cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4828915.v1
title: Dataset for: Post-exercise essential amino acid supplementation amplifies skeletal muscle satellite cell proliferation in older men 24 hours post-exercise

description: Aged skeletal muscle has an attenuated and delayed ability to proliferate satellite cells in response to resistance exercise. The mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway is a focal point for cell growth, however the effect of post-exercise mTORC1 activation on human skeletal muscle satellite cell (SC) proliferation is unknown. To test the proliferative capacity of skeletal muscle SC in aging muscle to a potent mTORC1 activator (i.e., EAA; essential amino acids) we recruited older (~72y) men to conduct leg resistance exercise (8sets x10reps) without (-EAA;n=8) and with (+EAA:n=11) ingestion of 10g of EAA 1h post exercise. Muscle biopsies were taken before exercise (Pre) and 24h post-exercise (Post) for assessment of expression and fiber type-specific Pax7+ SC, Ki67+Pax7+ SC and MyoD+ SC. -EAA did not show an increase in Pax7+ satellite cells at Post (p&gt;0.82). Although statistical significance for an increase in Pax7+ SC at 24 h post-RE was not observed in +EAA vs –EAA, we observed trends for a treatment difference (p&lt;0.1). When examining the change from Pre to Post trends were demonstrated (#/myofiber:p=0.076; and %/ myonuclei:p=0.065) for a greater increase in +EAA vs –EAA. Notably, we found an increases SC proliferation in +EAA, but not -EAA with increases in Ki67+ SC and MyoD+ cells (p&lt;0.05). Ki67+ SC also exhibited a significant group difference Post (p&lt;0.010). Pax7+ SC in fast twitch myofibers did not change and was not different between groups (p&gt;0.10). CDK2, MEF2C, RB1 mRNA only increased in +EAA (p&lt;0.05). Acute muscle satellite cell proliferative capacity may be partially rescued with post-exercise EAA ingestion in older men.
DOI: 10.6084/m9.figshare.4828669
title: WBD_Pools

description: 16S rRNA gene sequences for the white band disease pools.
DOI: 10.6084/m9.figshare.4828672
title: Stauffer-Olsen_Baetis_SoCal_vs_NorCal_rarefied

description: Alignment of COI gene region Baetis sequences generated by Natalie Stauffer-Olsen (UC Berkeley) and SCCWRP.
DOI: 10.6084/m9.figshare.4828606
title: Dataset for: Assessing the influence of rater and subject characteristics on measures of agreement for ordinal ratings

description: Widespread inconsistencies are commonly observed between physicians' ordinal classifications in screening tests results such as mammography. These discrepancies have motivated large-scale agreement studies where many raters contribute ratings. The primary goal of these studies is to identify factors related to physicians and patients' test results which may lead to stronger consistency between raters’ classifications. While ordered categorical scales are frequently used to classify screening test results, very few statistical approaches exist to model agreement between multiple raters. Here we develop a flexible and comprehensive approach to assess the influence of rater and subject characteristics on agreement between multiple raters' ordinal classifications in large-scale agreement studies. Our approach is based upon the class of generalized linear mixed models. Novel summary model-based measures are proposed to assess agreement between all, or a subgroup of raters, such as experienced physicians. Hypothesis tests are described to formally identify factors such as physicians' level of experience that play an important role in improving consistency of ratings between raters. We demonstrate how unique characteristics of individual raters can be assessed via conditional modes generated during the modeling process. Simulation studies are presented to demonstrate the performance of the proposed methods and summary measure of agreement. The methods are applied to a large-scale mammography agreement study to investigate the effects of rater and patient characteristics on the strength of agreement between radiologists.
DOI: 10.6084/m9.figshare.4828669.v1
title: WBD_Pools

description: 16S rRNA gene sequences for the white band disease pools.
DOI: 10.6084/m9.figshare.4828672.v1
title: Stauffer-Olsen_Baetis_SoCal_vs_NorCal_rarefied

description: Alignment of COI gene region Baetis sequences generated by Natalie Stauffer-Olsen (UC Berkeley) and SCCWRP.
DOI: 10.6084/m9.figshare.4828603
title: Dataset for: The retrosplenial cortex and object recency memory in the rat

description: It has been proposed that the retrosplenial cortex forms part of a “where/when” information network. The present study focussed on the related issue of whether retrosplenial cortex also contributes to “what/when” information, by examining object recency memory. In Experiment 1, rats with retrosplenial lesions were found to be impaired at distinguishing the temporal order of objects presented in a continuous series (‘Within-Block’ condition). The same lesioned rats could, however, distinguish between objects that had been previously presented in one of two discrete blocks (‘Between-Block’ condition). Experiment 2 used intact rats to map the expression of the immediate-early gene c-fos in retrosplenial cortex following performance of a between-block, recency discrimination. Recency performance correlated positively with levels of c-fos expression in both granular and dysgranular retrosplenial cortex (areas 29 and 30). Expression of c-fos in the granular retrosplenial cortex also correlated with prelimbic cortex and ventral subiculum c-fos activity, the latter also correlating with recency memory performance. The combined findings from both experiments reveal an involvement of the retrosplenial cortex in temporal order memory, which includes both between-block and within-block problems. The current findings also suggest that the rat retrosplenial cortex comprises one of a group of closely interlinked regions that enable recency memory, including the hippocampal formation, medial diencephalon, and medial frontal cortex. In view of the well-established importance of the retrosplenial cortex for spatial learning, the findings support the notion that, with its frontal and hippocampal connections, retrosplenial cortex has a key role for both what/when and where/when information.
DOI: 10.6084/m9.figshare.4828606.v1
title: Dataset for: Assessing the influence of rater and subject characteristics on measures of agreement for ordinal ratings

description: Widespread inconsistencies are commonly observed between physicians' ordinal classifications in screening tests results such as mammography. These discrepancies have motivated large-scale agreement studies where many raters contribute ratings. The primary goal of these studies is to identify factors related to physicians and patients' test results which may lead to stronger consistency between raters’ classifications. While ordered categorical scales are frequently used to classify screening test results, very few statistical approaches exist to model agreement between multiple raters. Here we develop a flexible and comprehensive approach to assess the influence of rater and subject characteristics on agreement between multiple raters' ordinal classifications in large-scale agreement studies. Our approach is based upon the class of generalized linear mixed models. Novel summary model-based measures are proposed to assess agreement between all, or a subgroup of raters, such as experienced physicians. Hypothesis tests are described to formally identify factors such as physicians' level of experience that play an important role in improving consistency of ratings between raters. We demonstrate how unique characteristics of individual raters can be assessed via conditional modes generated during the modeling process. Simulation studies are presented to demonstrate the performance of the proposed methods and summary measure of agreement. The methods are applied to a large-scale mammography agreement study to investigate the effects of rater and patient characteristics on the strength of agreement between radiologists.
DOI: 10.6084/m9.figshare.4828579
title: Skull morphometry of the two subspecies of long-finned Pilot Whale (Globicephala melas Trail 1809)

description: Skull morphometric data was collected from 93 adult specimens of both subspecies of the long-finned Pilot Whale, G. melas edwardii (Southern Ocean) and G. melas melas (North Atlantic Ocean,) with the aim of providing new information on their cranial characterizations and distinction between such subspecies. This brings a new line of evidence to help re-assess the current taxonomy of Globicephala melas.
DOI: 10.6084/m9.figshare.4828579.v1
title: Skull morphometry of the two subspecies of long-finned Pilot Whale (Globicephala melas Trail 1809)

description: Skull morphometric data was collected from 93 adult specimens of both subspecies of the long-finned Pilot Whale, G. melas edwardii (Southern Ocean) and G. melas melas (North Atlantic Ocean,) with the aim of providing new information on their cranial characterizations and distinction between such subspecies. This brings a new line of evidence to help re-assess the current taxonomy of Globicephala melas.
DOI: 10.6084/m9.figshare.4828408
title: Estimate of mortality reduction with implementation of advanced automatic collision notification

description: <b>Objective</b>: Advanced Automatic Collision Notification (AACN) is a system on a motor vehicle that notifies a public safety answering point (PSAP), either directly or through a third party, that the vehicle has had a crash. AACN systems enable earlier notification of a motor vehicle crash and provide an injury prediction that can help dispatchers and first responders make better decisions about how and where to transport the patient, thus getting the patient to definitive care sooner. The purposes of the current research are to identify the target population that could benefit from AACN, and to develop a reasonable estimate range of potential lives saved with implementation of AACN within the vehicle fleet. <b>Methods</b>: Data from the Fatality Analysis Reporting System (FARS) years 2009–2015 and National Automotive Sampling System–Crashworthiness Data System (NASS-CDS) years 2000–2015 were obtained. FARS data were used to determine absolute estimates of the target population who may receive benefit from AACN. These estimates accounted for a number of factors, such as whether a fatal occupant had nearby access to a trauma center and also was correctly identified by the injury severity prediction algorithm as having a “high probability of severe injury.” NASS-CDS data were used to provide relative comparisons among subsets of the population. Specifically, relative survival rate ratios between occupants treated at trauma centers versus at non-trauma centers were determined using the nonparametric Kaplan–Meier estimator. Finally, the fatality reduction rate associated with trauma center care was combined with the previously published fatality reduction rate for faster notification time to develop a range for possible lives saved. <b>Results</b>: Two relevant target populations were identified. A larger subset of 6893 fatalities can benefit only from earlier notification associated with AACN. A smaller subgroup of between 1495 and 2330 fatalities can benefit from both earlier notification and change in treatment destination (i.e., non-trauma center to trauma center). A Kaplan–Meier life curve and a multiple proportional hazard model were used to predict the benefits associated with transport to a trauma center. The resulting range for potential lives saved annually was 360 to 721. <b>Conclusions</b>: This analysis provides the estimates of lives that could potentially be saved with full implementation of AACN and universal cell coverage availability. This represents a fatality reduction of approximately 1.6% to 3.3% per year, and more than double the lives saved by earlier notification alone. In conclusion, AACN is a postcrash technology with a promising potential for safety benefit. AACN is therefore a key component of integrated safety systems that aim to protect occupants across the entire crash spectrum.
DOI: 10.6084/m9.figshare.4827373
title: Effects of exogenous GLP-2 and distal bowel resection on intestinal and systemic adaptive responses in rats Raw Data.xlsx

description: Raw data for plasma hormone levels, body composition, gross and microscopic gut morphometry, PCR and ENS - deidentified.
DOI: 10.6084/m9.figshare.4826737
title: DMLS_Periscope.STL

description: Periscope for DMLS manufacture for OCT imaging of autopsy eyes.
DOI: 10.6084/m9.figshare.4827373.v1
title: Effects of exogenous GLP-2 and distal bowel resection on intestinal and systemic adaptive responses in rats Raw Data.xlsx

description: Raw data for plasma hormone levels, body composition, gross and microscopic gut morphometry, PCR and ENS - deidentified.
DOI: 10.6084/m9.figshare.4828408.v2
title: Estimate of mortality reduction with implementation of advanced automatic collision notification

description: <b>Objective</b>: Advanced Automatic Collision Notification (AACN) is a system on a motor vehicle that notifies a public safety answering point (PSAP), either directly or through a third party, that the vehicle has had a crash. AACN systems enable earlier notification of a motor vehicle crash and provide an injury prediction that can help dispatchers and first responders make better decisions about how and where to transport the patient, thus getting the patient to definitive care sooner. The purposes of the current research are to identify the target population that could benefit from AACN, and to develop a reasonable estimate range of potential lives saved with implementation of AACN within the vehicle fleet. <b>Methods</b>: Data from the Fatality Analysis Reporting System (FARS) years 2009–2015 and National Automotive Sampling System–Crashworthiness Data System (NASS-CDS) years 2000–2015 were obtained. FARS data were used to determine absolute estimates of the target population who may receive benefit from AACN. These estimates accounted for a number of factors, such as whether a fatal occupant had nearby access to a trauma center and also was correctly identified by the injury severity prediction algorithm as having a “high probability of severe injury.” NASS-CDS data were used to provide relative comparisons among subsets of the population. Specifically, relative survival rate ratios between occupants treated at trauma centers versus at non-trauma centers were determined using the nonparametric Kaplan–Meier estimator. Finally, the fatality reduction rate associated with trauma center care was combined with the previously published fatality reduction rate for faster notification time to develop a range for possible lives saved. <b>Results</b>: Two relevant target populations were identified. A larger subset of 6893 fatalities can benefit only from earlier notification associated with AACN. A smaller subgroup of between 1495 and 2330 fatalities can benefit from both earlier notification and change in treatment destination (i.e., non-trauma center to trauma center). A Kaplan–Meier life curve and a multiple proportional hazard model were used to predict the benefits associated with transport to a trauma center. The resulting range for potential lives saved annually was 360 to 721. <b>Conclusions</b>: This analysis provides the estimates of lives that could potentially be saved with full implementation of AACN and universal cell coverage availability. This represents a fatality reduction of approximately 1.6% to 3.3% per year, and more than double the lives saved by earlier notification alone. In conclusion, AACN is a postcrash technology with a promising potential for safety benefit. AACN is therefore a key component of integrated safety systems that aim to protect occupants across the entire crash spectrum.
DOI: 10.6084/m9.figshare.4828408.v1
title: Estimate of mortality reduction with implementation of Advanced Automatic Collision Notification

description: <b>Objective</b>: Advanced Automatic Collision Notification (AACN) is a system on a motor vehicle that notifies a Public Safety Answering Point (PSAP), either directly or through a third party that the vehicle has had a crash. AACN systems enable earlier notification of a motor vehicle crash and provide an injury prediction that can help dispatchers and first responders make better decisions about how and where to transport the patient, thus getting the patient to definitive care sooner. The purpose of the current research is to identify the target population that could benefit from AACN, and develop a reasonable estimate range of potential lives saved with implementation of AACN within the vehicle fleet. <b>Methods</b>: Data from the Fatality Analysis Reporting System (FARS) years 2009–2015 and National Automotive Sampling System – Crashworthiness Data System (NASS-CDS) years 2000–2015 were obtained. FARS data were used to determine absolute estimates of the target population who may receive benefit from AACN. These estimates accounted for a number of factors, such as whether a fatal occupant had nearby access to a trauma center and also was correctly identified by the injury severity prediction algorithm as having a “high probability of severe injury”. NASS-CDS data were used to provide relative comparisons among subsets of the population. Specifically, relative survival rate ratios between occupants treated at trauma centers vs. non-trauma centers were determined using the non-parametric Kaplan-Meier estimator. Finally, the fatality reduction rate associated with trauma center care was combined with the previously published fatality reduction rate for faster notification time to develop a range for possible lives saved. <b>Results</b>: Two relevant target populations were identified. A larger subset of 6893 fatalities can benefit only from earlier notification associated with AACN. A smaller subgroup of between 1495 and 2330 fatalities can benefit from both earlier notification and change in treatment destination (i.e. non-trauma center to trauma center). A Kaplan-Meier life curve and multiple proportional hazard model were used to predict the benefits associated with transport to a trauma center. The resulting range for potential lives saved annually was 360 to 721. <b>Conclusions</b>: This analysis provides the estimates of lives that could potentially be saved with full implementation of AACN and universal cell coverage availability. This represents a fatality reduction of approximately 1.6% to 3.3% per year, and more than double the lives saved by earlier notification alone. In conclusion, AACN is a post-crash technology with a promising potential for safety benefit. AACN is therefore a key component of integrated safety systems that aim to protect occupants across the entire crash spectrum.
DOI: 10.6084/m9.figshare.4823530
title: Marchantia inflexa bacteriome: field habitat temperature and relative humidity

description: Environmental data was collected in June 2016. We monitored the relative humidity and temperature at each of 4 field sites on the island of Trinidad, Republic of Trinidad and Tobago at five minute intervals for 4-6 days (overlapping dates when possible) using sensors integrated in the WatchDog™ model 450 data logger (Spectrum® Technologies, Inc. Plainfield, IL, USA).
DOI: 10.6084/m9.figshare.4823587
title: QAPgenerator.tar.gz

description: Automatic instance generator for quadratic assignment problems with known optimal solution <br>
DOI: 10.6084/m9.figshare.4823530.v1
title: Marchantia inflexa bacteriome: field habitat temperature and relative humidity

description: Environmental data was collected in June 2016. We monitored the relative humidity and temperature at each of 4 field sites on the island of Trinidad, Republic of Trinidad and Tobago at five minute intervals for 4-6 days (overlapping dates when possible) using sensors integrated in the WatchDog™ model 450 data logger (Spectrum® Technologies, Inc. Plainfield, IL, USA).
DOI: 10.6084/m9.figshare.4823203
title: Facilitating Prediction of Adverse Drug Reactions by Using Knowledge Graphs and Multi-Label Learning Models

description: Data sets used in the experiments reported in the review article to predict adverse drug reactions.
DOI: 10.6084/m9.figshare.4823587.v1
title: QAPgenerator.tar.gz

description: Automatic instance generator for quadratic assignment problems with known optimal solution <br>
DOI: 10.6084/m9.figshare.4823212.v1
title: Inhibitory Stabilized Network models

description: Models of Inhibition Stabilized Networks in mammalian neocortex. Theoretical, firing-rate and spiking models of cortical networks with increasing realism, to explore how networks respond to perturbation of neural activity.<br>Provided as supplementary material to the paper Sadeh et al. 2017 (<i>in revision</i>).
DOI: 10.6084/m9.figshare.4823212.v2
title: Inhibitory Stabilized Network models

description: Models of Inhibition Stabilized Networks in mammalian neocortex. Theoretical, firing-rate and spiking models of cortical networks with increasing realism, to explore how networks respond to perturbation of neural activity.<br>Provided as supplementary material to the paper Sadeh et al. 2017 (<i>in revision</i>).
DOI: 10.6084/m9.figshare.4823026
title: Colour data from Human colour in mate choice and competition

description: Data on publications that have measured human colour
DOI: 10.6084/m9.figshare.4823026.v1
title: Colour data from Human colour in mate choice and competition

description: Data on publications that have measured human colour
DOI: 10.6084/m9.figshare.4822981
title: Supplemental Data S2

description: Nested random effects for the taxonomic categories (Order/Family/Species)<br>
DOI: 10.6084/m9.figshare.4822960
title: Supplementary Material for: Comparative Diagnostic Accuracy of the ACE-III, MIS, MMSE, MoCA, and RUDAS for Screening of Alzheimer Disease

description: <b><i>Background:</i></b> Our aim was to evaluate and compare the diagnostic properties of 5 screening tests for the diagnosis of mild Alzheimer disease (AD). <b><i>Methods:</i></b> We conducted a prospective and cross-sectional study of 92 patients with mild AD and of 68 healthy controls from our Department of Neurology. The diagnostic properties of the following tests were compared: Mini-Mental State Examination (MMSE), Addenbrooke's Cognitive Examination III (ACE-III), Memory Impairment Screen (MIS), Montreal Cognitive Assessment (MoCA), and Rowland Universal Dementia Assessment Scale (RUDAS). <b><i>Results:</i></b> All tests yielded high diagnostic accuracy, with the ACE-III achieving the best diagnostic properties. The area under the curve was 0.897 for the ACE-III, 0.889 for the RUDAS, 0.874 for the MMSE, 0.866 for the MIS, and 0.856 for the MoCA. The Mini-ACE score from the ACE-III showed the highest diagnostic capacity (area under the curve 0.939). Memory scores of the ACE-III and of the RUDAS showed a better diagnostic accuracy than those of the MMSE and of the MoCA. All tests, especially the ACE-III, conveyed a higher diagnostic accuracy in patients with full primary education than in the less educated group. Implementing normative data improved the diagnostic accuracy of the ACE-III but not that of the other tests. <b><i>Conclusions:</i></b> The ACE-III achieved the highest diagnostic accuracy. This better discrimination was more evident in the more educated group.