Find research datasets worth reusing

Risk Factors of Non-specific Low Back Pain in a Rural Community of Bangladesh

Risk Factors of Non-specific Low Back Pain in a Rural Community of Bangladesh

Host plant specificity of the monarch butterfly Danaus plexippus: A systematic review and meta-analysis

The preference-performance hypothesis explains host specificity in phytophagous insects, positing that host plants chosen by adults confer the greatest larval fitness. However, adults sometimes oviposit on plants supporting low larval success because the components of host specificity (adult preference, plant palatability, and larval survival) are non-binary and not necessarily correlated. Palatability (willingness to eat) is governed by chemical cues and physical barriers such as trichomes, while survival (ability to complete development) depends upon nutrition and toxicity. Absence of a correlation between the components of host specificity results in low-performance hosts supporting limited larval development. Most studies of specificity focus on oviposition behavior leaving the importance and basis of palatability and survival under-explored. We conducted a comprehensive review of 127 plant species that have been claimed or tested to be hosts for the monarch butterfly Danaus plexippus to classify them as non-hosts, low performance, or high performance. We performed a meta-analysis to test if performance status could be explained by the properties of neurotoxic cardenolides or trichome density. We also conducted a no-choice larval feeding experiment to identify the causes of low performance. We identified 34 high performance, 42 low performance, 33 non-hosts, and 18 species with unsubstantiated claims. Mean cardenolide concentration was greater in high- than low-performance hosts and a significant predictor of host status, suggesting possible evolutionary trade-offs in monarch specialization. Other cardenolide properties and trichome density were not significant predictors of host status. In the experiment, we found, of the 62% of larvae that attempted to eat low-performance hosts, only 3.5% survived to adult compared to 85% of those on the high-performance host, demonstrating that multiple factors affect larval host plant specificity. Our study is the first to classify all known host plants for monarchs and has conservation implications for this threatened species.

Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons

Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase substrate receptor TIR1. Rapid degradation of condensin I and condensin II – two essential regulators of mitotic chromosome structure - revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modeling drug activity in mammalian tissues.

Light and malaise traps tell different stories about the spatial variations in arthropod biomass and method-specific insect abundance

1. Conclusions reached in meta-analyses of changes in insect communities may be influenced by method-specific sampling biases, which may lead to inappropriate conservation measures. 2. We argue that the contradictory conclusions regarding terrestrial insect biomass, abundance and richness patterns are, at least partly, due to methodological limitations that reflect taxon-specific responses to environmental changes. 3. In this study, light and Malaise traps were simultaneously deployed to sample insects at 52 plots in a temperate forest in Germany along gradients of elevation (> 1000 m) and canopy openness (3 - 100 %). These gradients were used as predictors in models of total arthropod biomass according to the two trapping methods, and in models of abundance and richness of three commonly targeted groups: nocturnal moths, sampled using light traps, and hoverflies and bees, collected with Malaise traps. 4. A comparison of the total arthropod biomass obtained with the two methods revealed contrary results along the canopy openness gradient. Biomass in light traps showed a decreasing trend with increasing canopy openness while biomass in Malaise traps increased. The same opposing pattern was found for the abundance of selected taxa. 5. The different patterns describing spatial variation of arthropod communities obtained using light and Malaise traps can be explained by differences in the taxa predominantly collected. Regarding the ongoing debate on insect decline, our results demonstrate that comparing different taxa from different taxon-specific traps is inappropriate. Thus, we recommend that future meta-analyses take into account the sampling methods and taxon-specific responses to environmental changes.

Single-cell expression and TCR data from CD19-specific CAR T cells in a phase I/II clinical trial

By leveraging single-cell transcriptome and T cell receptor (TCR) sequencing, we aimed to track the transcriptional signatures of CAR T cell clonotypes throughout the course of treatment and furthermore identify molecular patterns leading to potent CAR T cell cytotoxicity. The data presented in this study encompass blood and bone marrow samples from patients ≤ 21 years of age with relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) participating in the SJCAR19 phase I/II clinical trial (<a href="https://clinicaltrials.gov/ct2/show/NCT03573700">NCT03573700</a>). In brief, patients enrolled in the clinical trial received either 1 x 10^6 (dose level 1) or 3 x 10^6 (dose level 2) per kilogram of body weight following successful generation of autologous CAR T cell products and lymphodepleting chemotherapy. Peripheral blood was drawn from each participant every week until week 4 post-infusion, at week 6 or 8, and month 3 or 6 if feasible. At week 4 post-infusion, blood marrow was also collected from participants. Total T cells (CD3+) were sorted from each post-infusion sample, as well as the pre-infusion CAR T cell products, and processed through 10x Genomics' single-cell gene expression and V(D)J sequencing platform using the standard protocol. We identified a unique and unexpected transcriptional signature in a subset of pre-infusion CAR T cells that shared TCRs with post-infusion cytotoxic effector CAR T cells. Functional validation of cells with even a subset of these pre-effector markers demonstrated their immediate cytotoxic potential and resistance to exhaustion.

Artifacts for the 2022 ATVA Paper: SISL: Concolic Testing of Structured Binary Input Formats via Partial Specification

Artifacts for the evaluation of the publication SISL: Concolic Testing of Structured Binary Input Formats via Partial Specification, which will be published as part of the 2022 International Symposium on Automated Technology for Verification and Analysis (<a href="https://atva-conference.org/2022/">ATVA</a>). Usage of the provided artifacts requires installing the SISL tooling first. In this regard, please refer to either the <a href="https://agra-uni-bremen.github.io/sisl/">SISL user manual</a> or the documentation in the <a href="https://github.com/agra-uni-bremen/sisl">sisl</a> and <a href="https://github.com/agra-uni-bremen/sisl-vp">sisl-vp</a> GitHub repositories. Both sisl and sisl-vp need to be installed to system-wide locations in order to be able to use the scripts provided as part of these artifacts. More information on using the artifacts is available in the README.md file.

Code and data for "Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer".

Code and data for "Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer". <ul> <li> The publicly available datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository (<a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a>) and UCSC Xena Browser (TCGA, <a href="https://xena.ucsc.edu/">https://xena.ucsc.edu/</a>). </li> </ul>

Urban environments have species-specific associations with invasive insect herbivores

Urban areas are expanding rapidly, with the majority of the global and US population inhabiting them. Urban forests are critically important for providing ecosystem services to the growing urban populace, but their health is threatened by invasive insects. Insect density and damage are highly variable in different sites across urban landscapes, such that trees in some sites experience outbreaks and are severely damaged while others are relatively unaffected. To protect urban forests against damage from invasive insects and support future delivery of ecosystem services, we must first understand the factors that affect insect density and damage to their hosts across urban landscapes. This study explores how a variety of environmental factors that vary across urban habitats influence density of invasive insects. Specifically, we evaluate how vegetational complexity, distance to buildings, impervious surface, canopy temperature, host availability, and density of co-occurring herbivores impact three invasive pests of elm trees: the elm leaf beetle (Xanthogaleruca luteola), the elm flea weevil (Orchestes steppensis), and the elm leafminer (Fenusa ulmi). Except for building distance, all environmental factors were associated with density of at least one pest species. Furthermore, insect responses to these factors were species-specific, with direction and strength of associations influenced by insect life history. These findings can be used to inform future urban pest management and tree care efforts, making urban forests more resilient in an era where globalization and climate change make them particularly vulnerable to attack. Keywords: urban forest, invasive species, impervious surface, temperature, species interactions.

Comprehensive Context-specific Genome-scale Metabolic Models for Mus Musculus

Comprehensive Context-specific Genome-scale Metabolic Models for  Mus Musculus. The data consists of 28 models for the combination 2 mouse strains (WT and Ob/Ob), 2 diets (WT and HFD) and 7 tissues (Aorta, Heart, Liver, Skeletal Muscle, Hippocampus, Hypothalamus and Epididymal fat).

Data and scripts for: Satellite-tracking reveals sex-specific migration distance in green turtles (Chelonia mydas)

Data derivates and analysis scripts (in R) used for the paper "Satellite-tracking reveals sex-specific migration distance in green turtles (Chelonia mydas)", published in Biology Letters, on analyzing male and female green turtle movements in West Africa.

High-density electrode recordings reveal strong and specific connections between retinal ganglion cells and midbrain neurons.

This is the source file to be use for debugging problems on your own set-up. This files is a good example to both the repository provided for visual processing on the Kremow GitHub: https://github.com/KremkowLab/Axon-on-Neuropixels-in-Kilosort https://github.com/KremkowLab/tangential_recording

Dataset for: Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks

The set of molecular dynamics trajectories generated and analyzed in the paper "Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks."  Citations should refer directly to the manuscript.  The preprint version is available at: https://doi.org/10.1101/2022.07.14.500085 The uploaded zip file "trajectory_data.zip" contains trajectories for the (1) apo (2) h3k27ac and (3) h3k9ac systems.  In each directory is a subdirectory corresponding to the wild-type, deletion, and insertion mutations.  In each of those subdirectories are 10 XTC files, which correspond to the trajectories for the 10 different simulations performed for each system, along with an AMBER-formated PRMTOP file. Solvent molecules were removed from each file, and trajectories were strided such that there is one frame per 500 ps.

Sex-specific shifts in morphology and diet in a frog after 50 years of anthropogenic habitat fragmentation

Aim: Phenotypic shifts are commonly observed when animals face insular habitat change and may reflect ongoing stresses on individuals. However, the generality and the driving processes of this 'island rule' remain equivocal, notably in amphibians. Here, we investigate both morphological and dietary shifts in a frog using a mosaic of human-created islands to assess the potential operating mechanisms underlying these phenotypic responses. Location: Thousand Island Lake, China. Taxon: The Chinese piebald odorous frog, Odorrana schmackeri. Results: We found insular dwarfism in female but not male frogs. Meanwhile, insular females also had smaller gape widths after accounting for snout-vent lengths (SVLs) than mainland females. According to SEMs, resource availability had a direct positive effect on body size. Finally, diet composition differed between island and mainland populations, but only in females. Males and females on islands exhibited greater overlaps in diet. Main conclusions: In contrast with most studies in amphibians, we found insular dwarfism rather than gigantism in females. The smaller gape width after accounting for SVL in insular females suggests potential changes in prey utilization or food availability on these human-created islands. This notion is further supported by the differentiation of diet composition between island and mainland females. The higher diet overlap between sexes implies stronger intersexual competition for food resources after habitat fragmentation. Overall, we found shifts in morphology and diet in frogs which may implicate the influence of habitat fragmentation and underscores the need to consider intersexual differences when assessing responses of species to anthropogenic disturbances.

opencc-by-4.0Feb 2023View details →

Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1)

Dataset supporting publication 'Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland. J. Geophys. Res. Earth Surf. <a href="https://doi.org/10.1029/2022JF006857">https://doi.org/10.1029/2022JF006857</a>.' This dataset provides GIS ready shapefiles of mapped terminus traces for 24 east Greenland glaciers between 2013 and 2020 for the aforementioned publication. Data are provided in both geographic (EPSG: 4326; WGS84) and projected (EPSG:3413; NSIDC Sea Ice Polar Stereographic North) coordinate systems. As each terminus trace has metadata appended, including the unique path identifier, it is possible to directly and easily identify the original image used in the mapping process. Both shapefiles are compatible for ingestion into the Google Earth Digitisation Tool (GEEDiT) Reviewer (<a href="https://liverpoolgee.wordpress.com/">https://liverpoolgee.wordpress.com/</a>) for reviewing and sub-setting the dataset (see Lea, J.M. [2018] Earth Surf. Dynam. 6, 551–561. <a href="https://doi.org/10.5194/esurf-6-551-2018">https://doi.org/10.5194/esurf-6-551-2018</a>).   When using this data product in a publication, please include the following citations: Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023). Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.6904219">https://doi.org/10.5281/zenodo.6904219</a>. Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland.  J. Geophys. Res. Earth Surf. <a href="https://doi.org/10.1029/2022JF006857">https://doi.org/10.1029/2022JF006857</a>.

Provisioning latency increases closer to roads and is associated with species-specific reproductive success in two urban adapters

Most research on urban avian ecology has focused on population- and community-level phenomena, whereas fewer studies have examined how urbanization affects individual behavioral responses to a sudden and novel stimulus, and how those translate to fitness. We measured between-individual variation in provisioning latency in two urban adapters - great tits and blue tits - in response to an infrared camera installed in the nestbox, encountered when offspring in the nest were at the peak of food demand (9–10-days old). For each nestbox, we quantified urbanization as intensity in human activity, distance to road and proportion of impervious surface area. In both species, provisioning latency increased significantly closer to roads. Moreover, increased provisioning latency when exposed to a novel object was associated with higher reproductive success in great tits whose nestboxes were surrounded by high amounts of impervious surface. In contrast, increased provisioning latency was consistently associated with lower reproductive success in blue tits. Our results suggest that provisioning latency changes in relation to the environment surrounding the nest, and may be context- and species-specific when exposed to a novel stimulus, such as a novel object in the nest. To better understand the role of initial behavioral responses towards novelty across an individual's lifetime and, ultimately, its impact on fitness in the urban mosaic, further research explicitly testing different behavioral responses across the entire breeding cycle in wild model systems is needed.

opencc-by-4.0Sep 2018View details →

Fig. 1 in The Spider Mite Schizotetranychus Spireafolia (Acari, Tetranychidae), Specific Pest Of Spiraea In The A. V. Fomin Botanical Garden

Fig. 1. Live mites and egg.

Data for: Forecasting shifts in habitat suitability of three marine predators suggests a rapid decline in inter-specific overlap under future climate change

Aim: To estimate spatiotemporal changes in habitat suitability and inter-specific overlap among three marine predators: Baltic grey seals (Halichoerus grypus grypus), harbour seals (Phoca vitulina), and harbour porpoises (Phocoena phocoena) under contemporary and future conditions. Location: The southwestern region of the Baltic Sea, including the Danish Straits and the Kattegat, one of the fastest-warming semi-enclosed seas in the world. Methods: Location data (>200 tagged individuals) were analysed within the maximum entropy (MaxEnt) algorithm to estimate changes in total area size and overlap of species-specific habitat suitability between 1997-2020 and 2091-2100. A total of eleven candidate predictor variables were considered representing anthropogenic activity, environmental, and climate sensitive oceanographic conditions in the area. Sea surface temperature and salinity data were taken from representative concentration pathways [RCPs] scenarios 6.0 and 8.5 to forecast potential climate change effects. Results: Model output suggests that habitat suitability of Baltic grey seals will decline drastically over space and time, largely driven by changes in sea surface salinity and a loss of currently available haulout sites following sea level rise in the future. A similar though weaker response was observed for harbour seals, while suitability of habitat for harbour porpoises was predicted to remain fairly stable over space and time. Inter-specific overlap in highly suitable habitat was predicted to increase slightly under RCP scenario 6.0 when compared to contemporary conditions but to largely disappear under RCP scenario 8.5. Main conclusions: Marine predators in the southwestern Baltic Sea and adjacent waters may respond differently to future climatic conditions, leading to divergent shifts in habitat suitability that are likely to decrease inter-specific overlap. We, therefore, conclude that climate change can lead to a marked redistribution of area use by marine predators in the region, which may influence local food-web dynamics and ecosystem functioning.

opencc-zeroAug 2022View details →

Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking

Mutations in the microtubule (MT)-binding protein doublecortin (DCX) or in the MT-based molecular motor dynein result in lissencephaly. However, a functional link between DCX and dynein has not been defined. Here, we demonstrate that DCX negatively regulates dynein-mediated retrograde transport by reducing dynein's association with MTs and by disrupting the composition of the dynein motor complex. Previous work showed an increased binding of the adaptor protein C-Jun-amino-terminal kinase-interacting protein 3 (JIP3) to dynein in the absence of DCX. Using purified components, we demonstrate that JIP3 forms an active motor complex with dynein and its cofactor dynactin with two dyneins per complex. DCX competes with the binding of the second dynein, resulting in a velocity reduction of the complex. We conclude that DCX negatively regulates dynein-mediated retrograde transport through two critical interactions by regulating dynein binding to MTs and by regulating the association of JIP3 to the dynein motor complex.

opencc-by-4.0Aug 2022View details →

Photoreactor and organic micropollutants specifications

Specifications of the operating parameters of a photoreactor used. Specifications of organic micropollutants used.