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6,335 results for “direct”
Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae)
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iEEG, Direct Electrical Stimulation, and Assessment of Mood in Human Subjects
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The direct and indirect effects of environmental toxicants on the health of bumble bees and their microbiomes
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Aquarius CAP Level 2 Sea Surface Salinity, Wind Speed & Direction Data V5.0
The version 5.0 Aquarius CAP Level 2 product contains the fourth release of the AQUARIUS/SAC-D orbital/swath data based on the Combined Active Passive (CAP) algorithm. CAP is a P.I. produced dataset developed and provided by JPL. This Level 2 dataset contains sea surface salinity (SSS), wind speed and wind direction data derived from 3 different radiometers and the onboard scatterometer. The CAP algorithm simultaneously retrieves the salinity, wind speed and direction by minimizing the sum of squared differences between model and observations. The main improvements in CAP V5.0 relative to the previous version include: updates to the Geophysical Model Functions to 4th order harmonics with the inclusion of sea surface temperature (SST) and stability at air-sea interface effects; use of the Canadian Meteorological Center (CMC) SST product as the new source ancillary sea surface temperature data in place of NOAA OI SST. Each L2 data file covers one 98 minute orbit. The Aquarius instrument is onboard the AQUARIUS/SAC-D satellite, a collaborative effort between NASA and the Argentinian Space Agency Comision Nacional de Actividades Espaciales (CONAE). The instrument consists of three radiometers in push broom alignment at incidence angles of 29, 38, and 46 degrees incidence angles relative to the shadow side of the orbit. Footprints for the beams are: 76 km (along-track) x 94 km (cross-track), 84 km x 120 km and 96km x 156 km, yielding a total cross-track swath of 370 km. The radiometers measure brightness temperature at 1.413 GHz in their respective horizontal and vertical polarizations (TH and TV). A scatterometer operating at 1.26 GHz measures ocean backscatter in each footprint that is used for surface roughness corrections in the estimation of salinity. The scatterometer has an approximate 390km swath.
Movement of Arginine Through OprD: The Energetics of Permeation and The Role of Lipopolysaccharide in Directing Arginine to The Protein
<p>The outer membrane channel OprD from <em>Pseudomonas aeruginosa</em> transports basic amino acids and clinically relevant carbapenem antibiotics. Understanding the molecular basis of substrate permeation across this channel will therefore lead to better therapeutic designs to treat infections. Using umbrella sampling simulations, we calculated the potential of mean force (PMF) for the arginine permeation pathway through OprD. The PMF reveals a deep free energy well of ∼6 <em>kT</em>around the putative substrate binding site followed by a shallower well of ∼4 <em>kT</em> close to the most constricted region of the pore. Despite becoming partially dehydrated during translocation, some water molecules are retained to shield the guanidinium side chain of arginine from the ladder of basic residues in the protein. Sugars of the lipopolysaccharide headgroups form contacts with arginine and could potentially play an important role in transferring substrate from the external medium to OprD. The PMF through bulk membrane shows a large energetic barrier of ∼45 <em>kT</em> within the hydrophobic core of the membrane, suggesting that spontaneous translocation without OprD is highly unlikely. This significant energetic penalty is likely caused by the extensive distortion of the lower leaflet of the outer membrane as phospholipid headgroups sink inwards to interact with charged groups of arginine. Our results provide quantitative insights into solute permeation across the bacterial outer membrane.</p>
Sealing. Oval sealing in terracotta with a three line inscription going in different directions.
<p>Sealing. Oval sealing in terracotta with a three line inscription going in different directions. British Museum 2005,0814.27.</p> <p> </p>
Supplementary material from: Ashurov S, Othman AHA, Bin Rosman R, Bin Haron R (2020) The determinants of foreign direct investment in Central Asian region: A case study of Tajikistan, Kazakhstan, Kyrgyzstan, Turkmenistan and Uzbekistan (A quantitative analysis using GMM). Russian Journal of Economics 6(2): 162-176. https://doi.org/10.32609/j.ruje.6.48556
Arellano–Bond dynamic panel-data estimation
A geotagged image dataset with compass directions for studying the drivers of farmland abandonment
<p>In this work, we present a dataset containing a collection of pictures taken during the fieldwork of a farmland abandonment study. Data was taken in 2010 with a compact camera which incorporates GPS and a digital compass sensor. The photographs are taken as a part of a GIS database. Using their Exif metadata we created a layer of Geographic Fields Of View (GeoFOVs) that can be used to perform very specific spatial queries. The dataset contains 2,235 pictures and GIS layers of GeoFOVs contextualizing the agricultural plots being photographed.</p>
Data from: Helping decisions and kin recognition in long-tailed tits: is call similarity used to direct help towards kin?
<p>Most cooperative breeders live in discrete family groups, but in a minority, breeding populations comprise extended social networks of conspecifics that vary in relatedness. Selection for effective kin recognition may be expected for individuals in such kin neighbourhoods to maximise indirect fitness. Using a long-term social pedigree, molecular genetics, field observations and acoustic analyses, we examine how vocal similarity affects helping decisions in the long-tailed tit <i>Aegithalos caudatus</i>. Long-tailed tits are cooperative breeders in which help is typically redirected by males that have failed in their own breeding attempts towards the offspring of male relatives living within kin neighbourhoods. We identify a positive correlation between call similarity and kinship suggesting that vocal cues offer a plausible mechanism for kin discrimination. Furthermore, we show that failed breeders choose to help males with calls more similar to their own. However, although helpers fine-tune their provisioning rates according to how closely related they are to recipients, their effort was not correlated with their vocal similarity to helped breeders. We conclude that although vocalisations are an important part of the recognition system of long-tailed tits, discrimination is likely to be based on prior association and may involve a combination of vocal and non-vocal cues.</p>
Parental investment does not directly affect reproductive success in the Saffron Finch
<p>In tropical species, the study of parental care and the description of the intraspecific variation of parental care remain relatively understudied, especially when compared to the vast works dedicated to species from the northern hemisphere. In Colombia, the Saffron Finch (<i>Sicalis flaveola</i>), is a species with a wide geographical distribution, and despite its abundance in open habitats and urban environments, little is known about its reproductive ecology. As a small‐bodied, short‐lived passerine, we postulated that the Saffron Finch should behave according to the "reproductive value hypothesis,'' investing in the current brood at the expense of future survival. Consequently, we predicted: (1) that parental investment would be associated with brood size and (2) parental investment would be positively associated with nestling growth rate and reproductive success (defined as the number of nestlings which reached fledging age). In 2018, two reproductive peaks of <i>S. flaveola flaveola</i> were documented in the Meléndez campus of Universidad del Valle, Cali. Direct observations and video cameras (> 1700 hours of recording) were used to monitor the nests from 38 different breeding pairs. We found that feeding visits and the number of regurgitation events were positively related to brood size. In an experiment of simulated nest predation, 85% of breeding pairs responded to the stimulus and parents who exhibited highly responsive behaviours (50%) raised nestlings with a higher growth rate. We also found that egg surface area positively affected the number of incubation bouts per hour. Whilst no relationship was found between overall parental investment and reproductive success, our results appear to show that the intensity of parental investment during reproduction was modulated by brood size. Our findings suggest that there are multiple ecological factors that influence reproductive success in the Saffron Finch, and reinforce the need for longer term studies of tropical passerines.</p>
Fast saccadic eye-movements in humans suggest that numerosity perception is automatic and direct.
<p><span>Fast saccades are rapid automatic oculomotor responses to salient and ecologically important visual stimuli such as animals and faces. Discriminating the number of friends, foe or prey may also have an evolutionary advantage. In this study participants were asked to saccade rapidly towards the more numerous of two arrays. Participants could discriminate numerosities with high accuracy and great speed, as fast as 190 ms. Intermediate numerosities were more likely to elicit fast saccades than very low or very high numerosities. Reaction-times for vocal responses (collected in a separate experiment) were slower, did not depend on numerical range, and correlated only with the slow, not the fast saccades, pointing to different systems. The short saccadic-reaction times we observe are surprising given that discrimination using numerosity estimation is thought to require a relatively complex neural circuit, with several relays of information through parietal and pre-frontal cortex. Our results suggest that fast numerosity-driven saccades may be generated on a single feed-forward pass of information recruiting a primitive system that cuts through the cortical hierarchy and rapidly transforms the numerosity information into a saccade command.</span></p>
Supplement (interactive Excel tool) to MAGIC Deliverable 6.4 'Intervention directed towards environmental protection: Biodiversity conservation on agricultural land'
<p>Interactive Excel data sheets to analyse potential interventions (i.e. changes in land use type and intensity) in the Dutch dairy production system towards conserving biodiversity. The tool uses the Dutch dairy sector as a case study and represents the current land use by dairy farmers in the Netherlands. The measures applied result in different landscapes that satisfy different biodiversity targets. At the same time, the tool measures the (negative) impact on food production.</p> <p>This interactive Excel tool is a supplement to: Kok A., Ripoll Bosch R., de Olde E.M., Muscat A., de Boer I.J.M. (2020), 'Intervention directed towards environmental protection: Biodiversity conservation on agricultural land', MAGIC (H2020–GA 689669) Project Deliverable 6.4, 24 February 2020, available online: <a href="https://magic-nexus.eu/documents/d64-intervention-directed-towards-environmental-protection">https://magic-nexus.eu/documents/d64-intervention-directed-towards-environmental-protection</a>.</p> <p> </p>
Supplementary material 1 from: Faulkner KT, Hulme PE, Pagad S, Wilson JRU, Robertson MP (2020) Classifying the introduction pathways of alien species: are we moving in the right direction? In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 143-159. https://doi.org/10.3897/neobiota.62.53543
Evidence used to assess the introduction pathway classification frameworks
Data from: Herring gulls respond to human gaze direction
Human-wildlife conflict is one of the greatest threats to species populations worldwide. One species facing national declines in the UK is the herring gull (Larus argentatus), despite an increase in numbers in urban areas. Gulls in urban areas are often considered a nuisance due to behaviours such as food-snatching. Whether urban gull feeding behaviour is influenced by human behavioural cues, such as gaze direction, remains unknown. We therefore measured the approach times of herring gulls to a food source placed in close proximity to an experimenter who either looked directly at the gull or looked away. We found that only 26% of targeted gulls would touch the food, suggesting that food-snatching is likely to be conducted by a minority of individuals. When gulls did touch the food, they took significantly longer to approach when the experimenter's gaze was directed towards them compared to directed away. However, inter-individual behaviour varied greatly, with some gulls approaching similarly quickly in both treatments while others approached much more slowly when the experimenter was looking at them. These results indicate that reducing human-herring gull conflict may be possible through small changes in human behaviour, but will require consideration of behavioural differences between individual gulls.
Data from: The core planar cell polarity gene, Vangl2, directs adult corneal epithelial cell alignment and migration
This study shows that the core planar cell polarity (PCP) genes direct the aligned cell migration in the adult corneal epithelium, a stratified squamous epithelium on the outer surface of the vertebrate eye. Expression of multiple core PCP genes was demonstrated in the adult corneal epithelium. PCP components were manipulated genetically and pharmacologically in human and mouse corneal epithelial cells in vivo and in vitro. Knockdown of VANGL2 reduced the directional component of migration of human corneal epithelial (HCE) cells without affecting speed. It was shown that signalling through PCP mediators, dishevelled, dishevelled-associated activator of morphogenesis and Rho-associated protein kinase directs the alignment of HCE cells by affecting cytoskeletal reorganization. Cells in which VANGL2 was disrupted tended to misalign on grooved surfaces and migrate across, rather than parallel to the grooves. Adult corneal epithelial cells in which Vangl2 had been conditionally deleted showed a reduced rate of wound-healing migration. Conditional deletion of Vangl2 in the mouse corneal epithelium ablated the normal highly stereotyped patterns of centripetal cell migration in vivo from the periphery (limbus) to the centre of the cornea. Corneal opacity owing to chronic wounding is a major cause of degenerative blindness across the world, and this study shows that Vangl2 activity is required for directional corneal epithelial migration.
Data from: Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population
A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation–selection balance. Here, we used a long-term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade-offs between fitness components, such as male and female fitness or fitness in high- and low-resource environments. "Animal model" analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population.
Data from: Non-coaxiality of sand under bi-directional shear loading
This study aims to investigate the effect of consolidation shear stress magnitude on the shear behaviour and noncoaxiality of soils. In previous drained bi-directional simple shear test on Leighton Buzzard sand, it is showed that the level of non-coaxiality, which is indicated by the angle difference between the principal axes of stresses and the corresponding principal axes of strain rate tensors, is increased by increasing angle difference between the direction of consolidation shear stress and secondary shearing. This paper further investigated the relation, and includes results with higher consolidation shear stresses. Results agree with previous relation, and further showed that increasing consolidation shear stresses decreased the level of non-coaxiality in tests with angle difference between 0 to 90 degrees, and increased the level of non-coaxiality in tests with angle difference between 90 to 180 degrees.
Data from: Sex-specific selection on plant architecture through 'budget' and 'direct' effects in experimental populations of a wind-pollinated herb
Sexual selection may contribute to the evolution of plant sexual dimorphism by favoring architecture traits that improve pollen dispersal to mates in males. In both sexes, larger individuals may be favored if large size allows the allocation of more resources to gamete production (a 'budget' effect of size). In wind-pollinated plants, large size may also benefit males if it allows them to liberate pollen from greater heights, fostering its dispersal (a 'direct' effect of size). To assess these effects and their implications for trait selection, we measured selection gradients on plant morphology in both males and females, as well as pollen production and dispersal in males, of the wind-pollinated dioecious herb Mercurialis annua. In two separate experimental common gardens established at different densities, selection strongly favored plants dispersing their pollen further. Selection for pollen production was observed in the high-density garden only and was weak. In addition, male morphologies associated with increased mean pollen dispersal differed between the two gardens as elongated branches were favored in the high-density garden while shorter plants with longer peduncles bearing inflorescences were advantaged the low-density garden. Larger females were selected in both gardens. Our results point to the importance of selection on male traits that affect pollen dispersal, and to a lesser extent pollen production.
Data from: Direct benefits of choosing a high fitness mate can offset the indirect costs associated with intralocus sexual conflict
Intralocus sexual conflict generates a cost to mate choice: high fitness partners transmit genetic variation that confers lower fitness to offspring of the opposite sex. Our earlier work in the fruit fly, Drosophila melanogaster, revealed that these indirect genetic costs were sufficient to reverse potential "good genes" benefits of sexual selection. However, mate choice can also confer direct fitness benefits by inducing larger numbers of progeny. Here, we consider whether direct benefits through enhanced fertility could offset the costs associated with intralocus sexual conflict in D. melanogaster. Using hemiclonal analysis, we found that females mated to high fitness males produced 11% more offspring compared to those mated to low fitness males, and high fitness females produced 37% more offspring than low fitness females. These direct benefits more than offset the reduction in offspring fitness caused by intralocus sexual conflict, creating a net fitness benefit for each sex to pairing with a high fitness partner. Our findings highlight the need to consider both direct and indirect effects when investigating the fitness impacts of mate choice. Direct fitness benefits may shelter sexually antagonistic alleles from selection, suggesting a novel mechanism for the maintenance of fitness variation.
Data from: Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies
Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with phenotype information voluntarily submitted via web-based surveys. These databases are having a transformative effect on human genomics research, yielding insights on increasingly complex traits, behaviors, and disease by including many thousands of individuals in genome-wide association studies (GWAS). The promise of consumer genomic data is not limited to human research, however. Genomic tools for dogs are readily available, with hundreds of causal Mendelian variants already characterized, because selection and breeding have led to dramatic phenotypic diversity underlain by a simple genetic structure. Here, we report the results of the first consumer genomics study ever conducted in a non-human model: a GWAS of blue eyes based on more than 3,000 customer dogs with validation panels including nearly 3,000 more, the largest canine GWAS to date. We discovered a novel association with blue eyes on chromosome 18 (P = 1.3x10-68) and used both sequence coverage and microarray probe intensity data to identify the putative causal variant: a 98.6-kb duplication directly upstream of the Homeobox gene ALX4, which plays an important role in mammalian eye development. This duplication is largely restricted to Siberian Huskies, is strongly associated with the blue-eyed phenotype (chi-square P = 5.2x10-290), and is highly, but not completely, penetrant. These results underscore the power of consumer-data-driven discovery in non-human species, especially dogs, where there is intense owner interest in the personal genomic information of their pets, a high level of engagement with web-based surveys, and an underlying genetic architecture ideal for mapping studies.
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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.