Find research datasets worth reusing

Development of a machine learning model to predict non- durable response to anti-TNF therapy in Crohn's disease using transcriptome imputed from genotypes

This is the expression value predicted using PrediXcan version 7 to find a gene feature that can distinguish between patients with and without effect on infliximab. Among the various tissue models provided by PrediXcan v7, three models were selected and used: whole blood, Colon transverse, and terminal ileum of small intestine, and the predicted gene counts of each model were 6,294, 5,612 and 3,107. For each of the three models, predicted gene expression values and phenotype information per sample were submitted.

opencc-zeroApr 2022View details →

Data from: Improving inferences and predictions of species environmental responses with occupancy data

Occupancy models represent a useful tool to estimate species distribution throughout the landscape. Among them, MacKenzie et al.'s model (2002, MC), is frequently used to infer species environmental responses. However, the assumption that detection probability is homogeneous or fully explained by covariates may limit its performance. Species should be more easily observed at sites with a higher number of individuals. We simulated data following Royle and Nichols (2003) occupancy model (RN) that accounts for abundance-driven heterogeneous detection and two variants with overdispersion in the detection probability and local abundances. Then, we compared the performance of the MC model against that of RN. In addition to model misspecifications, insufficient information in data (i.e. infrequent detections) can limit our ability to detect existing effects with affordable sampling designs. To deal with this source of error, we extended RN approach to a community-level joint species model (RN-JSM), where species responses and detectability depended on their traits and phylogeny. Then, we tested RN-JSM performance in simulated and out-of-sample field data. High abundance-driven heterogeneity in detection (i.e. common and secretive species) limited the ability of the MC model to quantify covariate effects; especially, when the number of visits was low. Both models (MC and RN), often failed to detect existing effects when data were overdispersed. Moreover, the RN model consistently lacked sufficient power when analyzing data from uncommon species (even when simulations and model specifications perfectly matched). This problem was solved by our RN-JSM, which yielded more precise and accurate estimates of species environmental responses. Increased accuracy in rare species held when the RN-JSM was tested with real and out-of-sample datasets. In the light of our results, we propose: (i) for common and secretive species analyze occupancy data with the RN model and prioritize revisiting sites; (ii) for species that may have overdispersed detectability or local abundances (e.g. with correlated behaviors or occurring in clusters), apply RN extensions that account for this extra variation (e.g. Poisson-beta or zero-inflated models). Finally, (iii) for uncommon species (mean abundances < 1), whenever possible, gather data at the community level and apply joint-species modeling techniques.

Estimation of groundwater flow rate by an actively heated fiber optics based thermal response test in a grouted borehole

The dataset contains the numerical data and the in-situ measurements in the manuscript titled "Estimation of groundwater flow rate by an actively heated fiber-optics-based thermal response test in a grouted borehole". The data is stored in MAT files, which are Binary MATLAB files. There are a series of codes used in this manuscript to estimate groundwater flow rates. The codes were written in MATLAB Live Script, version 2021b. <ul> <li>The numerical data contains temperatures of the heating stage in different thermal response tests in a numerical model, which considers the borehole effects. The model is set up by COMSOL Multiphysics, and a series of flow rates is set to the model respectively for different thermal response tests.</li> <li>The in-situ measurements include temperatures of the heating stage in an actively heated fiber-optics-based thermal response test, which was performed in July 2021 in the grouted borehole, which is located in the lower section of the Sima bend of the Yangtze River. The temperature for the flow rate estimation was thinned to 120 s records from 10s records for the limited computing resources.</li> <li>The data_process.mlx provides pre-processing for the observational data recorded by Silixa Ultima-M MK2 DTS. The estimation_process.mlx gives a groundwater flow estimation case in a grouted borehole.</li> </ul>

opencc-zeroApr 2022View details →

Interactions among multiple stressors vary with exposure duration and biological response

Coastal ecosystems are exposed to multiple anthropogenic stressors. Effective management actions would be better informed from generalized predictions of the individual, combined and interactive effects of multiple stressors; however, few generalities are shared across different meta-analyses. Using an experimental study, we present an approach for analysing regression-based designs with generalized additive models that allowed us to capture nonlinear effects of exposure duration and stressor intensity and access interactions among stressors. We tested the approach on a globally distributed marine diatom, using 72 h photosynthesis and growth assays to quantify the individual and combined effects of three common water quality stressors; photosystem II-inhibiting herbicide exposure, dissolved inorganic nitrogen (DIN) enrichment and reduced light (due to excess suspended sediment). Exposure to DIN and reduced light generally resulted in additivity, while exposure to diuron and reduced light resulted in additive, antagonistic or synergistic interactions, depending on the stressor intensity, exposure period and biological response. We thus find the context of experimental studies to be a primary driver of interactions. The experimental and modelling approaches used here bridge the gap between two-way designs and regression-based studies, which provides a way forward to identify generalities in multiple stressor interactions.

Manhattan and QQ plots of GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)

The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>. The raw GWAS outputs can be found <a href="https://zenodo.org/badge/DOI/10.5281/zenodo.5856310.svg">here</a>. This dataset represents Manhattan plots and QQ plots made out of the data.

A comparison of the World Health Organisation's HEAT model results using a non-linear physical activity dose response function with results from the existing tool

Datasets relating to the Wellcome Open Research publication of the same name.

opencc-by-4.0Dec 2021View details →

Data to reproduce the results presented in Sehgal et al. 2022. Water Resources Research, https://doi.org/10.1029/2021WR030624 ("Inferring suspended sediment carbon content and particle size at high-frequency from the optical response of a submerged spectrometer")

This repository consists data to reproduce results as presented in: "Inferring suspended sediment carbon content and particle size at high-frequency from the optical response of a submerged spectrometer", Water Resorces Research. Kindly refer to the readme.text file to navigate through the dataset.

opencc-zeroMay 2022View details →

β-cell-specific deletion of Zfp148 improves nutrient-stimulated β-cell Ca2+ responses

Insulin secretion from pancreatic β-cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β-cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. Here, we performed Ca2+ imaging of islets from β‑Zfp148KO and control mice on both a chow and a Western-style diet. β-Zfp148KO islets demonstrate improved sensitivity and sustained Ca2+ oscillations in response to elevated glucose. β-Zfp148KO islets also exhibit elevated sensitivity to amino acid-induced Ca2+ influx under low glucose conditions, suggesting enhanced mitochondrial phosphoenolpyruvate (PEP)-dependent KATP channel closure, independent of glycolysis. RNA sequencing and proteomics of β-Zfp148KO islets revealed altered levels of enzymes involved in amino acid metabolism (SLC3A2, SLC7A8, GLS, GLS2, PSPH, PHGDH, PSAT1) and intermediary metabolism (GOT1, PCK2), consistent with altered PEP cycling. In agreement with this, β-Zfp148KO islets displayed enhanced insulin secretion in response to L-glutamine and activation of glutamate dehydrogenase. Understanding pathways controlled by ZFP148 may provide promising strategies for improving β-cell function that are robust to the metabolic challenge imposed by a Western diet.

opencc-zeroMay 2022View details →

Optomotor response (eye movment) and avoidance responses (locomotor activity) of crabs Neohelice granulata for LP-lesioned, control lesioned and control crabs

When an animal rotates (whether it is an arthropod, a fish, a bird, or a human) a drift of the visual panorama occurs over its retina, termed optic flow. The image motion is stabilized by compensatory behaviors (driven by the movement of the eyes, head or the whole body depending on the animal) collectively termed optomotor response (OR). Dipteran lobula plate has been consistently linked with optic flow processing and the control of optomotor responses. Crabs have a neuropil similarly located and interconnected in the optic lobes, therefore referred to as a lobula plate also. Here we show that the crab's lobula plate is required for normal optomotor response since the response was lost or severely impaired in animals whose lobula plate had been lesioned. The effect was behavior-specific, since avoidance responses to approaching visual stimuli were not affected. Crabs require simpler optic flow processing than flies (because they move slower and in 2D instead of 3D), consequently their lobula plates are relatively smaller. Nonetheless, they perform the same essential role in the visual control of behavior. Our findings add a fundamental piece to the current debate on the evolutionary relationship between the lobula plates of insects and crustaceans.

opencc-zeroMay 2022View details →

Dataset, statistical analysis code, and supplementary material of juvenile ravens' responses towards acoustic cues of different social categories

Social competence i.e., defined as the ability to adjust the expression of social behaviour to the available social information, is known to be influenced by early-life conditions. Brood size might be one of the factors determining such early conditions, particularly in species with extended parental care. We here tested in ravens, whether growing up in families of different sizes affects the chicks' responsiveness to social information. We experimentally manipulated the brood size of 20 captive raven families, creating either small or large families. Simulating dispersal, juveniles were separated from their parents and temporarily housed in one of two captive non-breeder groups. After five weeks of socialization, each raven was individually tested in a playback setting with food-associated calls from three social categories: sibling, familiar unrelated raven they were housed with, and unfamiliar unrelated raven from the other non-breeder aviary. We found that individuals reared in small families were more attentive than birds from large families, in particular towards the familiar unrelated peer. These results indicate that variation in family size during upbringing can affect how juvenile ravens value social information. Whether the observed attention patterns translate into behavioural preferences under daily life conditions remains to be tested in future studies.

TPE-MI reveals proteome remodelling in response to pharmacological stimuli

Dataset contains raw and preprocessed data for fluorescence and proteomic studies respectively. In each case, protein foldedness was probed using thiol reactivity. The raw mass spectrometry proteomics data have also been deposited to the ProteomeXchange Consortium via the PRIDE partner repository, with the dataset identifiers PXD033152.

A dataset of measured spatial room impulse responses in different rooms including visualization

An open-source dataset of captured spatial room impulse responses (SRIRs) is presented. The data was collected in different enclosed spaces at the Technische Universität Ilmenau using an open self-build microphone array design following the spatial decomposition method (SDM) guidelines. The included rooms were selected based on their distinctive acoustical properties resulting from their general build and furnishing as required by their utility. Three different classes of spaces can be distinguished, including seminar rooms, offices, and classrooms. For each considered space different source-receiver positions were recorded, including 360° images for each condition. The dataset can be utilized for various augmented or virtual reality applications, using either a loudspeaker or headphone-based reproduction alongside the appropriate head-related transfer function sets. In future, we plan to add more rooms and more source-receiver positions. Please cite our corresponding paper: Klein, F., Surdu, T., Aretz, A., Birth, K., Edelmann, N., Seitelman, F., Ziener, C., Werner, S., and Sporer, T., “A dataset of measured spatial room impulse responses in different rooms including visualization,” in 152nd AES Convention, 2022, https://www.aes.org/e%E2%80%90lib/browse.cfm?elib=21728

Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing

Circulating tumor DNA (ctDNA) in blood may become a generic biomarker for non-invasive cancer diagnosis and monitoring. However, detection of ctDNA is challenged by the presence of many circulating DNA molecules from healthy cells. We found that single ctDNA molecules can be sequenced with high accuracy by a three-step process consisting of capturing, copying and concatenation of the original double-stranded ctDNA molecules. This innovative approach - called CyclomicsSeq -  is unparalleled by any other method in terms of cost-efficiency and speed, allowing point-of-care cancer diagnostics. Within this CPOC, subsidized by the Oncode institute, we have applied our CyclomicsSeq ctDNA test in patients with advanced head and neck cancer squamous cell carcinoma (HNSCC). Head and neck cancer (HNSCC) accounts for 380,000 cancer-related deaths worldwide. For these patients, determining whether a patient responds to the primary chemoradiation treatment is challenging, and non-responders are sometimes identified when other treatment options are no longer possible. By measuring the ctDNA levels in the blood of these patients prior to and during treatment, we aim to identify non-responders at an earlier stage. This dataset contains base calls of TP53 of 47 nanopore sequencing runs. We included 10 patients and 7 controls. For the patients, we have samples of multiple time points (0 = prior to treatment, 1 = 1 week after treatment initiation, etc).

Dataset: The effect of hydrogen enrichment, flame-flame interaction, confinement, and asymmetry on the acoustic response of a model can combustor

Complementary dataset for the article: The effect of hydrogen enrichment, flame-flame interaction, confinement, and asymmetry on the acoustic response of a model can combustor. This document provides a brief description of datasets associated with the paper by Æsøy et al. [1]. The datasets contain flame shapes, flame transfer functions (FTFs), and time series data for perfectly premixed methane/hydrogen/air flames operated in a model can combustor (see [1] for more details). The data is divided into four main categories listed below. Each of these are described in the read-me file in the subsequent sub-folder. • FTF flame interaction: The level of flame interaction was systematically varied through varying the spacing between flames and by varying the level of hydrogen enrichement of the fuel. • FTF confinement: The level of wall confinement was varied by varying the combustion chamber diameter. • FTF symmetry: The flame symmetry was varied through equipping the can with different injector geometries. • Time series: Time series data of pressure and heat release rate taken with different hydrogen concentrations and combustion chamber lengths. [1] E. Æsøy, T. Indlekofer, F. Gant, A. Cuquel, M. R. Bothien, J. R. Dawson, The effect of hydrogen enrichment, flame-flame interaction, confinement, and asymmetry on the acoustic response of a model can combustor, Combustion and Flame 242 (2022) 112176.

opencc-by-4.0Feb 2022View details →

Climate Response to ~23% Albedo Reduction in IPSL-CM5A2-LR

The dataset consists of IPSL-CM5A2-LR outputs from a present-day control (pdControl, Con) and 23% Arctic sea ice albedo reduction experiment (Alb). Both sets of experiments are annual means for 200 years of simulation. The Con has 12 members from two restarts (7 and 5) and the Alb experiment has 14 members from the same restarts (9 and 5). Annual datasets include: Winter (JFM) and summer (JAS) sea ice area fraction (SIA), Atlantic overturning streamfunction (zomsfatl,msftrho), sea level pressure (SLP), sea surface temperature (TOS), sea surface salinity (SOS), barotropic streamfunction (BSF), zonal windstress (TAUX), and meridional windstress (TAUY). Since there are two restarts from different model years, the time axis has been changed to count years of the experiment (i.e. 1,2,3,...200). The anomalies of the Alb experiment are also provided taking into account the respective control. The missing data is recorded as nan. The datasets are created from the IPSL-CM5A-LR output files, using CDO and Python3 commands to combine and create annual averages.

opencc-byJun 2022View details →

Piñon and Juniper Tree Removal Increases Available Soil Water, Driving Understory Response in a Sage-Steppe Ecosystem

This posting includes the dataset and accompanying metadata (variable definitions) used for analyses in the paper entitled, 'Pinon and Juniper Tree Removal Increases Available Soil Water, Driving Understory Response in a Sage-Steppe Ecosystem, to be published in Ecosphere, as part of the 'SageSTEP' Special Feature.

Characterization of the nuclear proteome of Chlamydomonas in response to salt stress

Supplementary Files and Figures for the manuscript "Characterization of the nuclear proteome of Chlamydomonas in response to salt stressCharacterization of the nuclear proteome of Chlamydomonas in response to salt stress"

opencc-by-4.0Jun 2022View details →

Hippocampal CA1 pyramidal cell membrane voltage recorded in response to noise stimuli at two temperatures.

Electrophysiological recording of the membrane voltage (whole-cell patch-clamp) of three hippocampal CA1 pyramidal cells. Cells are stimulated with a current step chosen to ensure a firing rate around 5-10Hz (amplitude of the current step is given in the filenames) and a noise stimulus with zero mean (Ornstein-Uhlenbeck process with 4ms timescale). Each CSV file contains three columns, the timepoints (saved at 10000Hz), the noise stimulus, and the voltage trace recorded in response to the given noise stimulus. Voltages are recorded at low temperatures (around 32 degrees Celsius) and at high temperatures (around 37 degrees Celsius for cell 1, around 40 degrees Celsius for cells 2 and 3), exact temperatures are given in the filenames. The file metadata.csv contains additional information.

opencc-zeroJun 2022View details →

Nitrogen availability determines ecosystem productivity in response to climate warming

One of the major uncertainties for carbon-climate feedback predictions is an inadequate understanding of the mechanisms governing variations in ecosystem productivity response to warming. Temperature and water availability are regarded as the primary controls over the direction and magnitude of warming effects, but some unexplained results signal that our understanding is incomplete. Using two complementary meta-analyses, we present evidence that soil nitrogen (N) availability drives the warming effects on ecosystem productivity more strongly than thermal and hydrological factors over a broad geographical scale. First, by synthesizing temperature manipulation experiments, meta-regression model analysis showed that the warming effect on productivity is mainly driven by its effect on soil N availability. Sites with higher warming-induced increase in N availability were characterized by stronger productivity enhancement and vice versa, suggesting that N is a limiting factor across sites. Second, a synthesis of full-factorial warming×N addition experiments demonstrated that N addition significantly weakened the positive warming effect, because the additional N induced by warming may not further benefit plant growth when N limitation is relieved, providing experimental evidence that N regulates the warming effect. Further, we demonstrated that warming effects on soil N availability were modulated by changes in dissolved organic N and soil microbes. Overall, our findings enrich a new mechanistic understanding of the varying magnitudes of observed productivity response to warming, and the N scaling of warming effects may help constrain climate projections.

Unexpected microbial metabolic responses to elevated temperatures and nitrogen addition in subarctic soils under different land-use

This repository contains all necessary raw data as well as the R code used to conduct statistical analysis and create figures of the publication   Unexpected microbial metabolic responses to elevated temperatures and nitrogen addition in subarctic soils under different land-useJulia Schroeder1, Tino Peplau1, Edward Gregorich2, Christoph C. Tebbe3, Christopher Poeplau11 Thünen Institute of Climate-Smart Agriculture, Bundesallee 68, 38116 Braunschweig, Germany 2 Research and Development Centre, Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada 3 Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, GermanyDOI: https://doi.org/10.1007/s10533-022-00943-7 This study investigated how subarctic soils under different land use will respond to warming and increasing N availability to allow for better predictions of C cycling under global change. The short-term temperature sensitivity as well as N-input effects on microbial CUE, respiration, growth and turnover were assessed in a one-day incubation experiment according to the 18O-CUE approach. The warming and N response of SOM decomposition were assessed in a 50-days incubation experiment via measurement of cumulative respiration. Both experiments were conducted with the following three treatments: incubation at 10 °C, incubation at 20 °C, and incubation at 20 °C plus N-fertiliser addition at an amendment rate of 100 kg N ha-1. The response to warming or N addition were expressed as response ratios RRT = 20°C/10°C and RRN = 20°C+N/20°C for warming and N response, respectively.The R code was developed under R v3.6.3 and adapted to work under version R v.4.1.2.The repository includes the following files:<ul><li>general_soil_parameters_per_sample.csv - general soil data for each field sample (n=27)</li><li>general_soil_parameters_per_plot.csv - general soil data assessed on pooled replicated field samples (n=9)</li><li>respiration_over_50d_incubation.csv - respiration rate and cumulative respiration for each time-point and laboratory sample over the 50-days incubation</li><li>sample_data.csv - data measured for each laboratory sample (n=81)</li></ul> <ul><li>Warming_and_nitrogen_response_of_CUE_in_subarctic_soils.Rproj - Rproject (load project to work on provided scripts and data)</li><li>load_data_script.R - loads required data</li><li>absolute_values_script.R - summary of absolute ranges of parameters per land-use type and site</li><li>absolute_linear_mixed_effects_model_script.R - run statistical analysis</li><li>correlograms_absolute_soil_params_script.R - correlation analysis to identify what drives absolute values</li><li>plot_correlations_absolute_soil_params_script.R - plot drivers of CUE and cumulative respiration</li><li>RRT_RRN_calculation_script.R - calculates response ratios</li><li>plot_RRT_RRN_script.R - plot response ratios</li><li>RRT_RRN_linear_mixed_effects_models_script.R - run statistical analysis</li><li>correlograms_RRT_RRN_soil_param_script.R - correlation analysis to identify drivers of response ratios</li><li>plot_correlations_RRT_RRN_soil_params_script.R - plot drivers of response ratios</li><li>RRT_RRN_resprate_cumulresp_over_time_50d_incubation_script.R - plot response ratios over time course</li></ul>