Find research datasets worth reusing

CAD-based Assembly Sequence Planning for Increased Operational Flexibility Dataset

Operational flexibility represents the ability to adapt to changes in production or assembly processes. It is a crucial aspect of assembly sequence planning for a dynamic environment (such as large-scale assembly systems). The choice of graph model, such as precedence graph or AND/OR graph, can significantly impact operational flexibility. The state-of-the-art research has demonstrated the utility of precedence graphs and AND/OR graphs for flexible assembly lines. However, AND/OR graphs offer the potential for even greater operational flexibility but with a higher computational cost. Further research is still needed on the detailed effects of precedence graphs and AND/OR graphs on operational flexibility and the limits for their application to large-scale assemblies. The trade-offs between different models and their impact on operational flexibility and computational costs is observed. 1st underlying research question: Which graph model, derived from CAD-based assembly-by- disassembly, can increase the operational flexibility in integrated assembly sequence planning and job scheduling problems? A hypothesis is formulated to answer this research question, which will be used to design an experiment and be tested. Hypothesis 1: The AND/OR graph can be utilized to improve the operational flexibility in comparison to the precedence graph.

opencc-by-4.0May 2023View details →

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"   compressed FASTA files for 16s amplicon sequences relating to two separate projects,  "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities" and "Habitat filtering leads to phylogenetic clustering in synthetic microbial communities". DADA22 pipeline is included, which pools all samples for better accuracy. A Julia script bioinfo.jl is then used to select only the samples relevant to spatial structure project.   All csv filenames are appended with "_q" indicating an increase in the stringency of quality filtering parameters (also increasing minimum hamming distance used in DADA2 algorithm to 5) to produce a taxa table with a sensible number of ASVs (given a known number of input strains) with each ASV uniquely aligning to an individual sequence from colony PCR of said input strains.

Negative sample sequences contained in datasets D1-D7

These are the negative sample sequences contained in datasets D1-D7, which do not contain the correct barcode.

Single Cell RNA sequencing data of ADT treated Prostate cancer patients

The data was generated from a study that was conducted according to guidelines approved by the Review Board at the University of Texas Southwestern Medical Center. We procured patient biopsy samples from two distinct studies. The first is titled "Tissue Collection and Results Gathering for Radiotherapy Patients & Healthy Individuals" (STU 072010-098), and the second is a Phase I Clinical Study on Stereotactic Ablative Radiotherapy (SABR) for Pelvic and Prostate Areas in High-Risk Prostate Cancer Patients (STU062014-027). The single-cell RNA sequencing (scRNA-seq) took place in Dr. Douglas Strand's laboratory, adhering to the method outlined in Henry et al1. We used a 1-hour treatment with 5mg/ml of collagenase type I, 10mM of ROCK inhibitor, and 1mg of DNase. Barcode labeling for 3' GEX was done using a 10X machine, and the sequencing process utilized an Illumina NextSeq 500 device.   1. Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J., ... & Strand, D. W. (2018). A cellular anatomy of the normal adult human prostate and prostatic urethra. Cell reports, 25(12), 3530-3542.

Revisit of 77 Clusters Candidates with Multiple Main Sequences using Gaia DR3

The data of 77 clusters with eMSTO.

opencc-zeroAug 2023View details →

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

opencc-zeroAug 2023View details →

Dataset for: mRNA vaccine quality analysis using RNA sequencing

The success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.

opencc-by-4.0Dec 2022View details →

Neuromorphic sequence learning with an event camera on routes through vegetation

code and dataset for paper 'Neuromorphic sequence learning with an event camera on routes through vegetation'.

opencc-zeroAug 2023View details →

Raw target enrichment of conserved element sequence data for 24 black coral species

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of "source" slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

opencc-by-nc-nd-4.0Sep 2023View details →

Models and Data associated with: Single-cell gene expression prediction from DNA sequence at large contexts

This archive holds trained models and associated data for the <a href="https://www.biorxiv.org/content/10.1101/2023.07.26.550634v1">manuscript</a>: "Single-cell gene expression prediction from DNA sequence at large contexts" Structure: <ul> <li>configs - example configs for the workflows to produce publication data </li> <li>data_* - pre-processed single cell data used for publication</li> <li>models_* - model checkpoints, hyperparameters and training progress in tensorboard logs</li> <li>preprocessing - additional data required to reproduce the pre-processing workflow</li> </ul>   "Copyright 2023 GlaxoSmithKline Research & Development Limited. All rights reserved."

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

opencc-by-4.0Sep 2023View details →

Phantom measurement data for 'Myelin water imaging at 0.55 T using a multi-gradient-echo sequence'

This dataset contains the phantom mGRE measurement data used in the submitted article Schäper et al. 'Myelin water imaging at 0.55 T using a multi-gradient-echo sequence'. The acquisitions were done with a 0.55 T MRI system (Magnetom Free.Max; Siemens Healthcare, Erlangen, Germany) using a 12 channel head coil and a 3 T MRI system (Magnetom Prisma; Siemens Healthcare, Erlangen, Germany) using a 20 channel head coil. For further measurement details, please refer to the mentioned original article.

Heatwave grazing kelp microbes sequences

The range-expansion of tropical herbivores due to ocean warming can profoundly alter temperate reef communities by overgrazing the seaweed forests that underpin them. Such ecological interactions may be mediated by changes to seaweed-associated microbiota in response to warming, but empirical evidence demonstrating this is rare. We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp Ecklonia radiata's microbiotain sustained warming and MHW treatments were enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid Sargassum linearifolium's microbiota was unaffected by temperature. Consumption by the tropical sea-urchin Tripneustes gratilla was greater on Ecklonia where the microbiota had been altered by higher temperatures, while Sargassum's consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. Effects of warming and MHWs on seaweed holobionts (host plus its microbiota) are likely species-specific. The effect of increased temperature on Ecklonia's microbiota and subsequent increased consumption suggest that changes to kelp microbiota may underpin kelp-herbivore interactions, providing novel insights into potential mechanisms driving change in species' interactions in warming oceans.

COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA

Developing systematic conservation plans depends on a wealth of information on a region's biodiversity. For 'dark taxa' such as arthropods, such data is usually very incomplete and in most cases left out from assessments. Sky islands are important and often fragile biodiversity hotspots. Southern Appalachian high-elevation spruce-fir forests represent a particularly threatened sky-island ecosystem, hosting numerous endemic and threatened species, but their arthropods remain understudied. Here we use voucher-based megabarcoding to explore genetic differentiation among leaf-litter arthropod communities of these highlands, and to examine the extent to which they represent dispersed communities of more or less coherent species, manageable as a distributed unit. We assembled a dataset comprising >6000 COI sequences representing diverse arthropod groups to assess species richness and sharing across peaks and ranges. Comparisons were standardized across taxa using automated species delimitation, measuring endemism levels by putative species. Species-richness was high, with sites hosting from 86-199 litter arthropod species (not including mites or myriapods). Community profiles suggest that around one-fourth of these species are unique to single sky islands and more than one-third of all species are limited to a particular range. Across major taxa, endemicity was lowest in Araneae, and highest in neglected groups like Isopoda, Pseudoscorpionida, Protura, and Diplura. Southern Appalachian sky islands of spruce-fir habitat host significantly distinct leaf litter arthropod communities, with high levels of local endemicity. This is the first work to provide such a clear picture of peak and range uniqueness for a taxonomically broad sample. Ensuring the protection of a sizeable fraction of high-elevation litter species richness will therefore require attention at a relatively fine spatial scale.

opencc-by-4.0Sep 2023View details →

The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2).  The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.

HLA class I Sanger sequences data of Honduras HIV cohort

HLA polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distribution can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency and the impact of these variants on HIV disease outcome. HLA class I (cI) loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, ART-naïve individuals from Honduras. HLA LD were assessed using Fisher's exact test. Using univariable and multivariable analyses we evaluated HLA associations with HIV pVL and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. Previously defined HLA associations were found: B*57:01/03, B*42:01, A*25:01 and C*12:03 (protective), and B*53:01 and A*68:01 (risk). Being consistent with our previous research in a Mesoamerican HIV cohort, Amerindian B*35:12 was associated to poor HIV control. Other HLA-HIV associations not previously described were C*03:04 and B*08:01 that were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness admixture of the Honduras population that express Amerindian, Caucasian and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association.

opencc-by-4.0Feb 2023View details →

Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing

Data and scripts of the manuscript "Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing" by Rosario Vanella, Christoph Küng, Alexandre A. Schoepfer, Vanni Doffini, Jin Ren and Michael A. Nash.

opencc-by-4.0Oct 2023View details →

Fragment-sequencing unveils local tissue microenvironments at single-cell resolution

This dataset contains the Resolve dataset that was used in the publication. Other data set can be found in GEO with the accession number GSE216189. The code that was used during the analysis can be found on our GitHub repository: https://github.com/Moors-Code/Fragment-sequencing

opencc-by-4.0Oct 2023View details →

HG002 data for Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

This dataset includes 6mA frequency data for the HG002 native DNA (untreated) sample sequenced on nanopore r9.4.1.