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10,812 results for “novels”
Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism
Open the record for dataset details and reuse information.
Negative outcomes of novel trophic interactions along mangrove range edges in the Gulf of Mexico: 2020-2021
Mangrove encroachment is shifting the food sources available to basal consumers in Gulf of Mexico salt marshes, so we sought to determine how two important basal consumers will respond to mangroves as a food source. We collected Littoraria irrorata and leaves of Spartina alterniflora, and Avicennia germinans from marshes in Galveston, Texas in summer of 2020 for a series of food preference and food quality studies. Additionally, we compared the physiological conditions of Littoraria irrorata and Uca rapax individuals collected from manipulated sites with varying levels of mangrove cover in Port Aransas, Texas in late 2020 and early 2021. These studies yielded results on the behavioral and physiological responses of basal consumers to mangrove plant matter as a food source.
A novel metabarcoding strategy for studying nematode communities
<p>Nematodes are most abundant soil metazoa. How, the ecology of this group of organism remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5, SSU_04F/SSU_22R, Nemf/18Sr2b from earlier studies; and MMSF/MMSR, a newly developed primer set from this study. In order to test these primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 mock communities in soil, and 4 root/rhizosphere soil samples. We successfully amplified the target regions (COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were very efficient in detecting soil nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets could be used to study nematode communities in agricultural environments.</p>
Resources for reproducing experiments in "Novel Entity Discovery from Web Tables"
<p>This repository contains resources developed for the paper: "S. Zhang, E. Meij, K. Balog, and R. Reinanda. Novel Entity Discovery from Web Tables. In: Proceeding of the The Web Conference 2020 (WWW ’20), April 2020".</p> <p>It includes the three test collections for novel entity discovery for Web tables, entity type and mention resolution, as well as the mention-entity and heading-property correspondences for 3M tables. The cited datasets were used in this work.</p> <p>Files to recreate the entity linking experiments:</p> <ul> <li>training_el.csv</li> <li>training_el_type.csv</li> <li>training_el_type_wiki.csv</li> <li>training_el_wiki.csv</li> <li>training_schema.csv</li> </ul> <p>Files to recreate the table matching experiments:</p> <ul> <li>me_corres.csv - textual cells algorithmically linked to Wikipedia entities</li> <li>hp_corres.csv - same but only table headings</li> </ul> <p>Files to recreate the entity resolution experiments:</p> <ul> <li>ec_golden.csv - 20K unlinked mentions textual cells, manually linked to Wikipedia</li> <li>er_sf_golden.csv - 1K cell values, manually clustered</li> <li>er_type_golden.csv - 1K cell values, manually linked to DBpedia types</li> </ul>
A dataset for evaluating one-shot categorization of novel object classes
<p>From just a single example, we can derive quite precise intuitions about what other class members look like. This stands in stark contrast to machine learning algorithms, which typically require tens or even hundreds of thousands of examples to learn a new category. One of the most important open questions in our field is: How do humans achieve this? The stimuli and data provided here (in MATLAB format) are from thousands of crowd-sourced human responses to novel objects. The data can be used to test machine learning generalization as compared to human and also can be used as a test bed for various kinds of category learning models. </p>
Dataset/Development of a novel calorimetry setup based on metallic paramagnetic temperature sensors
<p>Dataset related to the publication "Development of a novel calorimetry setup based on metallic paramagnetic temperature sensors" submitted to Review of Scientific Instruments.</p>
Experimental infection of bumble bees with honey bee associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts
<p>Pathogen spill-over represents an important cause of biodiversity decline. For wild bee species such as bumble bees, many of which are in decline, correlational data point toward viral spill-over from naged honey bees as a potential cause. Yet impacts of honey bee viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well characterised viral inocula, we show that three viral types isolated from honey bees (<i>Deformed wing virus</i> genotype A, <i>Deformed wing virus</i> genotype B and <i>Black queen cell virus</i>) readily replicate within hosts of the bumble bee <i>Bombus terrestris</i>. Impacts of these honey bee-derived viruses – either injected or fed – on the mortality of <i>B. terrestris </i>workers were, however, negligible and likely dependent on host condition. Our results highlight the potential threat of viral spill-over from honey bees to novel wild bee species, though they also underscore the importance of additional studies on this and other non- bee species under field-realistic conditions to evaluate whether pathogen spill-over has a negative impact on wild bee individuals and population fitness.</p>
Data from: Introduced bees (Osmia cornifrons) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences
<p><span><span><span><span><span><span><span><span><span><span><span>Studying the pollen preferences of introduced bees allows us to investigate how species utilize host-plants when establishing in new environments. <i>Osmia cornifrons</i> is a solitary bee introduced into North America from East-Asia for pollination of crops in the Rosaceae. We investigated whether <i>O. cornifrons</i> 1) more frequently collected pollen from host-plant species they coevolved with from their geographic origin, or 2) prefer hosts-plant species of specific plant taxa independent of origin. To address this question, using pollen metabarcoding we examined the identity and relative abundance of pollen in larval provisions from nests located in different habitats with varying abundance of East-Asian and non-Asian plant species. Our results show that <i>O. cornifrons</i> disproportionately, yet not exclusively, collected pollen from their native range. Plants in the family Rosaceae were their most preferred pollen hosts, where they differentially collected species native to East-Asia, Europe, or North America depending on the landscape. Our results suggest that while <i>O. cornifrons</i> more frequently collect pollen of East-Asian origin, the collection of pollen from novel species within their phylogenetic familial affinities can facilitate pollinator establishment. This phylogenetic preference highlights the effectiveness of <i>O. cornifrons</i> as crop pollinators of a variety of Rosaceae crops from different geographic origins. Ourresults imply that globalization of non-native plant species may ease the naturalization of their coevolved pollinators outside of their native range. </span></span></span></span></span></span></span></span></span></span></span></p>
Identification and characterization of novel splice variants of human farnesoid X receptor
<p>Dataset related to publication:</p> <blockquote> <p>Mustonen E-K, Lee SML, Nieß H, Schwab M, Pantsar T, Burk O: "Identification and characterization of novel splice variants of human farnesoid X receptor". <em>Archives of Biochemistry and Biophysics</em> <a href="https://doi.org/10.1016/j.abb.2021.108893">https://doi.org/10.1016/j.abb.2021.108893</a></p> </blockquote> <p> </p> <p>Including:</p> <p>I. Full-length raw-trajectories of the 1 microsecond Desmond simulations (-out.cms, trj)</p>
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes
<p>Intraspecific competition has long been considered a key driver of evolutionary diversification, but whether it can also promote evolutionary innovation is less clear. We examined the interplay between competition and phenotypic plasticity in fueling the origins of a novel, complex phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles (genus <i>Spea</i>) that specializes on fairy shrimp. We specifically sought to explore the possible origins of this phenotype by providing shrimp to <i>Scaphiopus holbrookii</i> tadpoles (the sister genus to <i>Spea </i>that does not produce carnivores) while subjecting them to competition for their standard diet of detritus. Previous research had shown that this species will eat shrimp when detritus is limited, and that these shrimp-fed individuals produce features that are redolent of a rudimentary <i>Spea </i>carnivore. In this study, we found that: 1) behavioral and morphological plasticity enabled some individuals to expand their diet to include shrimp; 2) there was heritable variation in this plasticity; and 3) individuals received a growth and development benefit by eating shrimp. Thus, novel resource use can arise via plasticity as an adaptive response to intraspecific competition. More generally, our results show how competition and plasticity may interact to pave the way for the evolution of complex, novel phenotypes, such as the distinctive carnivore morph in present-day <i>Spea</i>.</p>
Data from: Novel track morphotypes from new tracksites indicate increased Middle Jurassic dinosaur diversity on the Isle of Skye Scotland
<p>Dinosaur fossils from the Middle Jurassic are rare globally, but the Isle of Skye (Scotland, UK) preserves a varied dinosaur record of abundant trace fossils and rare body fossils from this time. Here we describe two new tracksites from Rubha nam Brathairean (Brothers' Point) near where the first dinosaur footprint in Scotland was found in the 1980s. These sites were formed in subaerially exposed mudstones of the Lealt Shale Formation of the Great Estuarine Group and record a dynamic, subtropical, coastal margin. These tracksites preserve a wide variety of dinosaur track types, including a novel morphotype for Skye: <i>Deltapodus</i> which has a probable stegosaur trackmaker. Additionally, a wide variety of tridactyl tracks shows evidence of multiple theropods of different sizes and possibly hints at the presence of large-bodied ornithopods. Overall, the new tracksites show the dinosaur fauna of Skye is more diverse than previously recognized and give insight into the early evolution of major dinosaur groups whose Middle Jurassic body fossil records are currently sparse.</p>
Data from: Behavioural and fitness effects of translocation to a novel environment: whole-lake experiments in two aquatic top predators
<p>Translocation into a novel environment through common fisheries-management practices, such as fish stocking, provides opportunities to study behavioural and fitness impacts of translocations at realistic ecological scales. The process of stocking, as well as the unfamiliarity with novel ecological conditions and the interactions with resident fish may affect translocated individuals, leading to alterations of behaviours and causing fitness impacts.</p> <p>Our objectives were to investigate how aquatic top-predators behaviourally establish themselves and compete with resident individuals following introduction in a novel lake environment and to investigate the resulting fitness consequences.</p> <p>Using high-resolution acoustic telemetry, we conducted whole-lake experiments and compared the activity, activity-space size and fate of translocated and resident individuals in two model top predators, northern pike (Esox lucius, n = 160) and European catfish (Silurus glanis, n = 33). Additionally, we compared the reproductive fitness of translocated and resident northern pike. The experiment was conducted with large (adult) individuals of different origins, resilient to predation, but subject to agonistic interactions and competition with resident fish.</p> <p>Over a period of several months, the translocated catfish exhibited consistently larger activity-space sizes than resident catfish, but did not differ from residents in activity and survival. The pike from one of the two translocated origins we tested also showed elevated space-use, and both translocated origins revealed higher mortality rates than their resident conspecifics, indicating maladjustment to their novel environment. When non-resident pike reproduced, they overwhelmingly produced hybrid offspring with resident fish, indicating that introductions fostered gene flow of non-native genes.</p> <p>Our study indicates that fish introductions result in behavioural and fitness impacts even in large-bodied top predators that experience low levels of natural predation risk. </p>
Data from: Wild samango monkeys, Cercopithecus mitis, balance risk and opportunity to interact with novel objects in village gardens
Research suggests that wild animals in urban areas exhibit heightened behavioral flexibility when they encounter novel human-made objects, but most such studies compared responses in urban populations with those from disjunct populations in less disturbed environments. We therefore know little about intrapopulation variation in cognitive or behavioral flexibility under different conditions of anthropogenic exposure. Here, we investigate object exploration and behavioral flexibility in a single group of samango monkeys (Cercopithecus mitis) in an environment where individuals forage in both gardens and natural forest. Over two months, we presented monkeys with novel, human-made objects in both natural and disturbed areas, varying the position of objects in trees to represent exposed or safer foraging zones. We video-recorded and analyzed interactions with these novel objects, assessing interaction times (an indicator of persistence), exploratory diversity (or motor diversity), and the occurrence of foraging innovations. Results from 67 interactions (29 in natural habitats and 38 in disturbed) indicate that samango monkeys exhibited a spatially complex response to novel objects: in contrast to other species, exploration diversity decreased significantly in anthropogenic environments, even as persistence remained largely static across contexts. Monkeys also exhibited foraging innovations by pulling on strings to bring objects closer. This may reduce exposure to danger, as string-pulling was most prevalent in the highest risk condition (ground level in human gardens). Significant intrapopulation variation in behavioral flexibility suggests that samango monkeys adjust the expression of problem-solving behaviors in relation to the degree of human disturbance in their immediate environment.
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
<p>Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3. </p>
Novel DMD mouse model carrying a multi-exonic Dmd deletion exhibit progressive muscular dystrophy and early-onset cardiomyopathy
Duchenne muscular dystrophy (DMD) is a life-threatening neuromuscular disease caused by the lack of dystrophin, resulting in progressive muscle wasting and locomotor dysfunctions. By adulthood, almost all patients also develop cardiomyopathy, which is the primary cause of death in DMD. While there has been extensive effort in creating animal models to study treatment strategies for DMD, most fail to recapitulate the complete skeletal and cardiac disease manifestations that are presented in affected patients. Here, we generated a mouse model mirroring a patient deletion mutation of exons 52-54 (<i>Dmd &[Delta]52-54</i>). The <i>Dmd &[Delta]52-54</i> mutation led to the absence of dystrophin, resulting in progressive muscle deterioration with weakened muscle strength. Moreover, <i>Dmd &[Delta]52-54</i> present with early-onset cardiomyopathy which is absent in current pre-clinical dystrophin deficient mouse models. Therefore, <i>Dmd &[Delta]52-54</i> presents itself as an excellent pre-clinical model to evaluate the impact on skeletal and cardiac muscles for both mutation dependent and independent approaches.
Data from: Evidence for normal novel object recognition abilities in developmental prosopagnosia
<p>The issue of the face specificity of recognition deficits in developmental prosopagnosia (DP) is fundamental to the organisation of high-level visual memory and has been increasingly debated in recent years. Previous DP investigations have found some evidence of object recognition impairments, but have almost exclusively used familiar objects (e.g., cars), where performance may depend on acquired object-specific experience and related visual expertise. An object recognition test not influenced by experience could provide a better, less contaminated measure of DPs' object recognition abilities. To investigate this, in the current study we tested 30 DPs and 30 matched controls on a novel object memory test (NOMT Ziggerins) and the Cambridge Face Memory Test (CFMT). DPs were impaired on the CFMT but showed no differences in accuracy or reaction times to controls on the NOMT. We found similar results when comparing DPs to a larger sample of 274 web-based controls. Additional individual analyses demonstrated that the rates of object recognition impairment in DPs did not differ from the rate of impairment in either control group. Together, these results demonstrate unimpaired object recognition in DPs for a class of novel objects that serves as a powerful index for broader novel object recognition capacity.</p>
Datasets to "Piecewise quadratic growth during the 2019 novel coronavirus epidemic"
<pre>This directory contains an index.html file with links to the run directories for Figs.8-11 and idl plotting routines with secondary data for the other figures for the paper "Piecewise quadratic growth during the 2019 novel coronavirus epidemic" by Axel Brandenburg (Nordita) with the URL https://arxiv.org/abs/2002.03638 </pre>
Novel developments in clamped geometries for fracture toughness testing
<p>Stable fracture toughness test geometries are useful in not only determining the monotonic fracture toughness, but also in capturing the R-curve behaviour and damage tolerance of materials under cyclic loading and extreme environments. The doubly clamped boundary condition offers such crack stability even in the most brittle materials. This talk will cover all aspects of clamped beams and wires in tension and bending as fracture toughness test geometries including their geometric factor solutions for linear elastic and elastic-plastic cases. Finite element simulations are used to explain the mechanics of crack stability for various beam and wire aspect ratios and crack configurations. Their varied applications in bulk materials, architectured systems, thin film multilayers and graded coatings will be shown.</p> <p><strong>Related publications</strong></p> <ol> <li>A. K. Mishra, A. Lambai and V. Jayaram, B. Nagamani Jaya, “The edge-notched clamped beam bend specimen as a fracture toughness test geometry”, Theoretical and Applied Fracture Mechanics, 105, 2020, 102409 (DOI: 10.1016/j.tafmec.2019.102409)</li> <li>B. Nagamani Jaya, Sanjit Bhowmick, S. A. Syed Asif, Oden L. Warren and Vikram Jayaram, “Optimization of clamped beam geometry for fracture toughness testing of micron-scale samples” Phil Mag Special Issue on Nanomech IV, Vol 95, 2015, 1945-1966 (DOI: 10.1080/14786435.2015.1010623)</li> <li>B. Nagamani Jaya and Vikram Jayaram, “Crack stability in edge notched clamped beam specimen under bending: modeling and experiments”, International Journal of Fracture, Vol 188, Issue 2, 2014, 213-228 (DOI: 10.1007/s10704-014-9956-2)</li> <li>B. Nagamani Jaya, Vikram Jayaram and Sanjay K. Biswas, “A new method for fracture toughness determination of graded (Pt,Ni)Al bond coats by microbeam bend tests”, Philosophical Magazine Special Issue on Nanomechanical Testing in Materials Research and Development III, Vol 92, Issue 25-27, 2012, 3326-3345. (DOI: 10.1080/14786435.2012.669068)</li> </ol>
A novel method for using RNA-seq data to identify imprinted genes in social Hymenoptera with multiply mated queens
<p>Genomic imprinting results in parent-of-origin dependent gene expression biased towards either the maternally- or paternally-derived allele at the imprinted locus. The kinship theory of genomic imprinting argues that this unusual expression pattern is a manifestation of intra-genomic conflict between the maternally- and paternally-derived halves of the genome that arises because they are not equally related to the genomes of social partners. The theory thus predicts that imprinting may evolve wherever there are close interactions among asymmetrically related kin. The social Hymenoptera with permanent caste differentiation are suitable candidates for testing the kinship theory because haplodiploid sex determination creates strong relatedness asymmetries and nursing workers interact closely with kin. However, progress in the search for imprinted genes in the social Hymenoptera has been slow, in part because tests for imprinting rely on reciprocal crosses that are impossible in most species. Here, we develop a method to systematically search for imprinting in haplodiploid social insects without crosses, using instead samples of pooled individuals collected from natural colonies. We tested this protocol using data available for the leaf-cutting ant <i>Acromyrmex echinatior</i>, providing the first genome-wide search for imprinting in any ant. While we identified several genes as potentially imprinted, none of the four genes tested could be verified as imprinted using digital droplet PCR, highlighting the need for higher quality genomic assemblies that accurately map duplicated genes.</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.