Find research datasets worth reusing

Data for GMD article: "Towards an improved treatment of cloud-radiation interaction in weather and climate models: exploring the potential of the Tripleclouds method for various cloud types using libRadtran 2.0.4"

Dataset for the publication by Nina Črnivec and Bernhard Mayer: "Towards an improved treatment of cloud-radiation interaction in weather and climate models: exploring the potential of the Tripleclouds method for various cloud types using libRadtran 2.0.4" submitted to Geoscientific Model Development in 2020. The repository contains data for stratocumulus, cirrus and cumulonimbus cloud case studies. It also contains MYSTIC benchmark radiation data (including atmosphering heating rate and net surface flux) for the aforementioned cloud cases. See README for additional information and description of data files.

Data and Code for: Comparative species abundance modeling of Capitellidae (Annelida) in Tampa Bay, Florida, USA

This publication contains the R-Scripts, RData, data frames, and other supplementary files necessary to reproduce the analyses and figures of Hilliard J, Karlen D, Dix T, Markham S, Schulze A (2020) Comparative species abundance modeling of Capitellidae (Annelida) in Tampa Bay, Florida, USA. Mar Ecol Prog Ser 653:105-119. <a href="https://doi.org/10.3354/meps13484">https://doi.org/10.3354/meps13484</a> All files are compressed into a single ZIP folder. The main directory contains a README file that explains the contents of the subdirectories.

Data Tables from contribution titled "Joint geophysical-petrological modeling on the Ivrea geophysical body beneath Valsesia, Italy: Constraints on the continental lower crust" published in Geochemistry, Geophysics, Geosystems

TABLE CAPTIONS Table 1: Average and specific bulk compositions of the representative exposed primitive rocks of the deep lower crust and upper mantle of the IVZ (Balmuccia and Lower Mafic Complex in Valsesia, Finero in Val Cannobina, and Sessera river in Val Sessera) used for the Perple_X calculations using the two thermodynamic models STX11 and HP02. Mn, Ni, P, and Cr were not used for the Perple_X calculations. Mg# is calculated as Mg / (Mg + Fe) (mole fractions). Symbols in the last row indicate the rock compositions that are reported (✓) and not reported (✗) in Figure 5. Average compositions are normalized to 100 wt.% on a volatile-free basis; specific compositions report original totals and H2O contents estimated based on the volumetric proportions hydrous minerals (amphibole and phlogopite) at the scale of the bulk rock. References: 1) Voshage et al. (1990); 2) Voshage et al. (1990), Shervais and Mukasa (1991), Hartmann and Wedepohl (1993), Rivalenti et al. (1995), and Mukasa and Shervais (1999); 3) Pin and Sills (1986); 4) Pin and Sills (1986), Shervais and Mukasa (1991), Hartmann and Wedepohl (1993), Rivalenti et al. (1995), and Mukasa and Shervais (1999); 5) Shervais and Mukasa (1991) and Mazzucchelli et al. (2009); 6) Sinigoi et al. (1991; 2011); 7) Hartmann and Wedepohl (1993); 8) Coltorti and Siena (1984); 9) Siena and Coltorti (1989), Lu et al. (1997a; b), and Stähle et al. (2001).   Table 2: Summary of VP and r from the thermodynamic calculations based on representative rock compositions listed in Table 1. Mineral abbreviations: Pl = plagioclase, Spl = spinel, Grt = garnet, Ky = kyanite, Px = pyroxene, Cr-Di = Cr-diopisde, Am = amphibole, Phl = phlogopite.

Data for "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics"

Experimental and precomputed data for the paper "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics" by Oesterle et al. 2020 (DOI: <a href="https://doi.org/10.7554/eLife.54997">10.7554/eLife.54997</a>). The cone bipolar cell data has been described and published in the paper "Inhibition decorrelates visual feature representations in the inner retina" by Franke et al. 2017 (DOI: <a href="https://doi.org/10.1038/nature21394">10.1038/nature21394</a>).  This data is both a supplement to the Oesterle et al. paper and the code for this paper. The code is available in this <a href="http://github.com/berenslab/CBC_inference">GitHub repository</a>. We recommend downloading the GitHub repository and to follow the instructions there.

opencc-zeroDec 2019View details →

Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size

Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites. Despite the extensive literature pertaining to host-parasite coevolution, the dynamics of genetic variation has not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone. The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally. By comparing host heterozygosity to the expectation in a single-species model of neutral genetic drift we find that while this is also largely true in finite populations two additional phenomena arise. First, reciprocal natural selection acting on stochastic perturbations in host and pathogen allele frequencies results in a slight increase or decrease in genetic variation depending on the parameter conditions. Second, following the fixation of an allele in the parasite, selection in the MAM becomes directional, which then rapidly erodes genetic variation in the host. Hence, rather than maintain it, we find that, on average, matching-alleles coevolution depletes genetic variation.

Data regarding the application of the inverse modeling (TsuSedMod) to the sediment deposits of CE 1755 Lisbon tsunami at Salgados, Algarve (Portugal)

This dataset contains data used to run TsuSedMod model. It contains the vertical textural distribution of 4 sediment samples (LV09, LV11,LV11a and LV13) retrieved at Salgados, southern Portugal and respective results.

opencc-zeroNov 2020View details →

Data from: Models of community-based primary care for epilepsy in low and middle income countries

Objective: To review systematically community-based primary care interventions for epilepsy in low and middle income countries to rationalize approaches and outcome parameters in relation to epilepsy care in these countries. Methods: A systematic search of PubMed, EMBASE, Global Index Medicus, CINAHL and Web of Science was undertaken to identify trials and implementation of provision of anti-seizure medications, adherence reinforcement and/or healthcare provider or community education in community-based samples of epilepsy. Data on populations addressed, interventions and outcomes were extracted from eligible articles. Results: Twenty-four reports were identified, mostly care programs addressing active convulsive epilepsy. Phenobarbital has been used most frequently though other conventional antiseizure medications have also been used but none of the newer. Tolerability rates in these studies are high but overall, attrition is considerable. Other approaches have included updating primary health care providers, reinforcing treatment adherence in clinics and raising community awareness. The coverage of existing treatment gap in the community, epilepsy-related mortality and comorbidity burden are fleetingly addressed in these programs. Conclusions: The cost-free provision, mostly of phenobarbital has resulted in short-term seizure freedom in roughly half of the people with epilepsy in LMICs. Future programs should include a range of antiseizure medications. These should cover apart from seizure control and treatment adherence, primary healthcare provider education, raising community awareness and referral protocols for specialist care. The programs should ensure sustainability and impact assessment at a community level.

opencc-zeroDec 2019View details →

Data for: Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models

Antagonistic coevolution has long been suggested to help maintain host genetic variation. While, ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. We find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the chance of allele fixation in the pathogen, as this results in directional selection and depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of allele fixation in the pathogen, especially in epidemiological models. Our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.

Standard Bouguer anomaly model achieved by multi-source Bouguer gravity anomaly Bayesian data fusion algorithm in Sichuan-Yunnan region

* Method: Based on the equivalent source inversion and Bayesian uncertainty quantization theory, a new multi-source gravity data fusion algorithm is developed, which effectively solves the multi-source data fusion problem with different noise and datum. * Standard Bouguer anomaly is Fused from WGM2012 Bouguer gravity anomaly model and 394 gravity profile data measured in Sichuan-Yunnan region. Fusion anomaly results can eliminate datum draft between multi-source gravity and reduce incoherent noise. * Spatial resolution of the standard Bouguer anomaly is about 20 kilometers. * Correcting deviations means the difference between the fused standard Bouguer anomaly model and the WGM2012 Earth gravity model.

opencc-zeroDec 2020View details →

Data from: Climate limitation at the cold edge – contrasting perspectives from species distribution modelling and a transplant experiment

The role of climate in determining range margins is often studied using species distribution models (SDMs), which are easily applied but have well-known limitations, e.g. due to their correlative nature and colonization and extinction time lags. Transplant experiments can give more direct information on environmental effects, but often cover small spatial and temporal scales. We simultaneously applied an SDM using high-resolution spatial predictors and an integral projection (demographic) model based on a transplant experiment at 58 sites to examine the effects of microclimate, light and soil conditions on the distribution and performance of a forest herb, Lathyrus vernus, at its cold range margin in central Sweden. In the SDM, occurrences were strongly associated with warmer climates. In contrast, only weak effects of climate were detected in the transplant experiment, whereas effects of soil conditions and light dominated. The higher contribution of climate in the SDM is likely a result from its correlation with soil quality, forest type, and potentially historic land use, which were unaccounted for in the model. Predicted habitat suitability and population growth rate, yielded by the two approaches, were not correlated across the transplant sites. We argue that the ranking of site habitat suitability is probably more reliable in the transplant experiment than in the SDM because predictors in the former better describe understory conditions, but that ranking might vary among years, e.g. due to differences in climate. Our results suggest that L. vernus is limited by soil and light rather than directly by climate at its northern range edge, where conifers dominate forests and create suboptimal conditions of soil and canopy-penetrating light. A general implication of our study is that to better understand how climate change influences range dynamics, we should not only strive to improve existing approaches but also to use multiple approaches in concert.

opencc-zeroDec 2020View details →

Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer's disease

Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sleep in males more so than in females. Diffuse TBI was induced in C57BL/6J mice and serial blood samples were collected (baseline, 1, 5, 7 days post‐injury [DPI]) to quantify peripheral immune cell populations and sleep regulatory cytokines. Brains and spleens were harvested at 7DPI to quantify central and peripheral immune cells, respectively. Mixed‐effects regression models were used for data analysis. Female TBI mice had 77%–124% higher IL‐6 levels than male TBI mice at 1 and 5DPI, whereas IL‐1β and TNF‐α levels were similar between sexes at all timepoints. Despite baseline sex differences in blood‐measured Ly6Chigh monocytes (females had 40% more than males), TBI reduced monocytes by 67% in TBI mice at 1DPI. Male TBI mice had 31%–33% more blood‐measured and 31% more spleen‐measured Ly6G+ neutrophils than female TBI mice at 1 and 5DPI, and 7DPI, respectively. Compared with sham, TBI increased sleep in both sexes during the first light and dark cycles. Male TBI mice slept 11%–17% more than female TBI mice, depending on the cycle. Thus, sex and TBI interactions may alter the peripheral inflammation profile and sleep patterns, which might explain discrepancies in disease progression based on sex.

model data of 90 ma

modeling data for the Asia

Dataset accompanying paper submission for "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"

This data set accompanies code archived at DOI: <a href="https://doi.org/10.5281/zenodo.3833186">10.5281/zenodo.3833186</a>, which was used in the experiments for the paper submission "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"

opencc-zeroDec 2020View details →

Data from: Implementation of Option B and a fixed-dose combination antiretroviral regimen for prevention of mother-to-child transmission of HIV in South Africa: a model of uptake and adherence to care

Introduction Initiating and retaining pregnant women on antiretroviral therapy (ART) to prevent mother-to-child HIV transmission (PMTCT) remains a major challenge facing African HIV programs, particularly during the critical final months prior to delivery. In 2013, South Africa implemented its "Option B" PMTCT regimen (three-drug ART throughout pregnancy and breastfeeding, regardless of maternal CD4 count) and introduced once-daily fixed-dose combinations and lifelong ART. Currently, the uptake of Option B and its possible impact on adherence to PMTCT during the critical final months of pregnancy is unclear. Materials and Methods We prospectively collected visit data from a cohort of adult, HIV-infected, pregnant women between July 2013-August 2014 to estimate three models of adherence to PMTCT during the final 16 weeks immediately preceding delivery. Adherence was defined according to possession of antiretroviral drugs, which was inferred from clinic visit records under varying assumptions in each model. We describe uptake of the PMTCT regimen, gestational age at initiation, and model possible scenarios of adherence through delivery after the implementation of Option B. Results Among 138 women enrolled (median (IQR) age 28 years (24-32), median CD4 count 378 cells/mm3), median (IQR) gestational age at initiation was 22 weeks (16-26). Estimates of adherence during the final 16 weeks of pregnancy prior to delivery ranged from 75% (52-89%) under the best case scenario assumptions to 52% (30-75%) under the worst case scenario assumptions. Estimates of the proportion of women who would achieve 80% adherence to PMTCT were <50% across all models. Conclusions Despite the switch to Option B and once-daily dosing, South African women continue to initiate PMTCT late in pregnancy, and estimations of regimen adherence, as modelled using PMTCT visit attendance data, is poor, with <50% of women reaching 80% adherence during final months of pregnancy across all models. Further guideline changes and interventions are needed to achieve vertical transmission goals. Trial Registration This study was nested within the original RapIT randomized controlled trial which was registered on ClinicalTrials.gov (Registration number) NCT01710397 on September 7, 2012 and the South African National Clinical Trials Register DOH-27-0213-4177. The first participant in the RapIT study was enrolled on May 8th, 2013.

opencc-zeroDec 2017View details →

Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation

Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.

opencc-byDec 2020View details →

Data for manuscript: An ecogeomorphic framework coupling sediment modeling with invasive riparian vegetation dynamics

Datasets (aside from the publicly available GIS datasets) used in the analyses presented in the manuscript "An ecogeomorphic framework coupling sediment modeling with invasive riparian vegetation dynamics."

opencc-by-4.0Jan 2021View details →

Data for: Free-Breathing Water, Fat, R2∗ and B0 Field Mapping of the Liver Using Multi-Echo Radial FLASH and Regularized Model-based Reconstruction (MERLOT)

Data for our manuscript with title "Free-Breathing Water, Fat, R2&lowast; and B0 Field Mapping of the Liver Using Multi-Echo Radial FLASH and Regularized Model-based Reconstruction (MERLOT)"

Status quo in data availability and predictive models of nano-mixture toxicity

Supplementary materials for manuscript: Status quo in data availability and predictive models of nano-mixture toxicity. This table contains the list of 183 curated literature used in this study.

opencc-zeroJan 2021View details →

Data from: Habitat modeling of Irrawaddy dolphins (Orcaella brevirostris) in the eastern Gulf of Thailand

Aim: The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean found throughout Southeast Asia. The main threat to this species is human encroachment, led by entanglement in fishing gear. Information on this data-poor species' ecology and habitat use is needed to effectively inform spatial management. Location: We investigated the habitat of a previously unstudied group of Irrawaddy dolphins in the eastern Gulf of Thailand, between the villages of Laem Klat and Khlong Yai, in Trat Province. This location is important as government groups plan to establish a marine protected area. Methods: We carried out boat-based visual line transect surveys with concurrent oceanographic measurements and used hurdle models to evaluate this species' patterns of habitat use in this area. Results: Depth most strongly predicted dolphin presence, while temperature was a strong predictor of group size. The highest probability of dolphin presence occurred at around 10.0 m with an optimal depth range of 7.50 to 13.05 m. The greatest number of dolphins was predicted at 24.93oC with an optimal range between 24.93 and 25.31oC. Dolphins are most likely to occur in two primary locations, one large region in the center of the study area (11o54'18"N to 11o59'23"N) and a smaller region in the south (11o47'28"N to 11o49'59"N). Protections for this population will likely have the greatest chance of success in these two areas. Main Conclusions: The results of this work can inform management strategies within the immediate study area by highlighting areas of high habitat use that should be considered for marine spatial planning measures, such as the creation of marine protected areas. Species distribution models for this species in Thailand can also assist conservation planning in other parts of the species' range by expanding our understanding of habitat preferences.