Find research datasets worth reusing

opencc-by-4.0Nov 2024View details →

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction"

Datasets used in "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". The provided zip file contains: <ul> <li>Datasets 1–3: For each dataset, directories include input sequences (FASTA), multiple sequence alignments (MSAs in AFA format), and normalized predicted structures from six deep learning tools. Dataset 3 also contains references - RNA chains extracted from complexes. These folders also include a CSV file with all metrics for all RNAs and tools.</li> <li>Dataset 4: A text file listing the PDB IDs of RNAs included in this dataset, which is a subset of Dataset 3.</li> <li>Dataset complexes: RNA chains extracted from predicted complexes, where predictions are made by AlphaFold 3 web server and, in some cases, RoseTTAFoldNA. There are also job files for the AlphaFold 3 web server used to obtain these predictions. Same as for previous datasets, this folder also includes a CSV file with all metrics for these RNA chains.</li> </ul> The structure of the dataset and details of each folder are explained in the included README file.

opennotspecifiedAug 2024View details →

Comparative Cytogenetics: Comparative Cytogenetics (554)

The Journal of Comparative Cytogenetics is a peer-reviewed, open-access, rapid online journal launched to accelerate research on all aspects of plant and animal cytogenetics, karyosystematics, and molecular systematics. All published papers can be freely copied, downloaded, printed and distributed at no charge for the reader. Authors are thus encouraged to post the pdf files of published papers on their homepages or elsewhere to expedite distribution. There is no charge for color.The Journal of Comparative Cytogenetics is a peer-reviewed, open-access, rapid online journal launched to accelerate research on all aspects of plant and animal cytogenetics, karyosystematics, and molecular systematics. All published papers can be freely copied, downloaded, printed and distributed at no charge for the reader. Authors are thus encouraged to post the pdf files of published papers on their homepages or elsewhere to expedite distribution. There is no charge for color.

opencc-by-4.0Dec 2023View details →

Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion

Abstract: Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson’s disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development. Zenodo contents: In this Zenodo archive we provide the post-QC and taxonomic and functional profiling "Source Data" used in all downstream analyses to generate tables and figures seen in our manuscript. We also provide the link to our GitHub repository where we have stored the code used to perform the bioinformatic processing of the shotgun metagenomic sequences and stastical analyses. Individual sample raw shotgun metagenomic sequences and metadata from our UFPF dataset are available on NCBI Sequence Read Archive (SRA) under BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/1096686">PRJNA1096686</a>.

opencc-by-4.0Oct 2021View details →

FIG. 6 in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance

FIG. 6. — The evolutionary grades of the studied species of Brassicaceae

opencc-by-4.0Oct 2021View details →

Establishing a Dual Generational Modality Dataset: Comparing the Ride-Sharing Adoption Trends and Perspectives of Consumers from two Generational Cohorts, Millennials and Gen-Xers - E2

Ride-hailing services such as Uber or Lyft are the latest tool in sustainable transportation strategies to come under scrutiny. Originally thought to be a way to reduce congestion, these services have actually been shown to increase it in some cases. Although the number of individuals driving around urban centers to find parking appears to decrease with the adoption of ride-hailing, Uber or Lyft drivers are instead circling around waiting for riders. Additionally, ride-hailing services have not led to the abandonment of personal vehicles, but rather to the abandonment of public transit in some cases. The purpose of this study is to evaluate the use of ride-hailing services in the two largest age cohorts in the United States: Millennials and Generation X-ers, focusing on the Southeastern states of Florida and North Carolina. This study seeks to determine how each generation has adopted these methods to help planners learn how to incorporate these strategies in transportation planning. The data provides information about the mode of transportation, trip details, and important socio-economic indicators of 1903 respondents from Florida and North Carolina.

opencc-by-4.0Oct 2021View details →

Supplementary material S24: Time course of the loudest Varroa jolting pulse compared to that of a honeybee colony and single bee individual.

Time course of the loudest Varroa jolt on brood-comb with the signal from the full colony and a single bee. The signal seen here in each panel is the integral of the magnitude of acceleration with respect to time. The background vibration that is inherent to the room was calculated and subtracted from this data. The loudest jolt (red) is here compared to the signal of a single bee (black) and the vibrations of the full colony at low and high signal (black). High signal is captured when the frame containing the accelerometer is empty of brood. Low signal is captured when the frame is fully loaded with brood and/or honey. The whooping signal (panel a) was captured during a period of high signal.

opencc-zeroNov 2021View details →

Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes

Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight Sinocyclocheilus species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including GNAQ, PKA, NRAS, and p38) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.

opencc-by-4.0Dec 2020View details →

The accuracy and efficiency of a reference-based adaptive selection algorithm for comparative judgement

Data and R code with article for Frontiers in Education special issue Validity, Reliability and Efficiency of Comparative Judgement to Assess Student Work. [Submitted] Abstract: Several studies have proven that comparative judgement (CJ) is a reliable and valid assessment method for a variety of competences, expert assessment and peer assessment, and CJ is emerging as a possible approach to help maintain standards over time. For consecutive pairs of student works (representations) assessors are asked to judge which representation is better. It has been shown that random construction of pairs leads to very inefficient assessments, requiring a lot of pairwise comparisons to reach reliable results. Some adaptive selection algorithms using information from previous comparisons were proposed to increase the efficiency of CJ. These adaptive algorithms appear however to artificially inflate the reliability of CJ results through increasing the spread of the results. The current article proposes a new adaptive selection algorithm using a previously calibrated reference set. Using a reference set should eliminate the reliability inflation. In a real assessment, using reference sets of different reliability, and in a simulation study it is proven that this adaptive selection algorithm is more efficient without reducing the accuracy of the results and without increasing the standard deviation of the assessment results. As a consequence, a reference-based adaptive selection algorithm produces high and correct reliability values in an efficient manner.

Comparing natural hydrogels to self-assembling peptides in spinal cord injury treatment: a systematic review

Abstract Background: In many cases, central nervous system (CNS) injury is unchanging due to the absence of neuronal regeneration and repair capabilities. In recent years, regenerative medicine, and especially hydrogels, have reached a significant amount of attention for their promising results for the treatment of spinal cord injury (SCI) currently considered permanent. Hydrogels are categorized based on their foundation: synthetic, natural, and combination. The objective of this study was to compare the properties and efficacy of commonly used hydrogels, like collagen, and other natural peptides with synthetic self-assembling peptide hydrogels in the treatment of SCI.  Methods: Articles were searched in PubMed, Scopus, Web of Science, and Embase. All studies from 1985 until January 2020 were included in the primary search. Eligible articles were included based on the following criteria: administering hydrogels (both natural and synthetic) for SCI treatment,  soley foucsing on spinal cord injury treatment, and published in a peer-reviewd journal. Data surronding xonal regeneration, revascularization, elasticity, drug delivery efficacy, and porosity were extracted. Results: A total of 24 articles were included for full-text review and data extraction. There were only one experimental study directly comparing Collagen I (as natural hydorgel) and PEG (as synthetic hydrogels) in an in vitro setting. The included study suggested PEG’s cell behavior is more expectable in the injury site, which makes it a more reliable scaffold. Conclusions: There is limited research comparing and evaluating both types of natural and self-assembling peptides (SAPs) in the same animal or in vitro study, despite its importance. Although we assume that the remodeling of natural scaffolds may lead to a stable hydrogel, there was not a definitive conclusion that synthetic hydrogels are more beneficial than natural hydrogels in neuronal regeneration.

opencc-zeroDec 2021View details →

Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation

This dataset contains data from a field experiment described in the publication "Wise, D. H. & Farfan, M.A. (2021) Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation. Ecology and Evolution, 00: 1-11. <a href="https://doi.org/10.1002/ece3.8375">https://doi.org/10.1002/ece3.8375</a>". The field experiment compared the response to increased input of nutrients and energy (artificial detritus) to an empirical model of intra-guild predation (IGP) to the predictions of published, simple mathematical models of asymmetric IGP (a generalist IG Predator that feeds both on a specialist IG Prey and a Resource that it shares with the IG Prey). The empirical model was a food-web module created by pooling species abundances across many families in a community of soil micro-arthropods into three response variables: IG Predator (large predatory mites), IG Prey (small predatory mites) and a shared Resource (fungivorous mites and springtails). The pattern of change over time in densities of the three response variables (IG Predator, IG Prey and Resource) was compared to the predictions of mathematical models of IGP to determine if the feeding relationships in this community of soil micro-arthropods could be abstracted into a simple IGP module. Thus, we were testing the hypothesis that IGP is a dominant organizing principle in this community. Simple mathematical models predict that increased input of nutrients and energy to the shared Resource will increase the equilibrium density of Resource and IG Predator, but will decrease that of IG Prey. By the experiment's end, densities of fungivores (Resource) had increased ~1.5x (ratio of pooled fungivore densities in the High treatment to plots with no addition of detritus (None treatment); and IG Predator densities had increased ~4x. Contrary to the prediction of mathematical models, IG Prey had not decreased, but instead had increased ~1.5x. We discuss possible reasons for the failure of the empirical model to agree with IGP theory.

opencc-zeroDec 2021View details →

Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism

Locusts exhibit one of nature's most spectacular examples of complex phenotypic plasticity, in which changes in density cause solitary and cryptic individuals to transform into gregarious and conspicuous locusts forming large migrating swarms. We investigated how these coordinated alternative phenotypes might have evolved by studying the Central American locust and three closely related non-swarming grasshoppers in a comparative framework. By experimentally isolating and crowding during nymphal development, we induced density-dependent phenotypic plasticity and quantified the resulting behavioural, morphological, and molecular reaction norms. All four species exhibited clear plasticity, but the individual reaction norms varied among species and showed different magnitudes. Transcriptomic responses were species-specific, but density-responsive genes were functionally similar across species. There were modules of co-expressed genes that were highly correlated with plastic reaction norms, revealing a potential molecular basis of density-dependent phenotypic plasticity. These findings collectively highlight the importance of studying multiple reaction norms from a comparative perspective.

Nordic comparative study on green space use during COVID-19 – Case Helsinki (NCS-Helsinki)

This dataset includes the data used in the Helsinki case study of an original research paper “Pandemic urban resilience in the Nordic context - a cross-city analysis on associations between outdoor recreation and green infrastructure” (Fagerholm et al., upcoming). The data were collected in the PLAN-Health (PLAN-H) research project (<a href="https://participatorymapping.org/project/health-promoting-urban-environment-plan-h/">https://participatorymapping.org/project/health-promoting-urban-environment-plan-h/</a>) and include point data of respondent-mapped outdoor locations visited in leisure time.

Comparative analysis of patient-specific aortic dissections through computational fluid dynamics suggests increased likelihood of degeneration in partially thrombosed aorta

Aortic dissection is a life-threatening cardiovascular disease associated with high rates of morbidity and mortality, especially in medically under-served communities. It compromises the hemodynamics of the arteries that originate from the aorta, and its outcomes include visceral ischemia and aortic rupture in the acute phase and aneurysmatic degeneration in the chronic phase. Understanding patients’ blood flow patterns is pivotal for non-invasive evidence-based treatment as they greatly influence both the disease onset and its outcome. In this paper, we combine diagnostic imaging techniques and computational fluid dynamics to analyze the flow patterns of three aorta dissections (fully perfused, partially thrombosed, and fully thrombosed), and compare them to a healthy aorta. Besides flow kinematics, we focus on time averaged wall shear stress and oscillatory shear index that are recognized risk factors for aneurysm and rupture. Our analysis shows that partially thrombosed dissection is the most prone to false lumen degeneration. In all dissections, the arteries connected to the false lumen are generally poorly supplied with blood. Further, both true and false lumens present higher turbulence levels than the healthy aorta, and critical stagnation points. Mesh sensitivity and a thorough comparison against literature data together support the methodology robustness.

opencc-by-4.0Aug 2021View details →

Comparative genomics reveals evolution traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae

Botryosphaeriaceae, as a major family of the largest class of kingdom fungi Dothideomycetes, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and bio-material plants. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted the first large-scale whole-genome comparison of 271 Dothideomycetes, including 19 species in Botryosphaeriaceae. The comparative genome analysis provided a clear classification of Botryosphaeriaceae in Dothideomycetes and indicated that Botryosphaeriaceae pathogenicity evolution undergoes multiple times. Mating strategies analysis demonstrated at least 3 transitions were found within Botryosphaeriaceae from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different species within Botryosphaeriaceae varied greatly, indicating that a secondary lineage expansion occurs in speciation. These findings cast new insights into evolution traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae.

opencc-zeroJan 2022View details →

Gene expression profiles compared in environmental and malnutrition enteropathy in Zambian children and adults

Background: Environmental enteropathy (EE) contributes to growth failure in millions of children worldwide, but its relationship to clinical malnutrition has not been elucidated. We used RNA sequencing to compare duodenal biopsies from adults and children with EE, and from children with severe acute malnutrition (SAM), to define key features of these malnutrition-related enteropathies. Methods: RNA was extracted and sequenced from biopsies of children with SAM in hospital (n=27), children with non-responsive stunting in the community (n=30), and adults living in the same community (n=37) using an identical sequencing and analysis pipeline. Two biopsies each were profiled and differentially expressed genes (DEGs) were computed from the comparisons of the three groups. DEG lists from these comparisons were then subjected to analysis with CompBio software to assemble a holistic view of the biological landscape and IPA software to interrogate canonical pathways. Findings: Dysregulation was identified in goblet cell/mucin production and xenobiotic metabolism/detoxification for both cohorts of children, versus adults. Within the SAM cohort, substantially greater induction of immune response and barrier function, including NADPH oxidases was noted, concordant with broadly reduced expression of genes associated with the brush border and intestinal structure/transport/absorption. Interestingly, down regulation of genes associated with the hypothalamic-pituitary-adrenal axis was selectively observed within the cohort of children with stunting. Interpretation: Gene expression profiles in environmental enteropathy and severe acute malnutrition have similarities, but SAM has several distinct transcriptional features. The intestinal capacity to metabolise drugs and toxins in malnourished children requires further study.

Supplementary data to publication "Growth efficiency, intestinal biology, and nutrient utilization and requirements of black soldier fly (Hermetia illucens) larvae compared to monogastric livestock species: a review"

The datasets provided in the excel file were used to generate Table 2 and Fig. 2 in the publication entitled "Growth efficiency, intestinal biology, and nutrient utilization and requirements of black soldier fly (Hermetia illucens) larvae compared to monogastric livestock species: a review" by Seyedalmoosavi et al., 2022 published in Journal of Animal Science and Biotechnology. https://doi.org/10.1186/s40104-022-00682-7

opencc-by-4.0Jan 2022View details →

Comparing black-carbon- and aerosol-absorption-measuring instruments – a new system using lab-generated soot coated with controlled amounts of secondary organic matter

A preprint of the publication can be found here: <a href="https://amt.copernicus.org/preprints/amt-2021-214/">AMTD - Response of black carbon and aerosol absorption measuring instruments to laboratory-generated soot coated with controlled amounts of secondary organic matter (copernicus.org)</a> (doi.org/10.5194/amt-2021-214). The files correspond to the raw data sets used for Figures 3 and 4 of the aforementioned publication. The date and start/stop time of the measurements are listed in the file "overview_measurements".

opencc-zeroFeb 2022View details →

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography

Phylogeography investigates historical drivers of species' geographic distribution. Special attention has been given to ecological, climatic, and geological processes in the diversification of the Neotropical biota. Several species sampled across the dry diagonal of South America (DDSA, comprising the Caatinga, Cerrado, and Chaco biomes) experienced range shifts coincident with Quaternary climatic changes. However, studies across different spatial, temporal, and biological scales on species from South America's dry biomes are still poorly represented. Here, we combine phylogeographic model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on both plant and animal species from the DDSA. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the historical demographic responses of 70 lineages. We then built a random forest model using both biotic and abiotic information to identify potential traits for predicting whether species underwent population expansion, contraction, or stasis during the Pleistocene. Finally, we estimated the temporal synchrony of species demographic responses using hierarchical approximate Bayesian computation (hABC). Biotic variables largely predicted how species responded to Pleistocene climatic changes, and demographic changes were mostly synchronous during the Middle Pleistocene. Although many DDSA species underwent demographic expansion, presumably associated with the spread of aridity during glacial Pleistocene periods, our findings suggest that some species exhibited the opposite response and that species-specific attributes might have been related to these differences.

opencc-by-4.0Nov 2021View details →

Comparative proteomic and metabolomic analyses of plasma reveal the novel biomarker panels for thyroid dysfunction

Abstract: Objectives: Thyroid dysfunction such as hypothyroidism (THO) and hyperthyroidism (THE) are the disease caused by pathological processes in the thyroid. The current diagnosis of thyroid dysfunction is variable because of ages and genders. The aim of this study was to explore the novel candidate biomarker panels for hypothyroidism and hyperthyroidism screening with mass spectrometry and bioinformatics. Methods: Plasma samples were collected from 15 THE patients, 9 THO patients, and 15 healthy controls. DIA-based proteomic and untargeted metabolomic analyses were performed to identify the novel biomarker panels for THO and THE. Finally, three candidate biomarkers were verified by ELISA in 34 samples. Results: A total of 2738 proteins and 6103 metabolites were identified, and 173 proteins and 2487 metabolites were found to be differentially expressed among THE, THO and control groups. The results of the ensemble feature selection, K-means clustering and the least absolute shrinkage and selection operator (LASSO) regression model showed that four proteins (C4A, C3/C5 convertase, APOL1, and ITIH4) and four metabolites (L-arginine, L-proline, cortisol, and cortisone) identified by plasma proteomics and metabolomics could help distinguish THO and THE patients from healthy controls. Conclusions: This study identified and verified two pairs of biomarker panels that can distinguish the THE and THO patients regardless of ages and genders. Consequently, our findings represent a comprehensive analyses of thyroid dysfunction plasma, which is significant for the clinical diagnosis.