Loading...
Loading...
DNA/RNA sequences, gene expression, protein structures, metagenomics, single-cell sequencing
27,650 datasets
Three alternative conformational states of the ATP-γS-bound human 26S proteasome, visualized by cryo-electron microscopy at near-atomic resolutions. The dataset, from a study by Yanan Zhu of Peking University, captures the nucleotide-driven remodeling of the AAA-ATPase channel controlling substrate translocation gate opening.
Gene expression profiles from male C57BL6/J mice across four brain regions following a five-day food restriction, authored by D. J. Guarnieri of Yale University. The dataset includes quantitative PCR validation, plasma corticosterone measurements, and progressive ratio behavioral tests. It was sourced from the paperswithcode platform.
Chris Vincent from University College London conducted an interview study with professionals from major medical device manufacturers. The study explores barriers and opportunities for user-centered design in medical device development. Findings are organized into four themes: collaborative working practices, understanding users, justifying user-centered approaches, and providing guidance.
1400 river gauging stations and 1800 river level monitoring sites across England and Wales provide water height measurements. The Environment Agency and Natural Resources Wales collect data via automatic field instruments, typically logging values every 15 minutes. During flooding incidents, update frequency can be increased if site technology allows.
Jean Morrison from the University of Chicago proposes rank conditional coverage (RCC) as a new criterion for confidence intervals in high-dimensional settings. The paper describes two bootstrap-based methods implemented in the R package 'rcc', available on CRAN, which aim to provide better coverage for the most significant parameter estimates. This work addresses the problem of marginal confidence intervals having low coverage rates for top-ranked parameters in multiple testing scenarios.
Tab-delimited files report calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues (Asp, Glu, Asn, Gln) in RNase H homologs. The dataset also includes complete 100ns molecular dynamics trajectory data for E. coli RNase H under apo and magnesium-bound conditions, authored by Kate A. Stafford of Columbia University.
Ye Tian from Columbia University proposes a new variable screening framework called Random Subspace Ensemble (RaSE). The method is designed to identify predictors that are jointly dependent with the response, even when they have no marginal effect. It includes theoretical guarantees like sure screening property and rank consistency, supported by simulation studies and real-data analysis.
Research data from Columbia University explores the role of conserved PHD finger protein ZFP-1 and RNAi factor RDE-4 in modulating insulin signaling and lifespan in Caenorhabditis elegans. The study identifies their negative regulation of PDK-1 transcription and links it to oxidative stress resistance and longevity. Findings suggest epigenetic and RNAi mechanisms significantly impact signaling pathway outcomes.
269 binding regions for the bacterial replication initiator DnaA were identified using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). The dataset, produced by Janet L. Smith at MIT, provides single nucleotide resolution binding data for ATP-DnaA and ADP-DnaA, refining the consensus sequence of the DnaA binding site. It serves as a backdrop for interpreting in vivo binding and regulation of DnaA.
Open access data and scripts for the figures in Colbois et al., PRB 2021. The repository contains raw data from micromagnetic simulations using MuMax, experimental spin configuration images, and analysis results for nearest-neighbor and J1-J2-J3 models. The data was produced by researchers at École Polytechnique Fédérale de Lausanne.
A database of 16 reinforced concrete walls with lap splices and 8 reference walls with continuous reinforcement, compiled from recent experimental tests. The dataset includes shell element models developed in Vector2 to simulate their inelastic force-displacement response. It was assembled by researchers from École Polytechnique Fédérale de Lausanne and published in 2017.
A psychology experiment by M. van Elk of École Polytechnique Fédérale de Lausanne investigated the relation between body semantics and spatial body representations. Participants judged word pairs referring to body parts under congruent or incongruent spatial layouts and varying distances. The findings suggest task-dependent activation of visuo-spatial body representations, discussed in the context of embodied cognition theories.
A randomized field experiment tested ways to stimulate savings by international migrants in their origin country. The study, by Claudia Martinez A. of Harvard University, offered U.S.-based migrants from El Salvador bank accounts with varying degrees of control over savings in El Salvador. It found migrants offered the greatest control accumulated the most savings, with impacts likely representing total savings increases rather than reallocations.
An experimental study by Felipe De Brigard of Harvard University examining the influence of repeated simulation on the perceived plausibility of episodic counterfactual thoughts. Participants recalled negative, positive, and neutral autobiographical memories and later re-simulated self-generated counterfactual alternatives either once or four times. The results indicate that repeated simulation decreases perceived plausibility while increasing ratings of ease, detail, and valence.
Datasets for the Virtual ChIP-seq software contain reference matrices, trained models, and pre-calculated features for predicting transcription factor binding. The data includes correlation matrices for TFs A-Z, genomic conservation scores, PWM scores from JASPAR, and ChIP-seq data from ENCODE and Cistrome. This repository was created by Mehran Karimzadeh of the University of Toronto.
The National Mooring Network Facility provides wave time-series observations from moorings deployed in Australian coastal ocean waters. The collection includes data from the Darwin and Yongala National Reference Stations and regional moorings at Beagle Gulf, Heron Island South, and One Tree East. Observations were made using acoustic Doppler current profilers (ADCPs) or AWAC ADCPs, with primary parameters likely including temperature, pressure, instrument depth, and wave-related metrics.
University of Helsinki researcher Jarno Alanko provides a Themisto v3 colored k-mer index for 639,981 high-quality bacterial genomes. The index contains 71 billion distinct 31-mers, each annotated with one of 2340 distinct species identifiers. This resource enables sensitive pseudoalignment of sequencing reads against a large collection of bacterial genomes.
Helsinki University Hospital collected multi-channel EEG recordings from 79 term neonates admitted to its NICU, with a median recording duration of 74 minutes. Three human experts annotated the EEGs for seizures, with an average of 460 seizure events annotated per expert, resulting in a consensus of seizures in 39 neonates and seizure-free status in 22. This dataset serves as a reference set for analyzing seizure characteristics and developing automated detection methods.
Deena Iskander from Imperial College London led a study using single-cell assays of patient-derived bone marrow to investigate mechanisms of failing erythropoiesis in Diamond-Blackfan anemia. The analysis delineated distinct cellular trajectories segregating with ribosomal protein genotypes, revealing differences in erythroid specification and inflammatory milieu. These findings may help facilitate therapeutic target discovery for this rare ribosomopathy.
DNA-encoded chemical libraries allow synthesis and screening of chemical compound collections of unprecedented size and diversity. This chapter by Jörg Scheuermann of ETH Zurich reviews concepts and applications related to Dual-pharmacophore DNA-encoded chemical libraries, characterizing a chelate effect improvement of ≥1000-fold for bidentate binding. The technology represents a complement to conventional fragment-based lead discovery strategies.