Find research datasets worth reusing

DoTA-seq processed datasets (barcode: read mappings)

Processed DoTA-seq sequencing reads to generate barcode: read mapping tables. This data is further processed to generate figures 1-3.

Data for 'Using 40 years of spot measurements to assess stream temperature response and recovery for different harvesting systems in northern hardwood forests' by Jason Leach, Danielle Hudson and R. Dan Moore. Submitted to Hydrological Processes.

This dataset contains spot stream temperature measurements taken at 5 headwater streams draining forested hillslopes (C31, C32, C33, C34, C35) in the Turkey Lakes Watershed, approximately 65 km northwest of Sault Ste. Marie, Ontario, Canada.

Datasets and Code for "Hypothesis Tests with Functional Data for Surface Quality Change Detection in Surface Finishing Processes"

This is the set of data and computer code used for reproducing the results in Jin, Tuo, Tiwari, Bukkapatnam, Aracne-Ruddle, Lighty, Hamza, and Ding, 2022, “Hypothesis tests with functional data for surface quality change detection in surface finishing processes,” IISE Transactions, in press.

opencc-zeroMay 2022View details →

Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains - Ecological Niche Modeling and Corridors files

Aim Ancient climatic fluctuations are invoked as the main driving force that generates the astonishing biodiversity in ancient mountains. As a result, endemism and spatial turnover are usually high and few species are widespread among entire mountain ranges, precluding the understanding of origins of macroevolutionary patterns. Here, we used a species endemic to, but widespread in, one of the most species-rich ancient mountains on the globe to test how environmental changes acted on them and how their macroevolutionary patterns were shaped. Location Espinhaço Range, Eastern Brazil. Taxon Vriesea oligantha species complex (Bromeliaceae). Methods We compiled data for plastidial regions and nuclear microsatellites to assess genetic diversity, population structure, migration rates and phylogenetic relationships. Using temperature and precipitation variables we modeled suitable areas for the present and the past, estimating corridors between isolated populations. We also implemented Bayesian demographic analyses to estimate ancient populations dynamics. Finally, we tested if population structure is driven by isolation by environment or by distance using a Bayesian modeling approach. Results Our results showed that the intraspecific divergence events of V. oligantha are older than those associated with the latest Pleistocene climatic oscillations, supporting the view that Quaternary climatic fluctuations are key components for understanding its population differentiation processes. Species distribution modeling estimated corridors between populations in the past, as also shown in the demographic analyses, depicting a major spatial reorganization during colder climates. Besides, the high genetic structure estimated results from both models of isolation by distance and by environment. Main conclusions V. oligantha is a remarkable model to test the effects of climatic oscillations over the biological community, since this species originated in the early-Pleistocene, prevailing over several cycles of climatic fluctuations until today. The estimated demographic dynamics of V. oligantha agrees with the species-pump mechanism, suggesting it as the main cause of speciation within the Espinhaço Range. Moreover, the phylogeographic patterns of V. oligantha reflect previously recognized spatial and temporal macroevolutionary patterns in the Espinhaço Range, providing insights into how microevolutionary processes may have given rise to this astonishing mountain biodiversity.

Data Availability - DRAFT - 'Process-based similarity' revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements

Datasets and R code related to confidential manuscript submission entitled "‘Process-based similarity’ revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements". Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency. Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency.

opencc-zeroMay 2022View details →

A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas

The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping by sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri-Atlantic distributions: the Narrow-billed Woodcreeper (Lepidocolaptes angustirostris), the Plain-crested Elaenia (Elaenia cristata), the Grassland Sparrow (Ammodramus humeralis), and the White-banded Tanager (Neothraupis fasciata). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri-Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.

opencc-zeroMay 2022View details →

Processed microphysical profiles of convective cloud scenes from satellite over ATTO

We present a new approach of analyzing and interpreting vertical profiles of cloud microstructure obtained by satellite remote sensing. The method is based on a spectral bin microphysics adiabatic parcel model and aims to elucidate the effects of aerosols on the evolution of convective clouds and related microphysical processes, including the activation of cloud condensation nuclei (CCN), the growth of cloud droplets, and the formation of precipitation. Characteristic features in the vertical profiles of effective radius (re) and temperature (T) reveal different microphysical zones in convective clouds related to the change increase of re with decreasing T. The classification of the different microphysical zones includes the (1) condensational growth of droplets, (2) growth by coalescence, (3) rainout, (4) secondary droplet activation zone (SAZ), (5) mixed-phase of ice particles and water droplets and (6) glaciation of the cloud. The detection of the SAZ is introduced here for the first time. This method allows us to identify the activation of aerosol particles above cloud base and their role in the invigoration of deep convective clouds.

opencc-by-nc-4.0Apr 2021View details →

Datasets and code for "Mapping the plague through natural language processing"

This project investigates the performance of various NLP libraries and geocoding services for the semi-automated generation of quantitative datasets from narrative texts. We provide the original files, several intermediate data products as well as the final plague datasets. Please note that some of the steps in this process were done manually, thus some of the scripts cannot be run completely.  This work is based on two plague treatises: - Sticker, G. 1908 Abhandlungen aus der Seuchengeschichte und Seuchenlehre. Band 1: Die Pest. Giessen, A. Töpelmann. - Biraben, J.-N. 1975 Les hommes et la peste en France et dans les pays européens et méditerranéens. Paris, Mouton. The final geocoded, plague datasets are: - plague_sticker_v1.csv - plague_biraben_v1.csv A data dictionary is available as plague_datadict.xlsx Other files: <table> <tbody> <tr> <td>file name</td> <td>content</td> </tr> <tr> <td>sticker_OCR_orig.txt</td> <td>Original OCR text</td> </tr> <tr> <td>sticker_OCR.txt</td> <td>Original OCR text without parenthesis (author names)</td> </tr> <tr> <td>sticker_textprep.rds</td> <td>Original OCR text with further preparations</td> </tr> <tr> <td>sticker_goldstandard_annotated_1.tsv</td> <td>manual annotations file 1</td> </tr> <tr> <td>sticker_goldstandard_annotated_2.tsv</td> <td>manual annotations file 2</td> </tr> <tr> <td>sticker_goldstandard_annotated_consensus.tsv</td> <td>consenus annotation file</td> </tr> <tr> <td>sticker_standard_toponyms.csv</td> <td>Gold standard for toponym recognition. Contains the tokenization, the start/end character respective to the OCR text (orig and without parenthesis) and whether a token is a location or other</td> </tr> <tr> <td>sticker_comparison_NER.rds</td> <td>Comparison of NER performance</td> </tr> <tr> <td>sticker_comparison_geocoding.rds</td> <td>Comparison of Geocoding performance</td> </tr> </tbody> </table>

Processed ground observation and WRF-CAMQ data for Greater Bay Area, 2015-2021

The pre-processed training and testing dataset for the paper Development of an LSTM-Broadcasting deep-learning framework for regional air pollution forecast improvement. The format of data is compatible with <a href="https://github.com/jvhs0706/regional-forecast-new">the official implementation</a>.

Datasets and Code for "A Gaussian process model-guided surface polishing process in additive manufacturing"

These are the datasets and computer code for reproducing the results in Jin, Iquebal, Bukkapatnam, Gaynor, and Ding, 2020, “A Gaussian process model-guided surface polishing process in additive manufacturing.” ASME Transactions, Journal of Manufacturing Science and Engineering, Vol. 142(1), pp. 011003.1–011003.12.

Can antioxidant responses be induced by habitat fragmentation process?

Animal populations are increasingly forced to live in small residual natural or semi-natural areas due to habitat loss and fragmentation. Here, the viability of populations is often compromised by intrinsic threat factors typical of small and isolated populations, such as inbreeding depression, genetic drift, and environmental and demographic stochasticity. Under these circumstances, organisms may have low fitness due to inadequate physiological responses needed to face environmental challenges. However, few studies have investigated the relationship between habitat fragmentation and stress defences. In this study, we aimed to test whether an increase in the level of individual inbreeding produced an increase in the antioxidant system response. To this purpose, we genotyped 151 individuals of Fire Salamander Salamandra salamandra (Amphibia: Urodela) within 5 sampling populations, located in forest landscapes with different degree of fragmentation in northern Italy. For 113 individuals we also measured the glutathione-S-transferase (GST) and catalase (CAT) enzyme activity. Results showed a significant increase in individual GST activity for increasing levels of inbreeding, whereas no relationship was found for CAT. We also measured acetylcholinesterase to test the possible confounding effects of pesticides that might have occurred in fragmented landscapes with forests interspersed with agricultural areas. However, no difference in this enzyme activity was found among sampling populations. We argue that high levels of GST activity may be symptomatic of oxidative stress derived from inbreeding. An increased frequency of homozygous deleterious alleles due to inbreeding may cause homeostatic alterations and trigger the expression of GST for protection against hydrogen peroxide reactive oxygen species. We suggest using GST as a biomarker for environmental stressors with great caution and not to underestimate that the sources of stress deriving from habitat fragmentation could lead to an unbalance in the oxidative status, possibly increasing population susceptibility to infectious diseases and, potentially, spillover events and zoonoses.

Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"

Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores.  For the details please see the original publication or the bioarxiv preprint:  https://doi.org/10.1101/2021.04.05.438521 The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment.  For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)

opencc-by-4.0Mar 2022View details →

Pre-processed data for "Does host plant drive variation in microbial gut communities in a recently shifted pest?"

Pre-processed fastqs files generated by Illumina sequencing associated with the publication by Javal et al. entitled "Does host plant drive variation in microbial gut communities in a recently shifted pest?".

opencc-by-4.0Dec 2021View details →

Data and code for "Non-local parameterization of atmospheric subgrid processes with neural networks" (Wang et al. 2022 submit to JAMES)

Data and code for "Non-local parameterization of atmospheric subgrid processes with neural networks" (Wang et al. 2022 submit to JAMES). Detailed description of the files in README.txt.

Turning summer into winter: nutrient dynamics, temperature, density dependence, and invasive species drive bioenergetic processes and growth of a keystone coldwater fish

A combination of global changes such as species invasions, climate change, and nutrient pollution have altered ecosystems, food webs, and the bioenergetic processes that control growth. These changes are especially pronounced in freshwater ecosystems and often lead to rapid variation in fish growth and dependent ecosystems services such as fishery yield. Understanding the mechanisms driving growth responses to environmental change is important for interpreting past dynamics and sustainably managing ecosystems. This study uses integrated bioenergetics and growth modeling to understand how nutrient dynamics, species invasions, and changing temperatures have altered growth of the keystone pelagic whitefish (Coregonus wartmanni) in Lake Constance, Germany from 1925 to 2020. Growth variation was modeled by allowing covariates to alter temperature-dependent consumption, while size-specific metabolism varied only with temperature. Consumption and growth increased strongly to a maximum with phosphorous, and this effect was stronger when intraspecific competition (measured as whitefish biomass) was low. Increasing whitefish biomass reduced growth under mesotrophic conditions, but had no effect under oligotrophic conditions. In contrast, increasing competition with invasive three-spined stickleback (Gasteosteus aculeauts) was predicted to reduce growth even under oligotrophic conditions. The invasion has effectively turned summer into winter for whitefish, with older fish ceasing to grow and younger fish losing up to 10% of their body weight during the normal growing season in subsequent years. Warming is predicted to further reduce whitefish growth due to competition with invasive stickleback, which would further alter zooplankton food availability and reduce already low fishery yields. These results demonstrate the importance of considering biotic interactions and synergistic effects in global change studies, as well as the value of mechanistic-based models for understanding effects. Similar growth responses to ecosystem change are likely within and across ecosystems, and bioenergetic models can help understand effects to support informed ecosystem management.

Dataset and R script for Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products

We provide raw data and R script for analysis of data published in: 1) Daher, E.; Cinosi, N.; Chierici, E.; Rondoni, G.; Famiani, F.; Conti, E. Field and Laboratory Efficacy of Low-Impact Commercial Products in Preventing Olive Fruit Fly, Bactrocera oleae, Infestation. Insects 2022, 13, 213. https://doi.org/10.3390/insects13020213 2) Daher, E.; Chierici, E.; Cinosi, N.; Rondoni, G.; Famiani, F.; Conti, E. Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products. Data 2022, 7,

Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period

Aim: Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. Methods: Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. Results: Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (Htr1a, Rims1, Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (Gpld1, Sirt1, Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (Mmp2, Itpr1, Nrf1, etc.). Conclusion: The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.

Beef Processing Microbiome Furbeck et al. FASTQ

FASTQ Files for the Manuscript "Investigating the Impact of Manufacturing Steps During Meat Processing of the Beef Microbiome". To use, download, and place in a folder called "fastq" within a directory containing .Rmd and .RDS from code linked described in manuscript.

Neural processing and perception of Schroeder‐phase harmonic tone complexes in the gerbil: Relating single‐unit neurophysiology to behavior

Schroeder-phase harmonic tone complexes have been used in physiological and psychophysical studies in several species to gain insight into cochlear function. Each pitch period of the Schroeder stimulus contains a linear frequency sweep; the duty cycle, sweep velocity, and direction are controlled by parameters of the phase spectrum. Here, responses to a range of Schroeder-phase harmonic tone complexes were studied both behaviorally and in neural recordings from the auditory nerve and inferior colliculus of Mongolian gerbils. Gerbils were able to discriminate Schroeder-phase harmonic tone complexes based on sweep direction, duty cycle, and/or velocity for fundamental frequencies up to 200 Hz. Temporal representation in neural responses based on the van Rossum spike-distance metric, with time constants of either 1 ms or related to the stimulus' period, was compared to average discharge rates. Neural responses and behavioral performance were both expressed in terms of sensitivity, d', to allow direct comparisons. Our results suggest that in the auditory nerve, stimulus fine structure is represented by spike timing while envelope is represented by rate. In the inferior colliculus, both temporal fine structure and envelope appear to be represented best by rate. However, correlations between neural d' values and behavioral sensitivity for sweep direction were strongest for both temporal metrics, for both auditory nerve and inferior colliculus. Furthermore, the high sensitivity observed in the inferior colliculus neural rate-based discrimination suggests that these neurons integrate across multiple inputs arising from the auditory periphery.

TimeSide API as an audio processing web service

Audio descriptors can help to analyze, classify and compare sounds by their own characteristics. For large datasets,it is often needed to store the results of the analyses in order to keep everything sustainable and comparable, especially in machine learning usecases. This demo will show how to use the TimeSide REST API as a remote service to process descriptors in order to embed the results in any web application. The new version of the TimeSide player will be presented as a general example of using the dedicated javascript SDK to produce new kinds of applications involving visualization and collaborative annotation.