Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal

Datasets and analysis notebooks for recreating the analysis described in the paper. biom tables of the original datasets used in the meta-analysis are not included due to privacy issues. Instead, we include the biom table containing the NRMD for each study/ASV Updated data and notebooks can also be found at the github page:  <a href="https://github.com/amnona/paper-metaanalysis">https://github.com/amnona/paper-metaanalysis</a> NOTE: files here are provided in a per-directory .zip file in order to preserve internal directory structure.

opencc-zeroFeb 2022View details →

Figure e-1.- Effect of APOE alleles on cognitive domain-specific composite measures.

Supplemental Figure of our original article "Association of APOE Genotype with Heterogeneity of Cognitive Decline Rate in Alzheimer's Disease" published in Neurology showing model 1-based trajectories of cognitive domain-specific composite measures by APOE genotype, as well as the difference of the APOEe2 and APOEe4 groups with respect to the APOEe3/e3 reference group.

Specific heat of tungsten from 23 °C to 3266 °C

This dataset contains specific heat values determined from 23 °C to 3266 °C by five laboratories on a batch of specimens machined in the same block of tungsten.

Specific heat of molybdenum from 23 °C to 2607 °C

This dataset contains specific heat values determined from 23 °C to 2607 °C by five laboratories on a batch of specimens machined in the same block of molybdenum.

Specific heat of isotropic graphite from 1000 °C to 2800 °C

This dataset contains specific heat values determined from 1000 °C to 2800 °C by three laboratories on a batch of specimens machined in the same block of isotropic graphite.

Sex-specific variation in R-loop formation in Drosophila melanogaster

Source Data for manuscript, "Sex-specific variation in R-loop formation in Drosophila melanogaster".

SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells

This dataset contains aggregated CellRanger output for six 10x Genomics (5'GEX+abTCR+Feature barcoding) experiments from the study by Minervina, Pogorelyy et al (<a href="https://www.medrxiv.org/content/10.1101/2021.07.12.21260227v3">medrxiv</a>).  The scripts to process it further are available at github (<a href="https://github.com/pogorely/COVID_vax_CD8">repository</a>).  Raw sequencing data is available at SRA (acc. PRJNA744851)

Raw Data for the article: Patient-Specific Analysis of Ascending Thoracic Aortic Aneurysm with the Living Heart Human Model

In ascending thoracic aortic aneurysms (ATAAs), aneurysm kinematics are driven by ventricular traction occurring every heartbeat, increasing the stress level of dilated aortic wall. Aortic elongation due to heart motion and aortic length are emerging as potential indicators of adverse events in ATAAs; however, simulation of ATAA that takes into account the cardiac mechanics is technically challenging. The objective of this study was to adapt the realistic Living Heart Human Model (LHHM) to the anatomy and physiology of a patient with ATAA to assess the role of cardiac motion on aortic wall stress distribution. Patient-specific segmentation and material parameter estimation were done using preoperative computed tomography angiography (CTA) and ex vivo biaxial testing of the harvested tissue collected during surgery. The lumped-parameter model of systemic circulation implemented in the LHHM was refined using clinical and echocardiographic data. The results showed that the longitudinal stress was highest in the major curvature of the aneurysm, with specific aortic quadrants having stress levels change from tensile to compressive in a transmural direction. This study revealed the key role of heart motion that stretches the aortic root and increases ATAA wall tension. The ATAA LHHM is a realistic cardiovascular platform where patient-specific information can be easily integrated to assess the aneurysm biomechanics and potentially support the clinical management of patients with ATAAs.

Corticosteroid therapy in patients with COVID-19 has little effect on the production of specific antibodies

This excel data includes our research, ”Corticosteroid therapy in patients with COVID-19 has little effect on the production of specific antibodies."

opencc-by-4.0Mar 2022View details →

Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)

Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper. PacBio.simulated_uniform_coverage.fasta.gz and ONT.simulated_uniform_coverage.fasta.gz files were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”. ONT.simulated_real_expression.fasta.gz file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". mouse.gencode.M26.spatial.15percent.reduced.gtf was used as the annotation file for all tools. mouse.gencode.M26.spatial.15percent.expressed.gtf contains the set of all expressed isoforms. mouse.gencode.M26.spatial.15percent.expressed_kept.gtf contains those of the isoforms that are in presented in the annotation file ("known" transcripts), mouse.gencode.M26.spatial.15percent.reduced.gtf contains expressed isoforms that were removed from the annotation ("novel" transcripts).

opencc-by-4.0Mar 2022View details →

Raw Data for the article: Complete intra-laboratory validation of a LAL assay for bacterial endotoxin determination in EBV-specific cytotoxic T lymphocytes

Endotoxin content is a critical factor that affects the safety of biological pharmaceutical products. International pharmacopoeias describe several reference methods to determine endotoxin levels in advanced therapy medicinal product (ATMP) preparations. Administration of ATMPs must be done as rapidly as possible to ensure complete viability and potency of the cellular product. To evaluate the endotoxin content in the shortest time possible, we chose to validate an alternative method based on the use of the Charles River Portable Testing System (PTS) and FDA-approved cartridges, compliant with the requirements of the European Pharmacopoeia and providing results in <20 min. Here, we describe a unique and complete validation approach for instrument, personnel, and analytical method for assessment of endotoxins in ATMP matrices. The PTS system provides high sensitivity and fast quantitative results and uses less raw material and accessories compared with compendial methods. It is also less time consuming and less prone to operator variability. Our validation approach is suitable for a validated laboratory with trained personnel capable of conducting the ATMP release tests, and with very low intra-laboratory variability, and meets the criteria required for an alternative approach to endotoxin detection for in-process and product-release testing of ATMPs.

opencc-by-4.0Jun 2022View details →

ISNAS-DIP: Image-Specific Neural Architecture Search for Deep Image Prior

Dataset for our CVPR paper: "ISNAS-DIP: Image-Specific Neural Architecture Search for Deep Image Prior".   The arxiv paper can be found: https://arxiv.org/abs/2111.15362

A synthesis of nitric oxide emissions across global fertilized croplands from crop-specific emission factors

Nitrogen (N)-fertilizer application to agricultural soils results in substantial emissions of nitric oxide (NO), a key substance in tropospheric chemistry involved in climate forcing and air pollution. However, estimates of global cropland NO emissions remain uncertain due to a lack of information on direct NO emission factors (EFds) of applied N for variours cropping systems at seasonal or annual scales. Here we quantified the crop-specific seasonal and annual-scale NO EFds through synthesizing 1094 measurements from 125 field-based studies worldwide. The global mean crop-specific seasonal EFd was 0.53%, with the highest for vegetables (0.75%). Among cereal crops, the EFd of maize (0.45%) or wheat (0.47%) was about three-times higher than for rice (0.12%). At annual scale, the mean EFd across all cropping systems was 0.58%, with tea plantations having the highest (1.54%). For other cropping systems, the annual-scale EFds ranged from 0.02% to 1.07%. Besides crop type, also soil organic carbon, total N and pH as well as N fertilizer type were the main factors explaining the variations of NO EFds. Based on obtained specific EFds for each crop type, we estimated that NO emissions due to the use of synthetic fertilizers from global croplands are about 0.42–0.62 Tg N yr−1. Our budgets are relatively lower if compared to estimates derived by the use of IPCC defaults for NO emissions (0.72–1.66 Tg N yr−1) or reported elsewhere (0.67–1.04 Tg N yr−1). In our estimates, cash crops (vegetable, tea and orchard), which cover only 9% of the world cropland area, contributed about 31% to total NO emissions from global fertilized croplands. Overall, our meta-analysis provides improved crop-specific NO EFds reflecting current stage of knowledge. The work also highlights the relative importance of cash crop production as sources for atmospheric NO, i.e., agricultural systems on which mitigation efforts may focus.

IIb-RAD-seq coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between sub-populations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection were also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.

Sex-specific evolution of brain size, brain structure, and covariation with eye size in Trinidadian killifish

Links between contrasting ecological conditions and evolutionary shifts in neurosensory components such as brain and eye size are accumulating. Whether selection operates differently on these traits between sexes is unclear. Trinidadian killifish (Anablepsoides hartii) are located in sites with and without predators. Male killifish from sites without predators have evolved larger brains and eyes than males from sites with predators. These differences in brain size are present early in life but disappear in adult size-classes. Here, we evaluated female brain growth allometries to determine if females exhibit similar size-specific brain size differences between sites that differ in predation intensity. We also quantified brain size, structure, and eye size to determine if these structures coevolve in a sex-specific manner. We found that female brain growth allometries did not differ across populations. Yet, female killifish from sites without predators exhibited a larger cerebellum, optic tectum, and dorsal medulla early in life (prior to maturation), but such differences disappeared in larger size-classes. Females from sites with predators exhibit similar patterns in brain growth as males in those sites, therefore shifts in brain size and structure are driven by differences between sexes in sites without predators. We also found evidence for covariation between brain and eye size in both sexes despite different levels of variation in both structures, suggesting that these structures may covary to fluctuating degrees in sex-specific ways. We conclude that differential investment in brain tissue in sites without predators may be linked to varying reproductive and cognitive demands across the sexes.

Genetic covariance in immune measures and pathogen resistance in decorated crickets (Gryllodes sigillatus) is sex and pathogen specific

Insects are important models for studying immunity in an ecological and evolutionary context. Yet, most empirical work on the insect immune system has come from phenotypic studies meaning we have a limited understanding of the genetic architecture of immune function in the sexes. We use nine highly inbred lines to thoroughly examine the genetic relationships between a suite of commonly used immune assays (haemocyte count, implant encapsulation, total phenoloxidase activity, antibacterial zone of inhibition, pathogen clearance) and resistance to infection by three generalist insect pathogens (the gram-negative bacterium Serratia marcescens, the gram-positive bacterium Bacillus cereus and the fungus Metarhizium robertsii) in male and female Gryllodes sigillatus. There were consistent positive genetic correlations between haemocyte count, antibacterial and phenoloxidase activity and resistance to S. marcescens in both sexes, but these relationships were less consistent for resistance to B. cereus and M. robertsii. In addition, the clearance of S. marcescens was genetically correlated with the resistance to all three pathogens in both sexes. Genetic correlations between resistances to the different pathogen species were inconsistent, indicating that resistance to one pathogen does not necessarily mean resistance to another. Finally, while there is ample genetic (co)variance in immune assays and pathogen resistance, these genetic estimates differed across the sexes and many of these measures were not genetically correlated across the sexes suggesting that these measures could evolve independently in the sexes. Our finding that the genetic architecture of immune function is sex and pathogen specific suggests that the evolution of immune function in male and female G. sigillatus is likely to be complex. Similar quantitative genetic studies that measure a large number of assays and resistance to multiple pathogens in both sexes are needed to ascertain if this complexity extends to other species.

Age-specific differences in Asian Elephant defecation, dung decay, detection and their implication for dung count

In vertebrate population estimation, converting faecal density into animal density requires information on faecal production rate, decay rate, and faecal density. Differences in the above factors for long-lived species across age classes were not evaluated. We have evaluated these factors associated with the dung count of Asian elephants (Elephas maximus) in the tropical forest of Southern India. The defecation rate of elephants was determined in semi-wild elephants at the Mudumalai elephant camp. The relationship between dung bolus diameter and age was determined to estimate the age of the elephant. Total and age-specific elephant density based on dung bolus diameter were estimated. A total of 24 transect lines of 2-4 km (125 km) were sampled in the study area. An experiment was conducted to assess detection probability across the age classes of dung piles. The dung decay rates across age classes and seasons were determined by marking fresh dung piles (n=1551). The dung-based age structure assessment and its limitations were evaluated. The mean defecation rate was 13.51±0.51 per day. The defecation rate was significantly lower for the younger age class and increased with the age of elephants. Defecation rates were significantly lower in the wet season than in the dry. The dung-boli diameter positively increased with the age of elephants, and the growth curve can be used to predict the age and age structure of the elephant population. The disparity in the dung production rate results in the lower availability of younger age class (Juvenile and calf) dung in the transect for counting, that results in lower dung abundance. The detection probability of dung piles of younger age classes was low (0.58). The survival rates of dung piles of younger age classes were lower and increased with the age of elephants in the wet season. Hence, demography assessment of the population based on dung needs to consider age-specific differences in dung production, decay, and detection probability. Through demography assessment using dung provides insight into population age structure, it has limitations in predicting age structure for young elephants.

Intra- and interspecific variability of specific leaf area mitigate the reduction of community stability in response to warming and nitrogen addition

Global environmental changes are reducing the diversity and affecting the functioning of natural ecosystems as well as their ability to reliably provide ecosystem functions and services to mankind. Many studies have shown that a greater plant diversity can stabilize community productivity against environmental fluctuations. However, most of these studies focused on plant species richness, thus overlooking the potential role of functional traits in stabilizing community productivity against environmental fluctuations. Whether and how functional trait mean and variability influence community stability in response to environmental changes and their relative contributions to community stability are largely unknown. Here, we used a 10-year experiment to investigate the role of species richness, as well as functional mean and intra- and interspecific variability of specific leaf area (SLA) of plants within- and among communities in driving community stability in response to nitrogen (N) addition and warming. We found that both N addition and warming reduced the temporal stability of community productivity by reducing species richness and its contribution to species asynchrony and species stability. In contrast, changes in the mean and variability of SLA in response to N addition and warming mitigated the reduction of community stability. Specifically, N addition reduced variation in SLA both by reducing interspecific differences in SLA within communities and differences in mean values of SLA among communities. Warming increased intraspecific differences in SLA among communities, leading to higher species stability that partly buffered the reduction of community stability. Our study demonstrates the role of trait mean and variability in mitigating the reduction of community stability in response to two pervasive global environmental changes. Gaining a deeper understanding of the processes linking global changes and the stability of our ecosystems requires integrating both trait mean values and trait variability.

opencc-zeroDec 2016View details →

Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.

Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on two traits, postnatal growth rate and birth date, in a population of North American red squirrels (Tamiasciurus hudsonicus). The strongest level of selection was typically within-acoustic social neighbourhoods (within 130m of the nest), where growing faster and being born earlier than nearby litters was key, while selection on growth rate was also apparent both within-litters and within-study areas. Higher population densities increased the strength of selection for earlier breeding, but did not influence selection on growth rates. Females experienced especially strong selection on growth rate at the within-litter level, possibly linked to the biased bequeathal of the maternal territory to daughters. Our results demonstrate the importance of considering multilevel and sex-specific selection in wild species, including those that are territorial and sexually monomorphic.

Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years

Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus Cephalotes. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that Cephalotes cospeciate with their most abundant adult symbionts. We find, also, that winged queens harbor worker-like microbiomes prior to colony founding, suggesting that vertical inheritance promotes ancient partner fidelity. While some adult-abundant symbionts colonize guts of larvae, microbiomes from this stage are by environmental bacteria from the Enterobacteriales, Lactobacillales, and Actinobacteria. Re-acquisition of such bacteria, each generation, for >40 million years suggests conserved environmental filtering and, hence, a second mechanism behind distinct symbioses divided by metamorphosis.