cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5533231
title: ADASS 2017: Extracting Insights from Astrophysics Simulations

description: Simulations inform all aspects of modern astrophysical research, ranging in scale from 1D and 2D test problems that can run in seconds on an astronomer's laptop all the way to large-scale 3D calculations that run on the largest supercomputers, with a spectrum of data sizes and shapes filling the landscape between these two extremes. In this talk I will review the diversity of astrophysics simulation data formats commonly in use by researchers, providing an overview of the most common simulation techniques, including pure N-body dynamics, smoothed particle hydrodynamics (SPH), adaptive mesh refinement (AMR), spectral methods, and unstructured meshes. Additionally, I will highlight methods for incorporating physical phenomena that are important for astrophysics, including chemistry, magnetic fields, radiative transport, and "subgrid" recipes for important physics that cannot be directly resolved in a simulation. In addition to the numerical techniques, I will also discuss the communities that have developed around these simulation codes and argue that increasing use and availability of open community codes has dramatically lowered the barrier to entry for novice simulators. Extracting scientific results from astrophysical simulation data requires detailed knowledge of the underlying data structures and data formats, as well as the semantic meaning of the data in relation to the physics problem posed by the simulation. As a solution to this problem, I will present yt, a community-developed python library for analyzing and visualizing simulation data. With support for most of the common astrophysics simulation research data formats, yt endeavors to provide a universal language for asking physically motivated questions of simulation data, regardless of the underlying data format. I will highlight the community of yt contributors and users, showcase scientific results where yt was used to facilitate the analysis.
DOI: 10.6084/m9.figshare.5533252.v1
title: Integrodifference equation solutions in R

description: This is the equivalent R code for malthus.m provided on Jim Powell's website: http://www.math.usu.edu/powell/wauclass/labs.html<br><br>This R code solves an integrodifference equation with 1 spatial dimension using the discrete fourier transform.<br>
DOI: 10.6084/m9.figshare.5534236.v3
title: Engagement and outreach for data management: FORCE 2017 presentation

description: My presentation for FORCE 2017, presented on 25 October 2017.
DOI: 10.6084/m9.figshare.5533231.v2
title: ADASS 2017: Extracting Insights from Astrophysics Simulations

description: Simulations inform all aspects of modern astrophysical research, ranging in scale from 1D and 2D test problems that can run in seconds on an astronomer's laptop all the way to large-scale 3D calculations that run on the largest supercomputers, with a spectrum of data sizes and shapes filling the landscape between these two extremes. In this talk I will review the diversity of astrophysics simulation data formats commonly in use by researchers, providing an overview of the most common simulation techniques, including pure N-body dynamics, smoothed particle hydrodynamics (SPH), adaptive mesh refinement (AMR), spectral methods, and unstructured meshes. Additionally, I will highlight methods for incorporating physical phenomena that are important for astrophysics, including chemistry, magnetic fields, radiative transport, and "subgrid" recipes for important physics that cannot be directly resolved in a simulation. In addition to the numerical techniques, I will also discuss the communities that have developed around these simulation codes and argue that increasing use and availability of open community codes has dramatically lowered the barrier to entry for novice simulators. Extracting scientific results from astrophysical simulation data requires detailed knowledge of the underlying data structures and data formats, as well as the semantic meaning of the data in relation to the physics problem posed by the simulation. As a solution to this problem, I will present yt, a community-developed python library for analyzing and visualizing simulation data. With support for most of the common astrophysics simulation research data formats, yt endeavors to provide a universal language for asking physically motivated questions of simulation data, regardless of the underlying data format. I will highlight the community of yt contributors and users, showcase scientific results where yt was used to facilitate the analysis.
DOI: 10.6084/m9.figshare.5533231.v1
title: ADASS 2017: Extracting Insights from Astrophysics Simulations

description: Simulations inform all aspects of modern astrophysical research, ranging in scale from 1D and 2D test problems that can run in seconds on an astronomer's laptop all the way to large-scale 3D calculations that run on the largest supercomputers, with a spectrum of data sizes and shapes filling the landscape between these two extremes. In this talk I will review the diversity of astrophysics simulation data formats commonly in use by researchers, providing an overview of the most common simulation techniques, including pure N-body dynamics, smoothed particle hydrodynamics (SPH), adaptive mesh refinement (AMR), spectral methods, and unstructured meshes. Additionally, I will highlight methods for incorporating physical phenomena that are important for astrophysics, including chemistry, magnetic fields, radiative transport, and "subgrid" recipes for important physics that cannot be directly resolved in a simulation. In addition to the numerical techniques, I will also discuss the communities that have developed around these simulation codes and argue that increasing use and availability of open community codes has dramatically lowered the barrier to entry for novice simulators. Extracting scientific results from astrophysical simulation data requires detailed knowledge of the underlying data structures and data formats, as well as the semantic meaning of the data in relation to the physics problem posed by the simulation. As a solution to this problem, I will present yt, a community-developed python library for analyzing and visualizing simulation data. With support for most of the common astrophysics simulation research data formats, yt endeavors to provide a universal language for asking physically motivated questions of simulation data, regardless of the underlying data format. I will highlight the community of yt contributors and users, showcase scientific results where yt was used to facilitate the analysis.
DOI: 10.6084/m9.figshare.5534236.v4
title: Engagement and outreach for data management: FORCE 2017 presentation

description: My presentation for FORCE 2017, presented on 25 October 2017.
DOI: 10.6084/m9.figshare.5533114
title: The combined effects of on-road and simulator training with feedback on older drivers' on-road performance: Evidence from a randomized controlled trial

description: <b>Objective</b>: A number of training programs that seek to improve driving performance among older drivers are available accompanied by a growing interest in their effectiveness. The purpose of the present investigation was to examine the combined effect of (1) basic in-class training (BT); (2) on-road training with individualized feedback (OR); and (3) training on a driving simulator (S). <b>Methods</b>: Using a randomized controlled trial study design, 78 older drivers were randomly assigned to one of 3 groups (BT, BT + OR, or BT + OR + S). All participants completed a pre- and postintervention on-road driving evaluation on a standardized route. The driving evaluations were recorded using video and Global Positioning System (GPS) equipment and were scored by a blind assessor. <b>Results</b>: The results indicated a significant reduction of approximately 30% in overall number of driving errors/omissions among participants in the BT + OR and the BT + OR + S groups in comparison to participants in the BT group. <b>Conclusions</b>: This study adds to the mounting evidence demonstrating the effectiveness of individualized driver training in improving safe driving among older adults.
DOI: 10.6084/m9.figshare.5534236.v5
title: Engagement and outreach for data management: FORCE 2017 presentation

description: My presentation for FORCE 2017, presented on 25 October 2017.
DOI: 10.6084/m9.figshare.5533114.v2
title: The combined effects of on-road and simulator training with feedback on older drivers' on-road performance: Evidence from a randomized controlled trial

description: <b>Objective</b>: A number of training programs that seek to improve driving performance among older drivers are available accompanied by a growing interest in their effectiveness. The purpose of the present investigation was to examine the combined effect of (1) basic in-class training (BT); (2) on-road training with individualized feedback (OR); and (3) training on a driving simulator (S). <b>Methods</b>: Using a randomized controlled trial study design, 78 older drivers were randomly assigned to one of 3 groups (BT, BT + OR, or BT + OR + S). All participants completed a pre- and postintervention on-road driving evaluation on a standardized route. The driving evaluations were recorded using video and Global Positioning System (GPS) equipment and were scored by a blind assessor. <b>Results</b>: The results indicated a significant reduction of approximately 30% in overall number of driving errors/omissions among participants in the BT + OR and the BT + OR + S groups in comparison to participants in the BT group. <b>Conclusions</b>: This study adds to the mounting evidence demonstrating the effectiveness of individualized driver training in improving safe driving among older adults.
DOI: 10.6084/m9.figshare.5533114.v1
title: The combined effects of on-road and simulator training with feedback on older drivers' on-road performance: Evidence from a randomized-controlled trial

description: Objective: A number of training programs that seek to improve driving performance among older drivers are available accompanied by a growing interest in their effectiveness. The purpose of the present investigation was to examine the combined effect of 1) basic in-class training (BT); 2) on-road training with individualized feedback (OR); and 3) training on a driving simulator (S). Method: Using a randomized controlled trial study design, 78 older drivers were randomly assigned to one of three groups (BT, BT+OR, or BT+OR+S). All participants completed a pre- and post-intervention on-road driving evaluation on a standardized route. The driving evaluations were recorded using video and GPS equipment and were scored by a blind assessor. Results: The results indicated a significant reduction of approximately 30% in overall number of driving errors/omissions among participants in the BT+OR and the BT+OR+S groups in comparison to participants in the BT group. Conclusions: This study adds to the mounting evidence demonstrating the effectiveness of individualized driver training in improving safe driving among older adults.
DOI: 10.6084/m9.figshare.5533036
title: Aerodynamic evaluation of the empty nose syndrome by means of computational fluid dynamics

description: The potential outcome of a surgical enlargement of internal nasal channels may be a complication of nasal breathing termed the Empty Nose Syndrome (ENS). ENS pathophysiology is not entirely understood because the expansion of air pathways would in theory ease inhalation. The present contribution is aimed at defining the biophysical markers responsible for ENS. Our study, conducted <i>in silico</i>, compares nasal aerodynamics in pre- and post-operative geometries acquired by means of computer tomography from the same individual. In this article, we elucidate and analyse the deviation of airflow patterns and nasal microclimate from the healthy benchmarks. The analysis reveals 53% reduction in flow resistance, radical re-distribution of nasal airflow, as well as dryer and colder nasal microclimate for the post-operative case.
DOI: 10.6084/m9.figshare.5533036.v1
title: Aerodynamic evaluation of the empty nose syndrome by means of computational fluid dynamics

description: The potential outcome of a surgical enlargement of internal nasal channels may be a complication of nasal breathing termed the Empty Nose Syndrome (ENS). ENS pathophysiology is not entirely understood because the expansion of air pathways would in theory ease inhalation. The present contribution is aimed at defining the biophysical markers responsible for ENS. Our study, conducted <i>in silico</i>, compares nasal aerodynamics in pre- and post-operative geometries acquired by means of computer tomography from the same individual. In this article, we elucidate and analyse the deviation of airflow patterns and nasal microclimate from the healthy benchmarks. The analysis reveals 53% reduction in flow resistance, radical re-distribution of nasal airflow, as well as dryer and colder nasal microclimate for the post-operative case.
DOI: 10.6084/m9.figshare.5532811
title: Supplementary Material for: Cellular Immunotherapy in B-Cell Malignancy

description: In recent years, cellular immunotherapy in B-cell malignancies has been driven by adoptive transfer of genetically engineered T cells expressing chimeric antigen receptors (CARs). CARs consist of a single chain variable fragment (scFv) of a monoclonal antibody, a spacer domain, a transmembrane domain, an intracellular signaling domain, and additional costimulatory domains. The bulk of clinical data available is on CD19-targeting CAR T cells for the treatment of B-cell acute lymphocytic leukemia (B-ALL), chronic lymphocytic leukemia, and B-cell non-Hodgkin lymphoma. Results so far have been promising with impressive rates and depth of remission especially among B-ALL patients. However, CAR T-cell therapy is a complex multi-step process, and clinical trials so far differ profoundly in CAR construct used, gene transfer method, composition of the cellular product, lymphodepletion, and CAR T-cell dose used. Randomized trials will be needed to conclusively evaluate the implications of these differences. The treatment concept is associated with significant neurotoxicity and potentially lethal cytokine release syndrome, both of which require specific management. Improvements in CAR design may help to overcome toxicity, the effects of an immunosuppressive microenvironment, and tumor escape by development of antigen-negative clones. This review will explain the mechanism of action, summarize the clinical experience with this treatment modality so far, and explore future developments in the field.
DOI: 10.6084/m9.figshare.5532763
title: Chickenpox and shingles ABM_connection and contact frequency profile

description: This files complements the chickenpox and shingles agent-based model, contains connection and contact frequency/exposure profile for the model and accompanies the scientific paper entitled "Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling".
DOI: 10.6084/m9.figshare.5532748
title: Supplementary Material for: Checkpoint Inhibition in Non-Hodgkin's Lymphoma

description: As patients continue to die from malignant lymphoma, novel treatment options continue to be warranted. To successfully grow and spread, tumor cells need to escape the immune system; therefore, the augmentation or restoration of immune effectors against the malignant cell could be of great value, as shown, e.g., for allogeneic transplantation. A deepened understanding of the regulation of activation and inhibition of the T cell-based effector mechanisms has led to the development of drugs that are able to modify specific checkpoints of this system and thereby raise an immune response against tumor cells. With dramatic responses observed in Hodgkin’s disease (HD), interest has risen to explore these drugs in non-Hodgkin’s lymphoma (NHL). Available data underline the potential of checkpoint inhibitors in a variety of lymphoma entities, such as primary mediastinal B cell lymphoma (PMBCL) or central nervous system (CNS) lymphoma, and there is hope that a significant proportion of patients will finally benefit. However, intensive efforts are needed to develop optimal screening tools, combinations, and sequences to explore the full potential of these new classes of therapeutic agents.
DOI: 10.6084/m9.figshare.5532757
title: Analysis of nectar from low-volume flowers: a comparison of collection methods for free amino acids

description: Data for the analysis of amino acids in Calluna vulgaris, published in Methods in Ecology and Evolution
DOI: 10.6084/m9.figshare.5532763.v1
title: Chickenpox and shingles ABM_connection and contact frequency profile

description: This files complements the chickenpox and shingles agent-based model, contains connection and contact frequency/exposure profile for the model and accompanies the scientific paper entitled "Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling".
DOI: 10.6084/m9.figshare.5532718
title: Night warming, spiders, grasshoppers

description: Data for Barton and Schmitz Ecology paper, " Opposite effects of daytime and nighttime warming on top-down control of plant diversity"<br>One file contains behavioral data for spiders and grasshoppers (height in plant canopy and feeding time). The other file contains plant community data for the multi-year mesocosm experiment.
DOI: 10.6084/m9.figshare.5532757.v1
title: Analysis of nectar from low-volume flowers: a comparison of collection methods for free amino acids

description: Data for the analysis of amino acids in Calluna vulgaris, published in Methods in Ecology and Evolution
DOI: 10.6084/m9.figshare.5532688
title: Supplementary Material for: Polymorphisms in Sex Hormone Metabolism Genes and Risk of Preeclampsia in Taiyuan, China

description: <i>Objective:</i> Aberrant synthesis and metabolism of sex hormone are likely to be associated with alterations in vascular function in preeclampsia (PE). The study aims to investigate whether single nucleotide polymorphisms (SNPs) in sex hormone-related genes are associated with PE. <i>Method:</i> We performed a nested case-control study including 436 pregnant women (203 PE and 233 healthy or normal pregnant women) to investigate associations between 96 SNPs in 28 sex hormone-related genes and risk of PE. <i>Results:</i><i>TXNRD2/COMT</i> rs3788314 and <i>SULT1A2/SULT1A1 </i>rs4788073 were associated with an increased risk of PE overall (<i>p</i><i>trend</i> = 0.004 and 0.003, respectively), early-onset PE (<i>p</i><i>trend</i> = 0.007 and 0.009, respectively), and severe PE (<i>p</i><i>trend</i> = 0.002 and 0.005, respectively). Additionally, <i>CYP17A1 </i>rs4919690 and rs4919687 and <i>LHCGR rs10180731</i>were associated with an increased risk of severe PE (<i>p</i><i>trend</i> = 0.005, 0.006, and 0.014, respectively), while <i>GNRHR</i> rs2630488 was associated with a decreased risk of severe PE (<i>p</i><i>trend</i> = 0.014). We also observed that <i>HSD17B3</i> rs8190512 was associated with a decreased risk of early-onset PE (<i>p</i><i>trend</i> = 0.003). We observed strong linkage disequilibrium in SULF1 (rs10106958, rs7813987, and rs6990375). <i>Conclusions:</i> Our study suggested that genetic polymorphisms in <i>TXNRD2/COMT, SULT1A2/SULT1A1, CYP17A1, HSD17B3, GNRHR, LHCGR, </i>and SULF1 might play a role in PE, especially in early-onset PE and severe PE. Future studies are warranted to replicate the observed associations and their functional mechanisms.
DOI: 10.6084/m9.figshare.5532718.v1
title: Night warming, spiders, grasshoppers

description: Data for Barton and Schmitz Ecology paper, " Opposite effects of daytime and nighttime warming on top-down control of plant diversity"<br>One file contains behavioral data for spiders and grasshoppers (height in plant canopy and feeding time). The other file contains plant community data for the multi-year mesocosm experiment.
DOI: 10.6084/m9.figshare.5532748.v1
title: Supplementary Material for: Checkpoint Inhibition in Non-Hodgkin's Lymphoma

description: As patients continue to die from malignant lymphoma, novel treatment options continue to be warranted. To successfully grow and spread, tumor cells need to escape the immune system; therefore, the augmentation or restoration of immune effectors against the malignant cell could be of great value, as shown, e.g., for allogeneic transplantation. A deepened understanding of the regulation of activation and inhibition of the T cell-based effector mechanisms has led to the development of drugs that are able to modify specific checkpoints of this system and thereby raise an immune response against tumor cells. With dramatic responses observed in Hodgkin’s disease (HD), interest has risen to explore these drugs in non-Hodgkin’s lymphoma (NHL). Available data underline the potential of checkpoint inhibitors in a variety of lymphoma entities, such as primary mediastinal B cell lymphoma (PMBCL) or central nervous system (CNS) lymphoma, and there is hope that a significant proportion of patients will finally benefit. However, intensive efforts are needed to develop optimal screening tools, combinations, and sequences to explore the full potential of these new classes of therapeutic agents.
DOI: 10.6084/m9.figshare.5532412
title: Lepidium didymum raw data from Sperber et al Nature Communications

description: This is the raw data from Sperber et al 2018 (Nature Comms).<br>
DOI: 10.6084/m9.figshare.5532673
title: Supplementary Material for: Checkpoint Inhibition in Hodgkin Lymphoma - a Review

description: Physiological immune checkpoint pathways are important to regulate self-tolerance, limit immune reactions, and moderate autoimmunity. Various cancers are commonly exploiting these mechanisms to evade the host immune system by restraining a durable, efficient anti-tumor immune response. Immune checkpoints include, but are not limited to, the programmed death 1 (PD1) and the cytotoxic T-lymphocyte-associated protein-4 (CTLA4) axis, which are both druggable by monoclonal antibodies referred to as checkpoint inhibitors (CIs). To date, the anti-PD1 antibodies nivolumab and pembrolizumab are approved for relapsed or refractory classical Hodgkin lymphoma (cHL) due to high response rates with a favorable yet distinct safety profile, and other agents are under investigation. This review summarizes the available preclinical and clinical data including the toxicity and efficacy of different CIs in cHL. It also provides future perspectives based on ongoing clinical trials, potentially synergistic combinatory approaches, and their fit in the therapeutic landscape in cHL.