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870 results for “boxing”
The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)
<p>Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (<i>Terrapene</i> spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.</p>
Data to accompany S. Boissier et al., "Coherent characterisation of a single molecule in a photonic black box," (2020)
<p>Data to accompany S. Boissier et al., "Coherent characterisation of a single molecule in a photonic black box," (2020). Data is in csv format and the "README.txt" file provides further details.</p>
Enhancing ecosystem services in apple orchards: Nest boxes increase pest control by insectivorous birds
<p>Ecological intensification in croplands aims to enhance biodiversity-based ecosystem services, helping to increase yield while reducing agricultural environmental impacts. Identifying ecological intensification tools of wide applicability and easily implemented by farmers is, therefore, an imperative. Here, we verify the efficiency of provisioning artificial nest boxes for insectivorous birds to reinforce pest biological control in apple orchards.</p> <p>The study was conducted in 24 cider-apple orchards in Asturias (NW Spain) over three years. We compared the effect of insectivorous birds between orchards with and without nest boxes occupied by different bird species, through insectivory estimates based on attack on a sentinel pest and measurements of arthropod abundance in apple trees. We also identified preys that birds of different species captured to feed nestlings.</p> <p>Bird occupancy of nest boxes was widespread, ranging 25.0-33.3% each year. Great tit was the dominant species, followed by blue tit and, occasionally, common redstart.</p> <p>Predation pressure on apple pests increased in orchards with nest boxes, as judged by the increased proportion of sentinel models attacked by birds (34.9% increase in 2018 and 41.1% in 2019), decreased biomass of tree-dwelling arthropods (-51.7%) and reduced probability of apple pest occurrence (from 57 to 40%), compared to orchards without nest boxes.</p> <p>Nesting species showed different predatory roles in apple orchards. Fewer attacks on sentinel pests but lower arthropod biomass was associated with blue tit rather than great tit. Besides, blue tit fed nestlings at a faster rate and included in their diet a higher proportion of apple pests than great tit, which preyed mostly on other herbivorous insects.</p> <p>Synthesis and applications. We demonstrated the usefulness of nest boxes for insectivorous birds in enhancing biological control of apple pests at a regional scale, identifying tit species as complementary predators of apple pests and herbivores. From the farmers' perspective, providing nest boxes in orchards may represent an efficient, easy to implement, cheap and attractive measure of ecological intensification, compatible with other actions fostering biodiversity in croplands.</p>
Data from: Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera
Patterns of spatial genetic structure (SGS), typically estimated by genotyping adults, integrate migration over multiple generations and measure the effective gene flow of populations. SGS results can be compared with direct ecological studies of dispersal or mating system to gain additional insights. When mismatches occur, simulations can be used to illuminate the causes of these mismatches. Here we report a SGS and simulation-based study of self-fertilization in Macrocystis pyrifera, the giant kelp. We found that SGS is weaker than expected in M. pyrifera, and used computer simulations to identify selfing and early mortality rates for which the individual heterozygosity distribution fits that of the observed data. Only one (of three) population showed both elevated kinship in the smallest distance class and a significant negative slope between kinship and geographic distance. All simulations had poor fit to the observed data unless mortality due to inbreeding depression was imposed. This mortality could only be imposed for selfing, as these were the only simulations to show an excess of homozygous individuals relative to the observed data. Thus, the expected data consistently achieved non-significant differences from the observed data only under models of selfing with mortality, with best fits between 32-42% selfing. Inbreeding depression ranged from 0.70-0.73. The results suggest that density-dependent mortality of early life stages is a significant force in structuring Macrocystis populations, with few highly-homozygous individuals surviving. The success of these results should help to validate simulation approaches even in data-poor systems, as a means to estimate otherwise difficult-to-measure life-cycle parameters.
Data from: Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia
Secondary cavity-nesting birds depend on tree cavities for nesting and roosting, but many studies of these birds are conducted using nest boxes. Implementation of effective conservation strategies for cavity-nesting species such as nest-site supplementation requires careful comparisons of fecundity and other vital rates for birds using both natural and artificial nest site types. We compared breeding phenology, clutch and brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor) nesting in tree cavities and nest boxes during 2001–2003 in British Columbia, Canada. Swallows using nest boxes initiated egg-laying and hatched young at approximately the same time as those in tree cavities (2 June, 23 June, respectively). Female Tree Swallows in boxes laid larger clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6 eggs, N = 67). The mean number of nestlings hatched was greater in nest boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0 nestlings, N = 58). Pairs in boxes were over twice as successful in producing fledglings (93.4%; 57 of 61 pairs fledged > 1 young) than those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests, pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest boxes averaged 60% larger in volume and 1.8 cm wider internally than tree cavities, we suggest that increased reproductive output was correlated with boxes enabling a larger clutch size. In previous research, we found that Tree Swallows were a poor competitor with other cavity-nesting passerines for tree cavities. The addition of nest boxes may serve as an effective way to supplement local reproduction for secondary cavity-nesting bird populations by reducing competition for limited nest sites. This is especially true in regions where the availability of natural nesting sites is highly variable, and where species compete with many other cavity-nesting passerines using a similar ecological niche and nesting cavities.
Data from: Nest-box temperature affects clutch size, incubation initiation, and nestling health in great tits
Prenatal maternal effects can be a source of phenotypic plasticity and may play a role in adaptation to climate change. However, we do not know how far temperature could influence such effects, if at all. We studied the influence of temperature during egg laying on maternal reproductive investment and on the phenotype of adult females, adult males, and nestlings. We expected temperature to have an effect, as it influences maintenance costs for females, who can also use it as a cue of the advancement of the breeding season. We experimentally increased night-time nest-box temperatures by approximately 1 °C throughout the entire laying period in great tits (Parus major). Clutch size was negatively correlated with laying date in heated females. Heated females did not delay incubation after clutch completion as frequently as control females did. Finally, blood sedimentation rate, which is an indicator of acute infections and inflammatory diseases, was positively correlated with hatching date in control broods. This suggests that nestlings were of lower quality in late-hatched broods than in early-hatched broods. This seasonal effect was not detected in heated nests. Our results show that a small increase in temperature during laying can influence breeding strategy and nestling characteristics. These results suggest that birds used temperature as a cue of seasonal advancement to adjust breeding phenology, with beneficial effects on nestling health. To better understand the consequences of maternal adjustments during egg laying, it would be interesting to combine studies with heating treatment during different periods of the breeding cycle.
Data from: Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box)
In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.
Data from: Smart nest box: a tool and methodology for monitoring of cavity-dwelling animals
1.Camera recording and video analysis have emerged as a successful non-invasive method for collecting a wide range of biological data on many different taxa of animals. However, camera monitoring has rarely been applied to long term surveillance of cavity or box-nesting species and ordinary off-the-shelf cameras are employed. 2.We present methodology and data on the effectiveness of nest box monitoring using a camera system embedded in four "smart nest boxes" (SNBoxes). We applied the SNBoxes to eight Tengmalm's owl (Aegolius funereus) nests in the Czech Republic during a five-month period in 2014. Each SNBox consisted of a pair of cameras with infrared lighting, an event detector, a radio-frequency identification reader, auxiliary sensors, and a 60 Ah 12 V battery to power the whole system. All devices used were centrally managed by an embedded computer with specifically developed software. 3.Using four SNBoxes, we observed owl nesting continually during the incubation, nestling, and fledgling phases, in total 309 days, resulting in 3382 owl video events. Batteries were changed every 6.5 days. A memory of 4 GB was found sufficient to store monthly data. We identified 12 types of male and female parental activities and their timing, the diet composition and frequency of prey delivery, the manner of prey storage, the light intensity at the time of each parental activity, the temperature inside the clutch and outside the box, and the duration of nestling period of each young. We also produced a video on owl nesting for the general public. 4.The SNBox and related methodology show enormous potential as a non-invasive tool for monitoring animals using boxes or natural cavities. The main advantage of the SNBox is the possibility to study both nocturnal and diurnal animal species and great flexibility in use of the software and hardware for different tasks. As a result, the SNBox provides an opportunity for novel insights into the breeding, roosting, hibernating, and food storage activities of a wide range of cavity-living birds, mammals, and reptiles.
The guide sRNA sequence determines the activity level of Box C/D RNPs
<p class="western">2'-O-rRNA methylation, which is essential in eukaryotes and archaea, is catalysed by the Box C/D RNP complex in an RNA-guided manner. Despite the conservation of the methylation sites, the abundance of site-specific modifications shows variability across species and tissues, suggesting that rRNA methylation may provide a means of controlling gene expression. As all Box C/D RNPs are thought to adopt a similar structure, it remains unclear how the methylation efficiency is regulated. Here, we provide the first structural evidence that, in the context of the Box C/D RNP, the affinity of the catalytic module fibrillarin for the substrate–guide helix is dependent on the RNA sequence outside the methylation site, thus providing a mechanism by which both the substrate and guide RNA sequences determine the degree of methylation. To reach this result, we develop an iterative structure calculation protocol that exploits the power of integrative structural biology to characterize conformational ensembles. </p> <p class="western"> </p>
Cardboard box
Low poly Cardboard box. Made in blander. Source: Objaverse 1.0 / Sketchfab
London Telephone Box
game ready, 6k polys total, 1 4k metalrough material. Source: Objaverse 1.0 / Sketchfab
Old Wood Tool Box [RAW]
Old Wood Tool Box Source: Objaverse 1.0 / Sketchfab
Coin Box
A box used to save coins. Source: Objaverse 1.0 / Sketchfab
Box
Photoscan 70 photos Source: Objaverse 1.0 / Sketchfab
Ancient metal box from Morocco
Ancient metal box from Morocco Source: Objaverse 1.0 / Sketchfab
Vintage Japanese Fujiya Chocolate Tin box
Vintage Japanese Fujiya's Chocolate Tin box Source: Objaverse 1.0 / Sketchfab
free press boxes a street lamp and a post
a nice chunk of sidewalk for the free press boxes Created with Polycam Source: Objaverse 1.0 / Sketchfab
Boxes And Barreles
Boxes And Barreles Source: Objaverse 1.0 / Sketchfab
Peanut Box
For more information about this item visit: https://bhpsite.org/ Source: Objaverse 1.0 / Sketchfab
Full data reduction Box Profile with Expressions
<p>This movie describes how to use DAWN to reduce a series of radiography images to a corrosion rate.</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.