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3,081 results for “array”
Experimental feeding validates nanofluidic array technology for DNA detection of ungulate prey in wolf scats
<p><span>The study of carnivores' diet is a key component to enhance knowledge on the ecology of predators and their effect on prey populations. Although molecular approaches to detect prey DNA in carnivore scats are improving, the validation of their accuracy, a prerequisite for reliable applications within ecological frameworks, is still lagging behind the methodological advances. Indeed, variation in detection probability among prey species can occur, representing a potentially insidious source of bias in food-habit studies of carnivores. Calibration of DNA-based methods involves the optimization of specificity and sensitivity and, whereas priority is usually given to the former to avoid false positives, sensitivity is rarely investigated so that false negatives may be largely overlooked. </span></p> <p><span>We conducted feeding trials with captive wolves (</span><em><span>Canis lupus</span></em><span>) to validate a nanofluidic array technology recently developed for detection of multiple prey species in scats. Using 371 scat samples from 12 wolves fed with a single-prey diet, the sensitivity of our nanofluidic array method varied between 0.45 and 0.95 for the six main ungulate prey species. The method sensitivity was enhanced by using multiple markers per species and by a relatively low threshold for the number of amplifying markers required to confirm a detection. Yet, at least two markers should be used to avoid false positives. By acknowledging sources of bias in sensitivity to reliably interpret results of DNA-based dietary methods, our study highlights the relevance of feeding experiments to optimally calibrate the relative thresholds to define a positive detection and investigate occurrence and extent of biases in sensitivity.</span></p>
Simple arrays for testing
<p>This are small arrays for testing that Zenodo can connect to Github Container registry and tests can be run over them.</p>
Photoelectrochemical performance of BiOI/TiO2 Nanotube Arrays (TNAs) p-n heterojunction synthesized by SILAR-ultrasonication-assisted methods
<p class="MsoNormal"><span>In order to extend the visible region activity of titania nanotube array (TNAs) films, the Successive Ionic Layer Adsorption and Reaction (SILAR)-ultrasonication-assisted method has been used to prepare BiOI-modified TiO<sub>2</sub> nanotube arrays (BiOI/TNAs). The band gap of BiOI/TNAs for all the variations reveals absorption in the visible absorption. The surface morphology of BiOI/TNAs is shown in the nanoplate, nanoflake, and nanosheet forms with a vertical orientation perpendicular to TiO<sub>2</sub>. The crystalline structure of BiOI did not change the structure of the anatase TNAs, with the band gap energy of the BiOI/TNAs semiconductor in the visible region. The photocurrent density of the BiOI/TNAs extends to the visible-light range. BiOI/TNAs with 1 mM Bi and 1 mM KI on TNAs 40 V 1 h 50 V 30 min shows the optimum photocurrent density. A tandem dye-sensitized solar cell (DSSC)-photoelectrochemical (PEC) was used for hydrogen production in salty water. BiOI/TNAs optimum was used as the photoanode of the PEC cell. Solar to hydrogen conversion efficiency (STH) of tandem DSSC-PEC reaches 1.34% in salty water.</span></p>
(SNP Array) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution
<p>Single nucleotide polymorphism (SNP) array data files related our publication titled "Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of <em>TP53 </em>mutant Leukaemic Evolution".</p>
Adaptations to the deep-sea alongside presence of a mega-array of homeobox genes in the genome of the cnidarian Actinernus
<p>Members of the phylum Cnidaria include sea anemones, corals, and jellyfishes, and have successfully colonised both marine and freshwater habitats throughout the world. Understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here we report the first chromosome-level deep-sea cnidarian genome, of the anemone <em>Actinernus</em>. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, ParaHox, NK cluster, and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. Analysis of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Compared to other sea anemones, circadian rhythm genes were lost in <em>Actinernus</em>, which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular and reveals some of the molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment.</p>
Dataset for: Biomimetic models of fish gill rakers as lateral displacement arrays for particle separation
<p class="MsoNormal">Ram suspension-feeding fish such as herring use gill rakers to separate small food particles from large water volumes while swimming forward with an open mouth. Fish gill raker function was tested using 3D-printed conical models and computational fluid dynamics (CFD) simulations over a range of slot aspect ratios. (See CFD simulation output in Dryad dataset: case and data files for ANSYS Fluent 19.1 CFD simulations.)</p> <p class="MsoNormal">Our hypothesis predicting the exit of particles based on mass flow rates, dividing streamlines (i.e., stagnation streamlines) at the slots between gill rakers, and particle size was supported by the results of experiments with physical models in a recirculating flume. (See R code with embedded comments in Dryad dataset to test Hypotheses 1 and 2 for particle exit/trapping.)</p> <p class="MsoNormal">Particle movement in suspension-feeding fish gill raker models was consistent with the physical principles of lateral displacement arrays ("bump arrays") for microfluidic and mesofluidic separation of particles by size. Although particles were smaller than the slots between rakers, particles skipped over the vortical region that was generated downstream from each raker. Particles "bumped" on anterior raker surfaces during posterior transport. (See particle movement data in Dryad dataset: three files for particle contact, exit, and retention in the physical models.)</p> <p class="MsoNormal">Experiments in a recirculating flume demonstrated that the shortest distance between the dividing streamline and the raker surface preceding the slot predicts the maximum radius of a particle that will exit from the model by passing through the slot. This theoretical maximum radius is analogous to the critical separation radius identified with reference to the stagnation streamlines in microfluidic and mesofluidic devices that use deterministic lateral displacement and sieve-based lateral displacement. These conclusions provide new perspectives and metrics for analyzing crossflow and cross-step filtration in fish with applications to filtration engineering. </p>
Datasets for "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents"
<p>Datasets used in the manuscript titled, "<strong>Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents</strong>" are uploaded here. </p> <p><strong>Brightfield and fluorescent stained images of brain tissue used for Fig. 5(a):</strong></p> <p>Malt3-20190624_Region 009_DAPI.png</p> <p>Malt3-20190624_Region 009_qCy5.png</p> <p>Malt3-20190624_Region 009_qFITC.png</p> <p>Malt3-20190624_Region 009_qTexasRed.png</p> <p>Malt3_BF20190628_Region 001.png</p> <p><strong>Fluorescent image of brain with embedded CFETs:</strong></p> <p>MALT2_Rat_100um_MOR1_x500_TSA_AF488.jpg</p> <p>Rat_100um_MOR1_x500_TSA.czi</p> <p><strong>In vivo dopamine recording data for Fig. 3:</strong></p> <p>ratarrays822_163.mat</p> <p>ratarrays822_57.mat</p>
Data from: Electrical imaging of cortical and spinal axons using high-density microelectrode arrays
<div> <div> <div> <p>Mammalian axons are specialized for transmitting action potentials to targets within the central and peripheral nervous system. A growing body of evidence suggests that, besides signal conduction, axons play essential roles in neural information processing, and their malfunctions are common hallmarks of neurodegenerative diseases. The technologies available to study axonal function and structure integrally limit the comprehension of axon neurobiology. </p> <p>Complementary-metal-oxide-semiconductor (CMOS) -based high-density microelectrode arrays (HD-MEAs) have been designed to record extracellular action potentials from neuronal cultures and allow tracking axonal signals across hundreds of microelectrodes. Thanks to a low-noise CMOS-design, HD-MEAs enable detection of APs across entire arbors of cortical axons. HD-MEAs provide noninvasive access to axonal action potentials and impose no constraints on the duration of the recording sessions. Here we present extracellular electrical activity recorded from rat's primary neurons using CMOS-based HD-MEA system (MaxWell Biosystems AG). Datasets comprise electrophysiological recordings obtained from primary motor and cortical neurons. Recorded signals were up-sampled to 200 kHz following the Whitaker-Shannon interpolation formula. Recorded signals were spike-sorted and spike-trigger averaged across an entire array (26400 electrodes). Such signal representation is referred to as 'axonal electrical image'. </p> </div> </div> </div>
The second data release from the European Pulsar Timing Array II. Customised pulsar noise models for spatially correlated gravitational waves
<p>Aims: The nanohertz gravitational wave background (GWB) is expected to be an aggregate signal of an ensemble of gravitational waves emitted predominantly by a large population of coalescing supermassive black hole binaries in the centres of merging galaxies. Pulsar tiNanohertz ming arrays (PTAs), which are ensembles of extremely stable pulsars at approximately kiloparsec distances precisely monitored for decades, are the most precise experiments capable of detecting this background. However, the subtle imprints that the GWB induces on pulsar timing data are obscured by many sources of noise that occur on various timescales. These must be carefully modelled and mitigated to increase the sensitivity to the background signal. Methods: In this paper, we present a novel technique to estimate the optimal number of frequency coefficients for modelling achromatic and chromatic noise, while selecting the preferred set of noise models to use for each pulsar. We also incorporated a new model to fit for scattering variations in the Bayesian pulsar timing package temponest. These customised noise models enable a more robust characterisation of single-pulsar noise. We developed a software package based on tempo2 to create realistic simulations of European Pulsar Timing Array (EPTA) datasets that allowed us to test the efficacy of our noise modelling algorithms. Results: Using these techniques, we present an in-depth analysis of the noise properties of 25 millisecond pulsars (MSPs) that form the second data release (DR2) of the EPTA and investigate the effect of incorporating low-frequency data from the Indian Pulsar Timing Array collaboration for a common sample of ten MSPs. We used two packages, enterprise and temponest, to estimate our noise models and compare them with those reported using EPTA DR1. We find that, while in some pulsars we can successfully disentangle chromatic from achromatic noise owing to the wider frequency coverage in DR2, in others the noise models evolve in a much more complicated way. We also find evidence of long-term scattering variations in PSR J1600-3053. Through our simulations, we identify intrinsic biases in our current noise analysis techniques and discuss their effect on GWB searches. The analysis and results discussed in this article directly help to improve the sensitivity to the GWB signal and they are already being used as part of global PTA efforts.</p>
The second data release from the European Pulsar Timing Array I. The dataset and timing analysis
<p>Pulsar timing arrays offer a probe of the low-frequency gravitational wave spectrum (1−100 nanohertz), which is intimately connected to a number of markers that can uniquely trace the formation and evolution of the Universe. We present the dataset and the results of the timing analysis from the second data release of the European Pulsar Timing Array (EPTA). The dataset contains high-precision pulsar timing data from25 millisecond pulsars collected with the five largest radio telescopes in Europe, as well as the Large European Array for Pulsars. The dataset forms the foundation for the search for gravitational waves by the EPTA, presented in associated papers. We describe the dataset and present the results of the frequentist and Bayesian pulsar timing analysis for individual millisecond pulsars that have been observed over the last∼25 years.We discuss the improvements to the individual pulsar parameter estimates, as well as new measurements of the physical properties of these pulsars and their companions. This data release extends the dataset from EPTA Data Release 1 up to the beginning of 2021, with individual pulsar datasets with timespans ranging from 14 to 25 years. These lead to improved constraints on annual parallaxes, secular variation of the orbital period, and Shapiro delay for a number of sources. Based on these results, we derived astrophysical parameters that include distances, transverse velocities,binary pulsar masses, and annual orbital parallaxes.</p>
Seismic node array data for iMUSH shot Y4
<p>Matlab file containing waveform data with a sample rate of 250 Hz from 20 s before to 120 s after shot Y4.</p>
Myomatrix arrays for high-definition muscle recording
Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous system's actual motor output – the activation of muscle fibers by motor neurons – typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices ("Myomatrix arrays") that record muscle activity at cellular resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a "motor unit", during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous system's motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and in identifying pathologies of the motor system.
The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.
<p><em>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.</em></p>
Source data for: Raman sideband cooling of molecules in an optical tweezer array
<p>Ultracold molecules, because of their rich internal structures and interactions, have been proposed as a promising platform for quantum science and precision measurement. Direct laser-cooling promises to be a rapid and efficient way to bring molecules to ultracold temperatures. For trapped molecules, laser-cooling to the quantum motional ground state remains an outstanding challenge. A technique capable of reaching the motional ground state is Raman sideband cooling, first demonstrated in trapped ions and atoms. In this work, we demonstrate for the first time Raman sideband cooling of molecules. Specifically, we demonstrate 3D Raman cooling for single CaF molecules trapped in an optical tweezer array, achieving average radial (axial) motional occupation as low as $\bar{n}_r=0.27(7)$ ($\bar{n}_z=7.0(10)$). Notably, we measure a 1D ground state fraction as high as 0.79(4), and a motional entropy per particle of $s = 4.9(3)$, the lowest reported for laser-cooled molecules to date. These lower temperatures could enable longer coherence times and higher fidelity molecular qubit gates desirable for quantum information processing and quantum simulation. With further improvements, Raman cooling could also be a new route towards molecular quantum degeneracy applicable to many laser-coolable molecular species including polyatomic ones. </p>
Sky model from the paper "Prospects for a survey of the Galactic plane with the Cherenkov Telescope Array" by the CTA Consortium
<p>The main source model definition file is provided in two formats.</p> <p>- models_gps.xml: readable using GammaLib/ctools, see http://cta.irap.omp.eu/ctools/users/user_manual/models.html</p> <p>- models_gps.yaml: readable using Gammapy, see https://docs.gammapy.org/1.1/tutorials/api/models.html#model-lists-and-serialisation</p> <p> </p> <p>We provide separately the three alternative interstellar emission models.</p> <p>- base: IEM_base.fits</p> <p>- varmin: IEM_varmin.fits.gz</p> <p>- varmin-rescaled: IEM_varmin_rescaled.fits.gz</p> <p>To use the interstellar models one can employ:</p> <p>- GammaLib/ctools, see http://cta.irap.omp.eu/ctools/users/user_manual/models_spatial.html#diffusemapcube</p> <p>- Gammapy, see https://docs.gammapy.org/1.1/tutorials/data/fermi_lat.html#galactic-diffuse-background</p> <p> </p> <p>This work was conducted in the context of the CTA Consortium. We gratefully acknowledge financial support from the agencies and organizations listed here: https://www.cta-observatory.org/consortium_acknowledgments/.</p>
Recording of Psyche with the Allen Telescope Array shortly after launch (decimated)
<p>This dataset contains an IQ recording of the X-band 8417.7 MHz telemetry signal from the Psyche spacecraft done with the Allen Telescope Array starting only 1 hour 30 minutes after launch. Antennas 1a and 5c from the ATA were used in dual linear polarization (X and Y polarizations).</p><p>The hardware configuration was as follows: the antennas were connected to RFCB LO d, which was tuned to a frequency of 8417 MHz and used an output IF of 512 MHz. A USRP N321 and N320 digitized both polarizations of each antenna. The USRPs used an external 10 MHz reference and PPS coming from the observatory distribution system, and LO sharing was set up among the four channels. The IQ sample rate of the USRPs was 4.096 Msps and a GNU Radio flowgraph was used to record IQ data to disk. The GNU Radio flowgraph stored the IQ data for each channel as 16-bin integers in the <a href="https://wiki.gnuradio.org/index.php/Metadata_Information">GNU Radio metatata file format</a>, with detached headers.</p><p>After recording, the data was downsampled to 128 ksps centered around 8417.525 MHz and formatted using <a href="https://github.com/gnuradio/SigMF">SigMF</a> with the script do_sigmf.py. This reduced bandwidth is sufficient to decode the low data rate (2 kbps) telemetry signal. There is a higher data rate (61.1 kbps) signal, as well as sequential ranging tones, near the end of the recording for which this bandwidth is insufficient. The original 4.096 Msps data for this part of the recording has been published for a single antenna and polarization in 8-bit resolution in the dataset "<a href="https://zenodo.org/records/10023378">Recording of Psyche with the Allen Telescope Array shortly after launch (wideband)</a>".</p>
Recording of Psyche with the Allen Telescope Array shortly after launch (wideband)
<p>This dataset contains an IQ recording of the X-band 8417.7 MHz telemetry signal from the Psyche spacecraft done with the Allen Telescope Array starting only 1 hour 30 minutes after launch. Antennas 1a and 5c from the ATA were used in dual linear polarization (X and Y polarizations).</p> <p>The hardware configuration was as follows: the antennas were connected to RFCB LO d, which was tuned to a frequency of 8417 MHz and used an output IF of 512 MHz. A USRP N321 and N320 digitized both polarizations of each antenna. The USRPs used an external 10 MHz reference and PPS coming from the observatory distribution system, and LO sharing was set up among the four channels. The IQ sample rate of the USRPs was 4.096 Msps and a GNU Radio flowgraph was used to record IQ data to disk. The GNU Radio flowgraph stored the IQ data for each channel as 16-bin integers in the <a href="https://wiki.gnuradio.org/index.php/Metadata_Information">GNU Radio metatata file format</a>, with detached headers.</p> <p>After recording, the data was formatted using <a href="https://github.com/gnuradio/SigMF">SigMF</a> with the script do_sigmf.py. This dataset contains only the last part of the recording in the original 4.096 Msps sample rate, and only one antenna and polarization. During most of the recording the spacecraft signal is a low rate signal (2 kbps) that fits in a much smaller bandwidth, so another dataset "<a href="https://zenodo.org/records/10003647">Recording of Psyche with the Allen Telescope Array shortly after launch (decimated)</a>" has been published with 128 ksps centered at this signal for each antenna and polarization.</p>
Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds
<p>Genotyping data in ped and map format (ped/map) for 72 goats and 53,347 genotypes.</p>
Clinical Assessment of a Novel Microprobe Array Continuous Glucose Monitor for Type 1 Diabetes
ClinicalTrials.gov study NCT01908530. IPD Sharing: NO. Countries: 1. Publications: 5.
Clinical and Histological Evaluation of the Picosure 755nm Laser With Cap Array for Facial Rejuvenation
ClinicalTrials.gov study NCT02107157. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.