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6,335 results for “direct”
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-2)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-2; the files are splited two two parts because of limitations of file size).</p>
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-1)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-1; the files are splited two two parts because of limitations of file size).</p>
Data from: "Glycerol-blended chitosan membranes with directional micro-grooves and reduced stiffness improve Schwann cell wound healing"
<h3>ABSTRACT</h3> <p>Regenerative medicine is continuously looking for new natural biocompatible and possibly biodegradable materials, but also mechanically compliant. Chitosan is emerging as a promising FDA-approved biopolymer for tissue engineering, however, its exploitation in regenerative devices is limited by its brittleness and can be further improved, for example, by blending it with other materials or by tuning its superficial microstructure. Here, we developed membranes made of chitosan and glycerol, by solvent casting and micropatterned them with directional geometries with different levels of axial symmetry. These membranes were characterized by light microscopy and atomic force microscopy (AFM), thermal, mechanical, and degradation assays, and also tested in vitro as scaffolds with Schwann cells. The glycerol-blended chitosan membranes are optimized in terms of mechanical properties, and present a physiological-grade Young's modulus (≈ 0.7 MPa). The directional topographies are effective in directing cell polarization and migration and in particular are highly performant substrates for collective cell migration. Here, we demonstrate that a combination of a soft compliant biomaterial and topographical micropatterning can improve the integration of these scaffolds with Schwann cells, which is a fundamental step in the peripheral nerve regeneration process.</p>
Direct electrochemical reduction of graphene oxide thin film for aptamer-based selective and highly sensitive detection of matrix metalloproteinase 2
<p>Simple and low-cost biosensing solutions are suitable for point-of-care applications aiming to overcome the gap between scientific concepts and technological production. To compete with sensitivity and <a title="Learn more about selectivity from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/selectivity">selectivity</a> of golden standards, such as <a title="Learn more about liquid chromatography from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/liquid-chromatography">liquid chromatography</a>, the functionalization of biosensors is continuously optimized to enhance the signal and improve their performance, often leading to complex chemical assay development. In this research, the efforts are made on optimizing the methodology for <a title="Learn more about electrochemical reduction from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/electrochemical-reaction">electrochemical reduction</a> of <a title="Learn more about graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/chemistry/graphene-oxide">graphene oxide</a> to produce thin film-modified gold electrodes. Under the employed specific conditions, 20 cycles of <a title="Learn more about cyclic voltammetry from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cyclic-voltammetry">cyclic voltammetry</a> (CV) are shown to be optimal for superior electrical activation of <a title="Learn more about graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/graphene-oxide">graphene oxide</a> into electrochemically <a title="Learn more about reduced graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/reduced-graphene-oxide">reduced graphene oxide</a> (ERGO). This platform is further used to develop a <a title="Learn more about matrix metalloproteinase 2 from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/mmp2">matrix metalloproteinase 2</a> (MMP-2) biosensor, where specific anti-MMP2 <a title="Learn more about aptamers from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/aptamer">aptamers</a> are utilized as a biorecognition element. MMP-2 is a protein which is typically overexpressed in tumor tissues, with important roles in tumor invasion, metastasis as well as in tumor <a title="Learn more about angiogenesis from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/angiogenesis">angiogenesis</a>. Based on impedimetric measurements, we were able to detect as low as 3.32 pg mL<sup>−1</sup> of MMP-2 in PBS with a dynamic range of 10 pg mL<sup>−1</sup> – 10 ng mL<sup>−1</sup>. Further experiments with real blood samples revealed a promising potential of the developed sensor for direct measurement of MMP-2 in complex media. High specificity of detection is demonstrated – even to the closely related <a title="Learn more about enzyme from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme">enzyme</a> MMP-9. Finally, the potential of reuse was demonstrated by signal restoration after experimental detection of MMP-2.</p>
Ultra II Directional RNA +UMI Qualification Data
<p>This is some of the data used to qualify the <a href="https://www.neb.com/en-us/products/e7416-nebnext-multiplex-oligos-for-illumina-unique-dual-index-umi-adaptors-rna-set-1">NEBNext® Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1)</a>.</p> <p>Libraries were prepared from 100 ng of UHR RNA (Agilent) using the <a href="https://www.neb.com/en-us/products/e7760-nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina">NEBNext Ultra II Directional RNA Library Prep Kit</a> with <a href="https://www.neb.com/en-us/products/e7400-nebnext-rrna-depletion-kit-v2-human-mouse-rat">ribosomal depletion</a>.</p> <p> </p>
Experimental data supporting the paper "Fluorescence from a single-molecule probe directly attached to a plasmonic STM tip"
<p>Experimental STM, STS and STML data studying the fluorescent behaviour of a PTCDA molecule attached to the metallic apex of a scanning tunneling microscope.</p> <p> </p> <p>Treated source data of all Figures included in the publication.</p>
Harnessing coupled nanolasers near exceptional points for directional emission - Figures Data
<p>Each figure's generative Matlab script is placed in a separate folder, along with the associated data.</p>
Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning
<p>Dataset used in "Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning"</p> <p>https://www.biorxiv.org/content/10.1101/2024.09.23.614484v1</p>
Associated data for "Optimisation strategies for directed evolution without sequencing"
<p>Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).</p>
Dataset for ''First comparison of MLT 3-dimensional wind retrieval methods and first direct extraction of vertical wind tides''
<p>This dataset supports the figures in the article "First comparison of the MLT vertical wind retrieval methods and first direct extraction of vertical wind tides" and the supporting information. The data are provided in MatLab format.</p>
Outward foreign direct investment and upgrading of enterprise export product quality——From the Perspective of Industrial Agglomeration
Open the record for dataset details and reuse information.
Fig. 4 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 4. Somatic embryos induction of P. vera L. Sarakhs variety from immature zygotic embryos under dark condition after 60 days. Somatic embryos exhibited by arrows (a) Somatic embryos in globular stage, (b) Somatic embryos in heart stage, (c) Cotyledonary somatic embryos. Bar 2 mm.
Fig. 6 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 6. Secondary somatic embryos produced from primay somatic embryos of P. vera L. Sarakhs variety. Bar 2 mm.
Fig. 8 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 8. Relative expression of selected embryogenesis-related genes on embryonic and non-embryonic samples of two genotypes (a: Sarakhs variety and b: Ghazvini cultivar) of P.vera L in three technical replication.ACT was used as a reference gene for data normalization.Mean value and standard deviation (SD) were presented for three biological replicates.The significance differences (p <.01) and non-significant differences showed with two stars and "ns", respectively.
Data from: Direct and indirect genetic effects on reproductive investment in a grasshopper
A fundamental part of the quantitative genetic theory deals with the partitioning of the phenotypic variance into additive genetic and environmental components. During interaction with conspecifics, the interaction partner becomes a part of the environment from the perspective of the focal individual. If the interaction effects have a genetic basis, they are called indirect genetic effects (IGEs) and can evolve along with direct genetic effects. Sexual reproduction is a classic context where potential conflict between males and females can arise from trade-offs between current and future investments. We studied five female fecundity traits, egg length and number, egg pod length and number and latency to first egg pod, and estimated the direct and IGEs using a half-sib breeding design in the grasshopper Chorthippus biguttulus. We found that the male IGEs were an order of magnitude lower than the direct genetic effects and were not significantly different from zero. However, there was some indication that IGEs were larger shortly after mating, consistent with the idea that IGEs fade with time after interaction. Female direct heritabilities were moderate to low. Simulation shows that the variance component estimates can appear larger with less data, calling for care when interpreting variance components estimated with low power. Our results illustrate that the contribution of male IGEs is overall low on the phenotypic variance of female fecundity traits. Thus even in the relevant context of sexual conflict, the influence of male IGEs on the evolutionary trajectory of female reproductive traits is likely to be small.
Data from: Direct effects of microalgae and protists on herring (Clupea harengus) yolk sac larvae
This study investigated effects of microalgae (Rhodomonas baltica) and heterotrophic protists (Oxyrrhis marina) on the daily growth, activity, condition and feeding success of Atlantic herring (Clupea harengus) larvae from hatch, through the end of the endogenous (yolk sac) period. Yolk sac larvae were reared in the presence and absence of microplankton and, each day, groups of larvae were provided access to copepods. Larvae reared with microalgae and protists exhibited precocious (2 days earlier) and ≥ 60% increased feeding incidence on copepods compared to larvae reared in only seawater (SW). In the absence and presence of microalgae and protists, survival and growth trajectories of yolk sac larvae were similar and digestive enzyme activity (trypsin) and nutritional condition (RNA-DNA ratio) markedly declined in all larvae directly after yolk sac depletion. Thus, microplankton promoted early feeding but was not sufficient to alter survival and growth during the yolk sac phase. Given the importance of early feeding, field programs should place greater emphasis on the protozooplankton-ichthyoplankton link to better understand match-mismatch dynamics and bottom-up drivers of year class success in marine fish.
Data from: Root herbivory indirectly affects above- and belowground community members and directly reduces plant performance
1.There is widespread recognition that above- and below-ground organisms are linked through their interactions with host plants that span terrestrial subsystems. In addition to direct effects on plants, soil organisms such as root herbivores can indirectly alter interactions between plants and other community members, with potentially important effects on plant growth and fitness. 2. We manipulated root herbivory by Acalymma vittatum in Cucumis sativus to determine indirect effects on arbuscular mycorrhizal fungi, leaf herbivory, the leaf pathogen downy mildew, and pollinators. We also manipulated pollen receipt by plants to determine if root herbivory reduced plant reproduction through changes in pollinator visitation. 3. Overall, root herbivory had strong net negative effects on plant growth and fitness, with 34% reductions in both leaf and fruit production by high root damage levels relative to control, despite reduced infection by downy mildew. High root herbivory also reduced floral visitation by 39%, apparently due to lower flower production, as flower size and scent were unaffected. Above-ground herbivory was not affected by root herbivores. 4. Although root herbivory reduced pollinator visits, pollen receipt manipulations had no effect on fruit set, indicating that reduced pollinator service did not affect plant reproduction. 5. Synthesis. Root herbivory had indirect effects on a range of community members, including mutualists and antagonists both above- and below-ground. Although reduced pathogen infection associated with root herbivory would be expected to benefit plants, root herbivory had an overall strong negative effect on plant growth and reproduction, indicating that direct negative effects over-rode any potential indirect benefits.
Data from: Nutrient distribution and absorption in the colonial hydroid Podocoryna carnea is sequentially diffusive and directional
The distribution and absorption of ingested protein was characterized within a colony of Podocoryna carnea when a single polyp was fed. Observations were conducted at multiple spatial and temporal scales at three different stages of colony ontogeny with an artificial food item containing Texas Red conjugated albumin. Food pellets were digested and all tracer absorbed by digestive cells within the first 2–3 hours post-feeding. The preponderance of the label was located in the fed polyp and in a transport-induced diffusion pattern surrounding the fed polyp. After 6 hours post-feeding particulates re-appeared in the gastrovascular system and their absorption increased the area over which the nutrients were distributed, albeit still in a pattern that was centered on the fed polyp. At later intervals, tracer became concentrated in some stolon tips, but not in others, despite the proximity of these stolons either to the fed polyp or to adjacent stolons receiving nutrients. Distribution and absorption of nutrients is sequentially diffusive and directional.
Data from: Direct effects of nitrogen addition on seed germination of eight semi-arid grassland species
<p>Seed germination plays an important role in mediating plant species composition of grassland communities under nitrogen (N) enrichment. Shifts of plant community structure with N-enhanced deposition in terrestrial ecosystems have occurred globally. Despite numerous studies about the effects of enhanced N deposition on mature plant communities, few studies have focused on seed germination. Using a laboratory experiment, we report the effects of five N concentrations, including 0, 5, 10, 20, and 40 mM N (NH<sub>4</sub>NO<sub>3</sub>) on seed germination of eight semi-arid grassland species. Results showed that low N concentrations (5- and 20-mM N) promoted mean final germination proportion of all eight species by 4.4% and 6.4%, but high concentrations (40 mM N) had no effect. The mean germination rate was decreased 2.1% and 5.1% by higher N concentration (20- and 40-mM N) levels, but germination start time showed the opposite trend, delayed by 0.7, 0.9, and 1.8 d for the 10, 20, and 40 Mm N treatments. Final germination proportion, mean germination rate, and germination start time were significantly different among species in response to N concentration treatments. The final germination proportion of <i>Allium tenuissimum </i>and<i> Chenopodium glaucum </i>were suppressed by increased N concentration, whereas it increased for<i> Potentilla bifurca, Plantago asiatica </i>and<i> Setaria viridis</i>. Our findings provide novel insights into N-deposition-induced species loss based on seed germination factors in semi-arid grassland communities.</p>
Source code and GCM data for 'Direct radiative effects of airborne microplastics'
<p>Source code and GCM data for 'Direct radiative effects of airborne microplastics' by Revell et al., (2021)</p>
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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.