m9.figshare.1434041.v2
title: Discerning enhanced dislocation plasticity in hydrogen-charged <i>α</i>-iron nano-crystals

description: Novel atomistic simulations of <i>α</i>-iron nano-crystals starting with pre-existing dislocation networks have been performed to identify the effect of high hydrogen concentrations on enhanced dislocation plasticity. Hydrogen is shown to decrease the dislocations free-surface nucleation stress, as well as increase the flow strength of crystals. The dislocation density is observed to increase in the presence of hydrogen due to dislocation pinning and enhanced dislocation self-multiplications. Hydrogen also changes the deformation morphology from discrete slip planes in hydrogen-free crystals to a homogeneous deformation in H-charged crystals due to the enhanced dislocations self-multiplication.
DOI: 10.6084/m9.figshare.1434037.v1
title: CAESAR_ConditionSeverity_Public_wSNOMED.xlsx

description: We present a method for classifying severity at the phenotype-level that uses the Systemized Nomenclature of Medicine – Clinical Terms. Our method is called the Classification Approach for Extracting Severity Automatically from Electronic Health Records (CAESAR). CAESAR combines multiple severity measures – number of comorbidities, medications, procedures, cost and treatment time, and a proportional index term. Using a random forest algorithm and these severity measures as input, CAESAR differentiates between severe and mild phenotypes (sensitivity = 91.67, specificity = 77.78) when compared to a manually evaluated gold standard (k=0.716). CAESAR enables researchers to measure phenotype severity from EHRs to identify phenotypes that are important for comparative effectiveness research.
DOI: 10.6084/m9.figshare.1434041.v1
title: Discerning enhanced dislocation plasticity in hydrogen-charged <i>α</i>-iron nano-crystals

description: Novel atomistic simulations of <i>α</i>-iron nano-crystals starting with pre-existing dislocation networks have been performed to identify the effect of high hydrogen concentrations on enhanced dislocation plasticity. Hydrogen is shown to decrease the dislocations free-surface nucleation stress, as well as increase the flow strength of crystals. The dislocation density is observed to increase in the presence of hydrogen due to dislocation pinning and enhanced dislocation self-multiplications. Hydrogen also changes the deformation morphology from discrete slip planes in hydrogen-free crystals to a homogeneous deformation in H-charged crystals due to the enhanced dislocations self-multiplication.
DOI: 10.6084/m9.figshare.1434028
title: Collection of NYT's most viewed articles between 2015-05-30T07:13:57.0+1:00 and 2015-06-02T17:44:11.0+1:00

description: The data was acquired through the NYT's REST API at http://api.nytimes.com/svc/mostpopular/v2/mostviewed/all-sections/1?api-key={your_api_key}. The intervals for data retrieval were irregular and are stored in the dataset in the column 'INSERT_DATE'. Each row also contains the raw JSON object retrieved by the API 'JSON', a SHA-512 hash of it 'HASH' and several parsed fields from the object. In total, there are 10 retrivals. The dataset can be used to monitor changes in the most viewed articles, query the changing number of hits for a keyword in the title, etc. Copyright (c) 2015 The New York Times Company. All Rights Reserved.
DOI: 10.6084/m9.figshare.1434029
title: Shame and guilt-proneness in adolescents: Gene-environment interactions

description: Data from a gene-environment interaction study (Szentagotai-Tatar et al., PLOS ONE, under revision), in which the BDNF Val66Met and 5-HTTLPR polymorphisms were examined as potential moderators in the relation between the intensity of early trauma and shame and guilt-proneness.
DOI: 10.6084/m9.figshare.1434011
title: Efficacy of berberine in patients with non-alcoholic fatty liver disease

description: human data of the article Efficacy of berberine in patients with non-alcoholic fatty liver disease
DOI: 10.6084/m9.figshare.1434028.v1
title: Collection of NYT's most viewed articles between 2015-05-30T07:13:57.0+1:00 and 2015-06-02T17:44:11.0+1:00

description: The data was acquired through the NYT's REST API at http://api.nytimes.com/svc/mostpopular/v2/mostviewed/all-sections/1?api-key={your_api_key}. The intervals for data retrieval were irregular and are stored in the dataset in the column 'INSERT_DATE'. Each row also contains the raw JSON object retrieved by the API 'JSON', a SHA-512 hash of it 'HASH' and several parsed fields from the object. In total, there are 10 retrivals. The dataset can be used to monitor changes in the most viewed articles, query the changing number of hits for a keyword in the title, etc. Copyright (c) 2015 The New York Times Company. All Rights Reserved.
DOI: 10.6084/m9.figshare.1434029.v1
title: Shame and guilt-proneness in adolescents: Gene-environment interactions

description: Data from a gene-environment interaction study (Szentagotai-Tatar et al., PLOS ONE, under revision), in which the BDNF Val66Met and 5-HTTLPR polymorphisms were examined as potential moderators in the relation between the intensity of early trauma and shame and guilt-proneness.
DOI: 10.6084/m9.figshare.1434009
title: Efficacy of berberine in patients with non-alcoholic fatty liver disease

description: Animal liver gene expression of the study Efficacy of berberine in patients with non-alcoholic fatty liver disease
DOI: 10.6084/m9.figshare.1434010
title: Efficacy of berberine in patients with non-alcoholic fatty liver disease

description: Animal study data on the manuscript Efficacy of berberine in patients with non-alcoholic fatty liver disease
DOI: 10.6084/m9.figshare.1434010.v1
title: Efficacy of berberine in patients with non-alcoholic fatty liver disease

description: Animal study data on the manuscript Efficacy of berberine in patients with non-alcoholic fatty liver disease
DOI: 10.6084/m9.figshare.1433996
title: Altered Resting-state Brain Activity and Connectivity in Depressed Parkinson’s Disease

description: ALFF file is all subjects' ALLF map, MCC-FC file is all subjects' MCC-FC map.
DOI: 10.6084/m9.figshare.1434009.v1
title: Efficacy of berberine in patients with non-alcoholic fatty liver disease

description: Animal liver gene expression of the study Efficacy of berberine in patients with non-alcoholic fatty liver disease
DOI: 10.6084/m9.figshare.1433993
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1433906
title: Bacterial 16S sequences from aerosol samples of Zero Carbon Building in Hong Kong

description: Currently, there is no information pertaining to the airborne bacterial communities (microbiota) of green buildings. In this study, the air bacterial community of a zero-carbon building (ZCB) in Hong Kong is characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment and occupant skin dominate the indoor air microbiota. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties are detected, which may be driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighed UniFrac distances) differ depending on the season and sampling location. A Bayesian source-tracking approach further supports the importance of adjacent outdoor air microbiota in sourcing the ZCB indoor microbiota. Despite the unique building attributes, the ZCB microbiota detected and its temporal characteristics are not dissimilar to that of built environments investigated previously. In the future, controlled experiments and microbiota investigations of other ZCB will undoubtedly uncover additional knowledge related to how microbiomes in green buildings are influenced by their distinctive architectural attributes.<b><br> </b>
DOI: 10.6084/m9.figshare.1433906.v2
title: Bacterial 16S sequences from aerosol samples of Zero Carbon Building in Hong Kong

description: Currently, there is no information pertaining to the airborne bacterial communities (microbiota) of green buildings. In this study, the air bacterial community of a zero-carbon building (ZCB) in Hong Kong is characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment and occupant skin dominate the indoor air microbiota. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties are detected, which may be driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighed UniFrac distances) differ depending on the season and sampling location. A Bayesian source-tracking approach further supports the importance of adjacent outdoor air microbiota in sourcing the ZCB indoor microbiota. Despite the unique building attributes, the ZCB microbiota detected and its temporal characteristics are not dissimilar to that of built environments investigated previously. In the future, controlled experiments and microbiota investigations of other ZCB will undoubtedly uncover additional knowledge related to how microbiomes in green buildings are influenced by their distinctive architectural attributes.<b><br> </b>
DOI: 10.6084/m9.figshare.1433993.v1
title: Numerical integration of the rate euqations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols "Timestep tightening" means "reduce timestep to avoid sign changes of the the rate of change of concentration of intermediates". This may be needed if consecutive rection steps have extremely small activation energies.
DOI: 10.6084/m9.figshare.1433906.v1
title: Bacterial 16S sequences from aerosol samples of Zero Carbon Building in Hong Kong

description: Currently, there is no information pertaining to the airborne bacterial communities (microbiota) of green buildings. In this study, the air bacterial community of a zero-carbon building (ZCB) in Hong Kong is characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment and occupant skin dominate the indoor air microbiota. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties are detected, which may be driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighed UniFrac distances) differ depending on the season and sampling location. A Bayesian source-tracking approach further supports the importance of adjacent outdoor air microbiota in sourcing the ZCB indoor microbiota. Despite the unique building attributes, the ZCB microbiota detected and its temporal characteristics are not dissimilar to that of built environments investigated previously. In the future, controlled experiments and microbiota investigations of other ZCB will undoubtedly uncover additional knowledge related to how microbiomes in green buildings are influenced by their distinctive architectural attributes.<b><br> </b>
DOI: 10.6084/m9.figshare.1433799
title: Taiwanin A incorporated polyurethane fiber sheets for prevention of postoperative cancer recurrence

description: In this study, we propose a single solution for prevention of postoperative complications and recurrence of highly metastatic gastrointestinal tract cancers. Here, we demonstrate preparation and characterization of Taiwanin A incorporated polyurethane fiber sheets with excellent mechanical properties and sustained drug release. Sheets with elastic modulus of 8 MPa and ultimate tensile strength of 30 MPa will provide support on surgical staple line preventing leakage at anastomosis. Slight burst release of the drug within 7 days (15%) and further sustained release will inhibit proliferation and migration of remaining cancer cells and maintain locoregional high drug concentration to prevent recurrence of the disease. High elasticity of the material will promote healing process without impeding natural peristalsis movement of gastrointestinal organs.
DOI: 10.6084/m9.figshare.1433993.v2
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols "Timestep tightening" means "reduce timestep to avoid sign changes of the the rate of change of concentration of intermediates". This may be needed if consecutive rection steps have extremely small activation energies.
DOI: 10.6084/m9.figshare.1433799.v2
title: Taiwanin A incorporated polyurethane fiber sheets for prevention of postoperative cancer recurrence

description: In this study, we propose a single solution for prevention of postoperative complications and recurrence of highly metastatic gastrointestinal tract cancers. Here, we demonstrate preparation and characterization of Taiwanin A incorporated polyurethane fiber sheets with excellent mechanical properties and sustained drug release. Sheets with elastic modulus of 8 MPa and ultimate tensile strength of 30 MPa will provide support on surgical staple line preventing leakage at anastomosis. Slight burst release of the drug within 7 days (15%) and further sustained release will inhibit proliferation and migration of remaining cancer cells and maintain locoregional high drug concentration to prevent recurrence of the disease. High elasticity of the material will promote healing process without impeding natural peristalsis movement of gastrointestinal organs.