cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3427406
title: Spatiotemporal Modeling of Node Temperatures in Supercomputers

description: Los Alamos National Laboratory is home to many large supercomputing clusters. These clusters require an enormous amount of power (∼500–2000 kW each), and most of this energy is converted into heat. Thus, cooling the components of the supercomputer becomes a critical and expensive endeavor. Recently, a project was initiated to investigate the effect that changes to the cooling system in a machine room had on three large machines that were housed there. Coupled with this goal was the aim to develop a general good-practice for characterizing the effect of cooling changes and monitoring machine node temperatures in this and other machine rooms. This article focuses on the statistical approach used to quantify the effect that several cooling changes to the room had on the temperatures of the individual nodes of the computers. The largest cluster in the room has 1600 nodes that run a variety of jobs during general use. Since extremes temperatures are important, a Normal distribution plus generalized Pareto distribution for the upper tail is used to model the marginal distribution, along with a Gaussian process copula to account for spatio-temporal dependence. A Gaussian Markov random field (GMRF) model is used to model the spatial effects on the node temperatures as the cooling changes take place. This model is then used to assess the condition of the node temperatures after each change to the room. The analysis approach was used to uncover the cause of a problematic episode of overheating nodes on one of the supercomputing clusters. This same approach can easily be applied to monitor and investigate cooling systems at other data centers, as well. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427406.v2
title: Spatiotemporal Modeling of Node Temperatures in Supercomputers

description: Los Alamos National Laboratory is home to many large supercomputing clusters. These clusters require an enormous amount of power (∼500–2000 kW each), and most of this energy is converted into heat. Thus, cooling the components of the supercomputer becomes a critical and expensive endeavor. Recently, a project was initiated to investigate the effect that changes to the cooling system in a machine room had on three large machines that were housed there. Coupled with this goal was the aim to develop a general good-practice for characterizing the effect of cooling changes and monitoring machine node temperatures in this and other machine rooms. This article focuses on the statistical approach used to quantify the effect that several cooling changes to the room had on the temperatures of the individual nodes of the computers. The largest cluster in the room has 1600 nodes that run a variety of jobs during general use. Since extremes temperatures are important, a Normal distribution plus generalized Pareto distribution for the upper tail is used to model the marginal distribution, along with a Gaussian process copula to account for spatio-temporal dependence. A Gaussian Markov random field (GMRF) model is used to model the spatial effects on the node temperatures as the cooling changes take place. This model is then used to assess the condition of the node temperatures after each change to the room. The analysis approach was used to uncover the cause of a problematic episode of overheating nodes on one of the supercomputing clusters. This same approach can easily be applied to monitor and investigate cooling systems at other data centers, as well. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427397
title: Parsimonious Tensor Response Regression

description: Aiming at abundant scientific and engineering data with not only high dimensionality but also complex structure, we study the regression problem with a multidimensional array (tensor) response and a vector predictor. Applications include, among others, comparing tensor images across groups after adjusting for additional covariates, which is of central interest in neuroimaging analysis. We propose parsimonious tensor response regression adopting a generalized sparsity principle. It models all voxels of the tensor response jointly, while accounting for the inherent structural information among the voxels. It effectively reduces the number of free parameters, leading to feasible computation and improved interpretation. We achieve model estimation through a nascent technique called the envelope method, which identifies the immaterial information and focuses the estimation based upon the material information in the tensor response. We demonstrate that the resulting estimator is asymptotically efficient, and it enjoys a competitive finite sample performance. We also illustrate the new method on two real neuroimaging studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427397.v1
title: Parsimonious Tensor Response Regression

description: Aiming at abundant scientific and engineering data with not only high dimensionality but also complex structure, we study the regression problem with a multidimensional array (tensor) response and a vector predictor. Applications include, among others, comparing tensor images across groups after adjusting for additional covariates, which is of central interest in neuroimaging analysis. We propose parsimonious tensor response regression adopting a generalized sparsity principle. It models all voxels of the tensor response jointly, while accounting for the inherent structural information among the voxels. It effectively reduces the number of free parameters, leading to feasible computation and improved interpretation. We achieve model estimation through a nascent technique called the envelope method, which identifies the immaterial information and focuses the estimation based upon the material information in the tensor response. We demonstrate that the resulting estimator is asymptotically efficient, and it enjoys a competitive finite sample performance. We also illustrate the new method on two real neuroimaging studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427370
title: Virtual Characters Experiment

description: This dataset is part of an unpublished study with the title:<br>Don't stand so close to me: Investigating the effect of control on the appeal of virtual humans using immersion and a proximity-based behavioral task
DOI: 10.6084/m9.figshare.3427370.v2
title: Virtual Characters Experiment

description: This dataset is part of an unpublished study with the title:<br>Don't stand so close to me: Investigating the effect of control on the appeal of virtual humans using immersion and a proximity-based behavioral task
DOI: 10.6084/m9.figshare.3427370.v1
title: New draft item

description: This dataset is part of an unpublished study with the title:<br>Don't stand so close to me: Investigating the effect of control on the appeal of virtual humans using immersion and a proximity-based behavioral task
DOI: 10.6084/m9.figshare.3427349
title: On Modeling and Estimation for the Relative Risk and Risk Difference

description: A common problem in formulating models for the relative risk and risk difference is the variation dependence between these parameters and the baseline risk, which is a nuisance model. We address this problem by proposing the conditional log odds-product as a preferred nuisance model. This novel nuisance model facilitates maximum-likelihood estimation, but also permits doubly-robust estimation for the parameters of interest. Our approach is illustrated via simulations and a data analysis. An R package implementing the proposed methods is available on CRAN. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427349.v2
title: On Modeling and Estimation for the Relative Risk and Risk Difference

description: A common problem in formulating models for the relative risk and risk difference is the variation dependence between these parameters and the baseline risk, which is a nuisance model. We address this problem by proposing the conditional log odds-product as a preferred nuisance model. This novel nuisance model facilitates maximum-likelihood estimation, but also permits doubly-robust estimation for the parameters of interest. Our approach is illustrated via simulations and a data analysis. An R package implementing the proposed methods is available on CRAN. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3427349.v1
title: On Modeling and Estimation for the Relative Risk and Risk Difference

description: A common problem in formulating models for the relative risk and risk difference is the variation dependence between these parameters and the baseline risk, which is a nuisance model. We address this problem by proposing the conditional log odds-product as a preferred nuisance model. This novel nuisance model facilitates maximum-likelihood estimation, but also permits doubly-robust estimation for the parameters of interest. Our approach is illustrated via simulations and a data analysis.
DOI: 10.6084/m9.figshare.3427322
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: Freezing percentages]

description: <b>D</b><b>escription</b><br>A group of mice was trained and tested for memory retrieval 4 weeks after context (C) or context shock (CS) exposure (10 mice per condition). Several mice have also been tested for freezing behavior 30 minutes and 24 hours after exposure to shock (10 and 14 mice, respectively), and compared with basal freezing behavior. The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The table contains the freezing percentages separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427322.v1
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record X: freezing percentages]

description: <b>Description</b><br>A group of mice was trained and tested for memory retrieval 30 minutes, 24 hours and 4 weeks after context (C) or context shock (CS) exposure (10, 14 and 10 mice per condition, respectively). The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The table contains the freezing percentages separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427322.v2
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: freezing percentages]

description: <b>Description</b><br>A group of mice was trained and tested for memory retrieval 30 minutes, 24 hours and 4 weeks after context (C) or context shock (CS) exposure (10, 14 and 10 mice per condition, respectively). The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The table contains the freezing percentages separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427322.v3
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: freezing percentages]

description: <b>D</b><b>escription</b><br>A group of mice was trained and tested for memory retrieval 4 weeks after context (C) or context shock (CS) exposure (10 mice per condition). Several mice have also been tested for freezing behavior 30 minutes and 24 hours after exposure to shock (10 and 14 mice, respectively), and compared with basal freezing behavior. The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The table contains the freezing percentages separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427322.v4
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: freezing percentages]

description: <b>D</b><b>escription</b><br>A group of mice was trained and tested for memory retrieval 4 weeks after context (C) or context shock (CS) exposure (10 mice per condition). Several mice have also been tested for freezing behavior 30 minutes and 24 hours after exposure to shock (10 and 14 mice, respectively), and compared with basal freezing behavior. The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The table contains the freezing percentages separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427304
title: One-year Mortality in COPD After an Exacerbation: The Effect of Physical Activity Changes During the Event

description: Mortality is one of the most important outcomes in patients with chronic obstructive pulmonary disease (COPD). Different predictors have been associated with mortality, including the patient's level of physical activity (PA). The objective of this work was to establish the relationship between changes in PA during a moderate-to-severe COPD exacerbation (eCOPD) and 1-year mortality after the index event. This was a prospective observational cohort study with recruitment of 2,484 patients with an eCOPD attending the emergency department (ED) of 16 participating hospitals. Variables recorded included clinical and sociodemographic data from medical records, dyspnea, health-related quality of life, and PA before the index eCOPD and 2 months after the hospital or ED discharge, as reported by the patient. In the multivariate analysis worsening changes in PA from baseline to 2 months after the ED index visit [odds ratio (ORs) from 2.78 to 6.31] was related to 1-year mortality, using the age-adjusted Charlson comorbidity index (OR: 1.22), and previous use of long-term domiciliary oxygen therapy or non-invasive mechanical ventilation at home (OR: 1.68). The same variables were also predictive in the validation sample. Areas under the receiver operating characteristic curve in the derivation and validation sample were 0.79 and 0.78, respectively. In conclusion, PA is the strongest predictor of dying in the following year, i.e., those with worsened PA from baseline to 2 months after an eCOPD or with very low PA levels have a higher risk.
DOI: 10.6084/m9.figshare.3427304.v1
title: One-year Mortality in COPD After an Exacerbation: The Effect of Physical Activity Changes During the Event

description: Mortality is one of the most important outcomes in patients with chronic obstructive pulmonary disease (COPD). Different predictors have been associated with mortality, including the patient's level of physical activity (PA). The objective of this work was to establish the relationship between changes in PA during a moderate-to-severe COPD exacerbation (eCOPD) and 1-year mortality after the index event. This was a prospective observational cohort study with recruitment of 2,484 patients with an eCOPD attending the emergency department (ED) of 16 participating hospitals. Variables recorded included clinical and sociodemographic data from medical records, dyspnea, health-related quality of life, and PA before the index eCOPD and 2 months after the hospital or ED discharge, as reported by the patient. In the multivariate analysis worsening changes in PA from baseline to 2 months after the ED index visit [odds ratio (ORs) from 2.78 to 6.31] was related to 1-year mortality, using the age-adjusted Charlson comorbidity index (OR: 1.22), and previous use of long-term domiciliary oxygen therapy or non-invasive mechanical ventilation at home (OR: 1.68). The same variables were also predictive in the validation sample. Areas under the receiver operating characteristic curve in the derivation and validation sample were 0.79 and 0.78, respectively. In conclusion, PA is the strongest predictor of dying in the following year, i.e., those with worsened PA from baseline to 2 months after an eCOPD or with very low PA levels have a higher risk.
DOI: 10.6084/m9.figshare.3427271
title: COMBINE Archive Show Case

description: A fully featured COMBINE archive of syncytial mitotic cycles in Drosophila embryos, including (i) the original publication, (ii) model code, (iii) simulation descriptions, and (iv) simulation results. A COMBINE archive is a standardised container for data files related to a simulation study in computational biology. The archive can be used for both, educational and research purposes. Anyone may reuse, extend and update the archive to make it a valuable resource for the scientific community. The archive is developed and maintained at https://github.com/SemsProject/CombineArchiveShowCase - everyone is invited to use and improve it!
DOI: 10.6084/m9.figshare.3427250.v1
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record X: freezing percentages]

description: <b>Description</b><br>A group of mice was trained and tested for memory retrieval 30 minutes, 24 hours and 4 weeks after context (C) or context shock (CS) exposure (10, 14 and 10 mice per condition, respectively). The motion of mice was tracked and the percentage of freezing (i.e. percentage of total testing time the mice were recorded as frozen) was calculated using the Video Freeze ® automated monitoring system (Med Associates). The freezing percentages is available as a table in Data Record X, separated by tested time after exposure and conditioning.<br>
DOI: 10.6084/m9.figshare.3427172
title: Next-generation sequencing reveals germline mutations in an infant with synchronous occurrence of nephro- and neuroblastoma

description: Although neuro- and nephroblastoma are common solid tumors in children, the simultaneous occurrence is very rare and is often associated with syndromes. Here, we present a unique case of synchronous occurrence of neuro- and nephroblastoma in an infant with no signs of congenital anomalies or a syndrome. We performed genetic testing for possible candidate genes as underlying mutation using the next-generation sequencing (NGS) approach to target 94 genes and 284 single-nucleotide polymorphisms (SNPs) involved in cancer. We uncovered a novel heterozygous germline missense mutation p.F58L (c.172T→C) in the anaplastic lymphoma kinase (<i>ALK</i>) gene and one novel heterozygous rearrangement Q418Hfs<sup>*</sup>11 (c.1254_1264delins TTACTTAGTACAAGAACTG) in the Fanconi anemia gene <i>FANCD2</i> leading to a truncated protein. Besides, several SNPs associated with the occurrence of neuroblastoma and/or nephroblastoma or multiple primary tumors were identified. The next-generation sequencing approach might in the future be useful not only in understanding tumor etiology but also in recognizing new genetic markers and targets for future personalized therapy.
DOI: 10.6084/m9.figshare.3427172.v1
title: Next-generation sequencing reveals germline mutations in an infant with synchronous occurrence of nephro- and neuroblastoma

description: Although neuro- and nephroblastoma are common solid tumors in children, the simultaneous occurrence is very rare and is often associated with syndromes. Here, we present a unique case of synchronous occurrence of neuro- and nephroblastoma in an infant with no signs of congenital anomalies or a syndrome. We performed genetic testing for possible candidate genes as underlying mutation using the next-generation sequencing (NGS) approach to target 94 genes and 284 single-nucleotide polymorphisms (SNPs) involved in cancer. We uncovered a novel heterozygous germline missense mutation p.F58L (c.172T→C) in the anaplastic lymphoma kinase (<i>ALK</i>) gene and one novel heterozygous rearrangement Q418Hfs<sup>*</sup>11 (c.1254_1264delins TTACTTAGTACAAGAACTG) in the Fanconi anemia gene <i>FANCD2</i> leading to a truncated protein. Besides, several SNPs associated with the occurrence of neuroblastoma and/or nephroblastoma or multiple primary tumors were identified. The next-generation sequencing approach might in the future be useful not only in understanding tumor etiology but also in recognizing new genetic markers and targets for future personalized therapy.
DOI: 10.6084/m9.figshare.3427040
title: Data from Unterseer et.al 2016 Genome Biology

description: This data package accompanies the following publication:<br><br>Unterseer et al. 2016 (Genome Biology 2016,<strong> 17</strong>:137)<br>A comprehensive study of the genomic differentiation<br>between temperate Dent and Flint maize.<br><strong>DOI: </strong>10.1186/s13059-016-1009-x<br><br>It contains a copy of the data files used in this paper as well as further accompanying files (see README.txt).<br><br>
DOI: 10.6084/m9.figshare.3426986
title: OpenAccessDataFacialAnimationExperiment

description: This dataset contains the retrieved data from the experiments described in the papers:<br><br>Kokkinara, E., & McDonnell, R. (2015, November). Animation realism affects perceived character appeal of a self-virtual face. In Proceedings of the 8th ACM SIGGRAPH Conference on Motion in Games (pp. 221-226). ACM.<br>and <br>Kokkinara, E., & McDonnell, R. (2015). The Effect of Animation Realism on Face Ownership and Engagement. FAAVSP-The 1 st Joint Conference on Facial Analysis, Animation, and Auditory-Visual Speech Processing. <br><br><br><br><br>
DOI: 10.6084/m9.figshare.3426986.v2
title: OpenAccessDataFacialAnimationExperiment

description: This dataset contains the retrieved data from the experiments described in the papers:<br><br>Kokkinara, E., & McDonnell, R. (2015, November). Animation realism affects perceived character appeal of a self-virtual face. In Proceedings of the 8th ACM SIGGRAPH Conference on Motion in Games (pp. 221-226). ACM.<br>and <br>Kokkinara, E., & McDonnell, R. (2015). The Effect of Animation Realism on Face Ownership and Engagement. FAAVSP-The 1 st Joint Conference on Facial Analysis, Animation, and Auditory-Visual Speech Processing. <br><br><br><br><br>
DOI: 10.6084/m9.figshare.3426986.v1
title: OpenAccessDataWalkingExperiment.rar

description: This dataset contains the retrieved data from the experiments described in the papers:<br><br>Kokkinara, E., & McDonnell, R. (2015, November). Animation realism affects perceived character appeal of a self-virtual face. In Proceedings of the 8th ACM SIGGRAPH Conference on Motion in Games (pp. 221-226). ACM.<br>and <br>Kokkinara, E., & McDonnell, R. (2015). The Effect of Animation Realism on Face Ownership and Engagement. FAAVSP-The 1 st Joint Conference on Facial Analysis, Animation, and Auditory-Visual Speech Processing. <br><br><br><br><br>
DOI: 10.6084/m9.figshare.3426890
title: Metabolism, personality and pace of life in the Trinidadian guppy, Poecilia reticulata

description: Data used in the study
DOI: 10.6084/m9.figshare.3426890.v1
title: Metabolism, personality and pace of life in the Trinidadian guppy, Poecilia reticulata

description: Data used in the study
DOI: 10.6084/m9.figshare.3426887
title: Muscle contributions to medial tibiofemoral compartment contact loading following ACL reconstruction using semitendinosus and gracilis tendon grafts

description: This data contains outputs of muscle force, activations, torques, fiber lengths and joint contact forces of 34 MTU's for 25 participants each doing 3 walks, 3 runs and 3 cuts. Data for Standard model and an adjusted model, that models the morbidity associated with