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12,455 results for “Promoters”
Data from: Seasonality promotes grassland diversity: interactions with mowing, fertilization and removal of dominant species
1. Current biodiversity declines in species-rich grasslands are connected with the cessation of management, eutrophication and the expansion of dominant grass species. One of the theoretical mechanisms limiting biodiversity loss is the ability of subordinate species to avoid competitive exclusion by seasonal niche separation from dominant species. Here we explore how seasonality underpins the maintenance of diversity in temperate meadows under different management regimes and competition intensities in relation to species functional traits. 2. We studied eight different communities in a long-term meadow experiment that manipulated mowing, fertilization and dominant species (Molinia caerulea) removal. In each community, species-specific trait and biomass data were taken five times during the year to test whether seasonal variation in species composition and functional strategies enable species to coexist. 3. Mown unfertlized meadows exhibited pronounced seasonal variations in community composition and structure, linked to differences in resource-use strategies between mid-summer dominants and the spring and autumn subordinates. Higher specific leaf area and foliar nitrogen concentration in the fast-growing dominants, and increased water use (δ13C) and nutrient acquisition (δ15N) efficiency in resource-retentive subordinates, best predicted their temporal niche separation. Seasonal segregation of species with contrasting strategies increased after mowing cessation, and the resulting summer dominance of Molinia. Conversely, the seasonal dynamics were markedly reduced by fertilization, promoting tall grasses over sedges and forbs throughout the entire year, thereby decreasing the overall taxonomic and functional diversity. When Molinia was removed the compositional changes during the season became less pronounced, being significant only in mown unfertilized plots. 4. Seasonal shifts in community composition reduced the competitive interactions and promoted the coexistence of dominant and subordinate species. Seasonality reversed the negative mid-summer diversity-productivity relationship to a positive one during the spring and autumn, and seasonality only prevented diversity loss in unfertilized conditions possibly because competition is most intense in summer. In fertilized meadows, subordinate species are not able to escape competitive exclusion by shifting their phenological peaks to the spring or autumn periods because asymmetric competition is intense over the entire growing season. Studying seasonal dynamics is key to understanding the maintenance of grassland diversity under ongoing land use change.
Data S1. Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors
<p>Supplementary data S1 for Henssen et al. "</p> <p>Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors"</p>
Asynchronous updates can promote the evolution of cooperation on multiplex networks
<p>Code is included to run the model described for varying enhancement factors, and the different versions of the social dilemmas (public goods game and prisoners dilemma) described in the publication. Code is also included to calculate the payoff probabilities described in the publication. The data used to plot the mean cooperation against the enhancement factors is also included for each of the models permutations. Which code files are for which permutation are described in the accompanying pdf.</p>
Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)
<div>This contains data necessary to reproduce the figures in the CLIPNET paper (preprint <a href="https://www.biorxiv.org/content/10.1101/2024.03.13.583868">here</a>) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: <a href="https://github.com/Danko-Lab/clipnet_paper/">https://github.com/Danko-Lab/clipnet_paper/</a></div> <div> </div> <div>Pretrained CLIPNET models are archived separately at <a href="../doi/10.5281/zenodo.10408622">DOI 10.5281/zenodo.10408622</a></div> <div> </div> <div>V5: Fixed bug in calculation of profile attribution scores causing them to be off by a factor of exactly 500. Genome-wide DeepSHAP tracks & TF-MoDISco tracks have been accordingly updated. I have not updated the individual examples, as these can be quickly fixed by simply multiplying by 500 when plotting. Additionally, I have uploaded profile and quantity motif calls, which contain genome-wide seqlet annotations. The columns in these files are [chrom, start, end, peak_idx, motif_annotation].</div> <div>V4: Uploaded individual bigWigs. These have been lifted over using CrossMap from the original hg19 (GSE110638) to hg38 and RPM normalized.</div> <div>V3: Final version prior to journal submission. Don't recall exact details of what's changed.</div> <div>V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.</div>
Ultrafast Vibrational Control of Organohalide Perovskite Optoelectronic Devices Using Vibrationally Promoted Electronic Resonance
<p>2D PC/PL-VIPER Maps, and results of molecular dynamics simulations for the above titled paper</p>
Raw data for "Lithium carbonate-promoted mixed rare earth oxides as a generalized strategy for oxidative coupling of methane with exceptional yields"
<p>Raw data for "Lithium carbonate-promoted mixed rare earth oxides as a generalized strategy for oxidative coupling of methane with exceptional yields"</p>
Data from: Protection promotes energetically efficient structures in marine communities
<p>The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.</p>
Reception of a physical activity intervention program in German older adults. Data from a feedback analysis of PROMOTE II.
<p>As part of the<strong> AEQUIPA </strong>prevention research network, the aim of the <strong>PROMOTE II</strong> study was to gain insights into primary prevention for healthy aging. One focus was on the development and dissemination of ready-to-use tools and work aids to promote physical activity.</p><p>As part of a nine-month randomized trial with a cross-over design among adults aged 60 and above, eligible participants from 14 districts in Bremen in proximity to the two study centers (one in the North and one in the East of the city of Bremen, Germany) were randomly assigned to either a) a print-based intervention (PRINT) or b) a web-based intervention (WEB). Randomly selected thirty percent of the web-based intervention group received an activity tracker in addition (WEB+).</p><p>Usage of program components, attendance of group sessions and acceptance of the intervention were assessed via self-administered paper-based questionnaires three and nine months after baseline as well as feedback interviews and class recordings. Participant feedback was analyzed using quantitative methods on a descriptive basis, as well as using qualitative content analysis of open-ended questions, group-interviews and protocols based on the socio-ecological model as coding framework.</p><p>This publication provides the coding matrix, including the participant feedback data.</p>
A Framework to Promote Diversity & Inclusion in Workforce Development in the Southeast States
<p>The lack of workforce diversity has made it challenging for transportation agencies to </p><p>incorporate resiliency into their long-term plans effectively. This project developed a </p><p>framework for creating an inclusive and functional workforce environment for transportation </p><p>agencies in the southeast region. The project identifies existing gaps, predicts future needs, and </p><p>captures the role transportation agencies, research centers, Departments of Transportations </p><p>(DOTs), and professional organizations can play to recruit, train, and maintain a diverse and </p><p>inclusive workforce. This research will ultimately contribute to creating a resilient </p><p>transportation workforce structure in the southeast region. The goal of this project is to present </p><p>an Equity, Diversity, and Inclusion (EDI) -focused framework for promoting diversity and </p><p>inclusion within the workforce. </p>
RAD54L2 counters TOP2-DNA adducts to promote genome stability (Etoposide treated RPE1 CRISPR screens in TP53 and RAD53L2 knock outs)
<p>The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anti-cancer agents such as etoposide operate by stabilising TOP2ccs, ultimately generating genotoxic TOP2-DNA protein crosslinks that require processing and repair. Here, we identify RAD54-like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with TDP2 and TOP2 (ZATT/ZNF451) and independent of tyrosyl-DNA phosphodiesterase 2 (TDP2). Our work suggests a model wherein RAD54L2 recognises sumoylated-TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer-therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.</p>
Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons
<p><span>Living in dynamic environments such as the social domain, where interaction with others determines the reproductive success of individuals, requires the ability to recognize opportunities to obtain natural rewards and cope with challenges that are associated with achieving them. As such, actions that promote survival and reproduction are reinforced by the brain reward system, whereas coping with the challenges associated with obtaining these rewards is mediated by stress-response pathways, the activation of which can impair health and shorten lifespan. While much research has been devoted to understanding mechanisms underlying the way by which natural rewards are processed by the reward system, less attention has been given to the consequences of failure to obtain a desirable reward. As a model system to study the impact of failure to obtain a natural reward, we used the well-established courtship suppression paradigm in <em>Drosophila</em> <em>melanogaster</em> as means to induce repeated failures to obtain sexual reward in male flies. We discovered that beyond the known reduction in courtship actions caused by interaction with non-receptive females, repeated failures to mate induce a stress response characterized by persistent motivation to obtain the sexual reward, reduced male-male social interaction, and enhanced aggression. This frustrative-like state caused by the conflict between high motivation to obtain sexual reward and the inability to fulfill their mating drive impairs the capacity of rejected males to tolerate stressors such as starvation and oxidative stress. We further show that sensitivity to starvation and enhanced social arousal is mediated by the disinhibition of a small population of neurons that express receptors for the fly homologue of<em> neuropeptide Y</em>. Our findings demonstrate for the first time the existence of social stress in flies and offers a framework to study mechanisms underlying the crosstalk between reward, stress, and reproduction in a simple nervous system that is highly amenable to genetic manipulation.</span></p>
Matrix N, TEs vs promoters, 100kb-wide windows, hg38
<p>Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.</p>
Matrix N, TEs vs promoters, weighted with L = 2.5e5kb, hg38
<p>Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 2.5e5kb. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.</p>
Divergence in cold tolerance promotes niche differentiation between diploid and polyploid kiwifruits along an altitudinal gradient in Southwest China
<p>Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved in the freezing resistant ability of polyploids remain unclear. In <em>Actinidia chinensis</em> (kiwifruits), the tetraploids and hexaploids occupy higher altitude habitats with colder climates than the diploids, providing a study system to investigate mechanisms responsible for differentiation in freezing resistance between cytotypes. We characterized environmental conditions of their natural distribution areas, and measured leaf-level traits of cold damages and water relations at typical sites of each cytotype along an altitudinal gradient. Polyploids showed lower semi-lethal temperature (LT<sub>50</sub>) than ice nucleation temperature (INT), reflecting a tolerance strategy to cope with freezing events in the plateau regions. More negative turgor loss points and larger cell elastic modulus of polyploids could help to alleviate damages from freezing-induced cell dehydration, thus strengthening their tolerance to lower subzero temperatures (lower LT<sub>50</sub>). The increased supercooling capacity of polyploids (lower INT) might correlate with less extracellular ice formation due to lower osmotic potential at full turgor, apoplastic water fraction and tissue capacitance. Our study uncovers a greater cold tolerance in polyploid kiwifruits than diploids, and suggests the potential linkage between freezing tolerance and water relations. Taken together, such a divergence in stress resistance may underlie the niche shift of polyploid plants towards harsh environments.</p>
Tree diversity across multiple scales and environmental heterogeneity promote ecosystem multifunctionality in a large temperate forest region
<p><strong>Aim</strong>: Biodiversity across different scales provides multidimensional insurance for ecosystem functioning. Although the positive effects of local scale (α-diversity) biodiversity on ecosystem multifunctionality are widely accepted, species turnover across communities (β-diversity) which is often an important driver of ecosystem functioning did not receive the same attention. This study broadens the understanding of how multiple attributes of biodiversity maintain ecosystem multifunctionality from local to regional scales, across diverse environmental gradients.</p> <p><strong>Location</strong>: North-eastern China.</p> <p><strong>Time period</strong>: 2017.</p> <p><strong>Major taxa studied</strong>: Woody plants.</p> <p><strong>Methods</strong>: We estimate ecosystem multifunctionality using both averaging and modified multiple thresholds (50%, 70% and 90%) approaches. Multiple dimensions of biodiversity across varying spatial scales were measured within the framework of Hill‒Chao numbers. Linear and nonlinear models were used to evaluate the optimal patterns of multifunctionality and biodiversity along the latitude. Using variance decomposition, structural equation modeling and linear mixed models, we explored how multiple attributes of tree diversity at varying spatial scales affect multifunctionality, and how these relationships are modulated by environmental drivers.</p> <p><strong>Results</strong>: Our results show that multifunctionality decreased with increasing latitude, mirroring the pattern of tree diversity along latitudinal gradients. Phylogenetic β-diversity and species α-diversity emerged as crucial diversity indices for sustaining multifunctionality in these temperate forests. Soil and climatic conditions had either direct effects on multifunctionality, or indirect ones mediated by tree diversity. Environmental heterogeneity played a pivotal role in maintaining high levels of multifunctionality, exerting influence both directly and indirectly via phylogenetic β-diversity.</p> <p><strong>Main conclusions</strong>: This study underscores the positive effects of biodiversity on multifunctionality across multiple dimensions. Based on our findings, we conclude that any design of a forested landscape that is aimed at maximizing multifunctionality should consider maintaining high local diversity as well as forest community heterogeneity at varying scales.</p>
Dataset for "Beyond Self-Promotion: How Software Engineering Research Is Discussed on LinkedIn"
<p>This repository contains the artifacts of our study on how software engineering research papers are shared and interacted with on LinkedIn, a professional social network. This includes:</p> <ul> <li><em>included-papers.csv</em>: the list of the 79 ICSE and FSE papers we found on LinkedIn</li> <li><em>linkedin-post-data.csv</em>: the final data of the 98 LinkedIn posts we collected and synthesized</li> <li><em>linkedin-post-scraping.zip</em>: the scripts used to automatically collect several attributes of the LinkedIn posts</li> <li><em>analysis.zip</em>: the Jupyter notebook used to analyze and visualize <em>linkedin-post-data.csv</em></li> </ul>
Extended data for behavioural change for Parkinson's disease: A randomised controlled feasibility study to promote physical activity and exercise adherence among people with Parkinson's, study protocol
<p><strong>Background: </strong>Parkinson's is a common progressive neurological condition characterized by motor and non-motor deficits. Physical activity and exercise can improve health, but many people with Parkinson's have trouble reaching the recommended dosage. Our recent literature review found improvements in exercise adherence with behavioural change interventions, but it remains unclear which are most effective. Further qualitative research and patient and public involvement has informed a novel behavioural change support intervention to be tested alongside an existing exercise program.<strong> </strong></p> <p><strong>Objective: </strong>To examine the feasibility of behavioural change support techniques delivered alongside an exercise programme to improve physical activity, function, and self-efficacy in PwP (and study procedures) to inform a future pilot RCT trial.<strong> </strong></p> <p><strong>Methods: </strong>A parallel-arm single blinded randomised feasibility study. Twenty participants with Parkinson's (Hoehn and Yahr stage 1-3) will be recruited from a physiotherapy primary-care waiting list. Following written consent, and baseline assessment, the participants will be randomly allocated to the intervention (n=10) or the control group (n=10). Both groups will receive usual care, which includes a weekly program of a multidisciplinary education, a supervised exercise class and a prescribed home exercise program. The intervention group will receive additional behavioural change techniques, targeting behaviour regulation, belief about capabilities and social influences. Class and home exercise adherence, behavioural component uptake and adherence, and negative events will be recorded. Outcomes will include enrolment and maintenance rates, physical function, falls, physical activity, and exercise self-efficacy measured pre- and post- the 12- week program (in-person). Surveys will be used to compare experiences and satisfaction between groups. Exit interviews will be completed with the intervention group only, exploring their experience of the behavioural change techniques. </p> <p><strong>Discussion: </strong>The results will help inform a future pilot RCT, based on the intervention acceptability, consent rate, maintenance, and protocol integrity.</p>
Data from: Heterogeneity promotes resilience in restored prairie: implications for the 'environmental heterogeneity hypothesis'
<p>Enhancing resilience in formerly degraded ecosystems is an important goal of restoration ecology. However, evidence for the recovery of resilience and its underlying mechanisms requires long-term experiments and comparison to reference ecosystems. We used data from an experimental prairie restoration that featured long-term soil heterogeneity manipulations and data from comparable remnant (reference) prairie to (1) quantify the recovery of ecosystem functioning (i.e., productivity) relative to remnant prairie, (2) compare resilience of restored and remnant prairies to a natural drought, and (3) test whether soil heterogeneity enhances resilience of restored prairie. We compared sensitivity and legacy effects between prairie types (remnant and restored) and among four prairie sites that included two remnant prairie sites and prairie restored under homogeneous and heterogeneous soil conditions. We measured sensitivity and resilience as the proportional change in aboveground net primary productivity (ANPP) during and following drought (sensitivity and legacy effects, respectively) relative to average ANPP based on four pre-drought years (2014-2017). In non-drought years, total ANPP was similar between remnant and restored prairie, but remnant prairie had higher grass productivity and lower forb productivity compared to restored prairie. These ANPP patterns generally persisted during drought. Sensitivity of total ANPP to drought was similar between restored and remnant prairie, but grasses in restored prairie were more sensitive to drought. Post-drought legacy effects were more positive in restored prairie, and we attributed this to the more positive and less variable legacy response of forb ANPP in restored prairie, especially in the heterogeneous soil treatment. Our results suggest that productivity recovers in restored prairie and exhibits similar sensitivity to drought as remnant prairie. Furthermore, imparting heterogeneity promotes forb productivity and enhances prairie resilience to drought.</p>
Data from: Plant canopies promote climatic disequilibrium in Mediterranean recruit communities
<p>Current rates of climate change are exceeding the capacity of many plant species to track climate, thus leading communities to be in disequilibrium with climatic conditions. Plant canopies can contribute to this disequilibrium by buffering macro-climatic conditions and sheltering poorly adapted species to the oncoming climate, particularly in their recruitment stages. Here we analyze differences in climatic disequilibrium between understory and open ground woody plant recruits in 28 localities, covering more than 100,000 m<sup>2</sup>,<sup> </sup>across an elevation range embedding temperature and aridity gradients in the southern Iberian Peninsula. This study demonstrates higher climatic disequilibrium under canopies compared with open ground, supporting that plant canopies would affect future community climatic lags by allowing the recruitment of less arid-adapted species in warm and dry conditions, but also it endorse that canopies could favor warm-adapted species in extremely cold environments as mountain tops, thus pre-adapting communities living in these habitats to climate change.</p>
Different photoperiodic responses in diapause induction can promote the maintenance of genetic diversity via the storage effect in Daphnia pulex
<p>Understanding mechanisms that promote the maintenance of biodiversity (genetic and species diversity) has been a central topic in evolution and ecology. Previous studies have revealed that dormancy can contribute to coexistence of competing genotypes or species in fluctuating environments via the storage effect. However, they tended to focus on differences in reproductive success (e.g., seed yield) and diapause termination (e.g., germination) timing. Here we tested whether different photoperiodic responses in diapause induction can promote coexistence of two parthenogenetic (asexual) genotypes of <em>Daphnia pulex </em>in Lake Fukami-ike, Japan. Through laboratory experiments, we confirmed that short day length and low food availability induced the production of diapausing eggs. Furthermore, we found that one genotype tended to produce diapausing eggs in broader environmental conditions than the other. Terminating parthenogenetic reproduction earlier decreases total clonal production, but the early-diapausing genotype becomes advantageous by assuring reproduction in "short" years where winter arrival is earlier than usual. Empirically parameterized theoretical analyses suggested that different photoperiodic responses can promote coexistence via the storage effect with fluctuations of the growing season length. Therefore, timing of diapause induction may be as important as diapause termination timing for promoting the maintenance of genetic diversity in fluctuating environments.</p>
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.