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3,576 results for “strain”
3D lookup tables for helium-graphene interaction for uniaxially strained graphene in the armchair direction
<p>Data files containing the 3D lookup tables for the helium-graphene Lennard Jones interaction for uniaxially strained graphene in the armchair direction from 0$\AA$ to 10$\AA$. Path integral Monte Carlo simulations can be performed using these data files and our open source code located <a href="https://code.delmaestro.org/">here</a>.</p>
Data from: Silence of the killers: discovery of male-killing suppression in a rearing strain of the small brown planthopper, Laodelphax striatellus
<p>According to evolutionary theory, sex ratio distortions caused by reproductive parasites such as <i>Wolbachia</i> and <i>Spiroplasma</i> are predicted to be rapidly normalised by the emergence of host nuclear suppressors. However, such processes in the evolutionary arms race are difficult to observe because sex ratio biases will be promptly hidden and become superficially unrecognisable. The evolution of genetic suppressors has been reported in just two insect species so far. In the small brown planthopper,<i> Laodelphax striatellus</i>,<i> </i>female-biases caused by <i>Spiroplasma</i>, which is a 'late' male-killer, have been found in some populations. During the continuous rearing of <i>L. striatellus</i>, we noticed that a rearing strain had a 1:1 sex ratio even though it harboured <i>Spiroplasma</i>. Through introgression crossing experiments with a strain lacking suppressors, we revealed that the <i>L. striatellus</i> strain had the zygotic male-killing suppressor acting as a dominant trait. The male-killing phenotype was hidden by the suppressor even though<i> Spiroplasma</i> retained its male-killing ability. This is the first study to demonstrate the existence of a late male-killing suppressor and its mode of inheritance. Our results, together with those of previous studies, suggest that the inheritance modes of male-killing suppressors are similar regardless of insect order or early or late male-killing.</p>
Enhanced polarization in epitaxially strained monoclinic potassium niobate for lead-free electromechanical applications
<p>Atomic structure files used to study the anisotropic structural index for ferroelectric properties of strained KNbO3 perovskite polymorphs.</p>
Fibronectin-Based Nanomechanical Biosensors to Map 3D Surface Strains in Live Cells and Tissue (Raw Data)
<p>This is the raw microscope imaging data for the manuscript titled "Fibronectin-Based Nanomechanical Biosensors to Map 3D Surface Strains in Live Cells and Tissue."</p>
Dataset for "Strain induced electrochemical behaviours of ionic liquid electrolytes in an electric double layer capacitor: Insights from molecular dynamics simulations"
<p>The datafile contains molecular dynamics simulation results for analysing the electrochemical behaviour of ionic liquid based EDLC under compression and tension.</p>
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.
DIC performance for huge strains: The X-Strain DIC Challenge (GeM/ECN batch images)
<p>There are in this repository <strong>2 sets of images </strong>of flat elastomeric membranes that are severely deformed (up to several hundred % deformation). A speckle and dots have been deposited on the membranes in order to perform image analysis and measure the deformation fields. The document ’<em>Large_strain_images.pdf’</em> explains how the images were obtained. These images can be used as a benchmark for digital image correlation codes in case of very large deformations (i.e. The X-Strain DIC Challenge, <a href="http://sem.org/dicchallenge">https://sem.org/dicchallenge</a>).</p> <ul> <li>First set of images : 360 bmp images of size 38.8 Mo (<a href="https://zenodo.org/api/files/dbac452a-e701-4b5d-b05c-edafa7e442c8/20190926.zip">20190926.zip</a>)</li> <li>Second set of images : 820 bmp images of size 32.5 Mo (<a href="https://zenodo.org/api/files/dbac452a-e701-4b5d-b05c-edafa7e442c8/20191220.zip">20191220.zip</a>) </li> <li>Technical data sheet of the materials (<a href="https://zenodo.org/api/files/dbac452a-e701-4b5d-b05c-edafa7e442c8/Data_sheet.zip">Data_sheet.zip</a>)</li> <li>A technical report on how the images where obtained (<a href="https://zenodo.org/api/files/dbac452a-e701-4b5d-b05c-edafa7e442c8/Large_strain_Images.pdf">Large_strain_Images.pdf</a>)</li> </ul>
BONE STRAIN INDEX AS A PREDICTOR OF FURTHER VERTEBRAL FRACTURE IN OSTEOPOROTIC WOMEN
<p>Background: Osteoporosis is an asymptomatic disease of high prevalence and incidence, leading to bone fractures burdened by high mortality and disability, mainly when several subsequent fractures occur. A fragility fracture predictive model, Artificial Intelligence-based, to identify dual X-ray absorptiometry (DXA) variables able to characterise those patients who are prone to further fractures called Bone Strain Index, was evaluated in this study.</p> <p>Methods: In a prospective, longitudinal, multicentric study 172 female outpatients with at least one vertebral fracture at the first observation were enrolled. They performed a spine X-ray to calculate spine deformity index (SDI) and a lumbar and femoral DXA scan to assess bone mineral density (BMD) and bone strain index (BSI) at baseline and after a follow-up period of 3 years in average. At the end of the follow-up, 93 women developed a further vertebral fracture. The further vertebral fracture was considered as one unit increase of SDI. We assessed the predictive capacity of supervised Artificial Neural Networks (ANNs) to distinguish women consistently with a further fracture from those without a further fracture and to identify the variables expressing the maximal amount of relevant information to discriminate the two groups. ANNs were allowed to choose relevant input data automatically (TWIST-system). Moreover, we constructed a semantic connectivity map with Auto Contractive Map to offer some insight regarding the complex biological connections among the studied variables and the two conditions (further fracture vs no further fracture).</p> <p>Results: TWIST system selected 5 out of 13 available variables: age, menopause age, BMI, FTot BMC, FTot BSI. With training testing procedure, ANNs reached predictive accuracy of 79.36%, with a sensitivity of 75% and a specificity of 83.72%. The semantic connectivity map highlighted the role of BSI in predicting the risk of a further fracture.</p> <p>Conclusions: Artificial Intelligence is a useful method to analyse a complex system like that regarding osteoporosis, able to identify patients prone to a further fragility fracture. BSI appears to be a useful DXA index in identifying those patients who are at risk of further vertebral fractures.</p>
FeSe_nematicity_and_strain
<p>Data related to the paper "Nanoscale decoupling of electronic nematicity and structural anisotropy in FeSe thin films".</p>
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
<p>Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.</p>
Strain fields in twisted bilayer graphene: Dataset 18 of 19
<p>See supplemental materials of Kazmierczak & Van Winkle et al for more information.</p> <p>02262020_3.h5 : dataset s1-3 corresponding to a mean angle of 0.9999</p>
Strain fields in twisted bilayer graphene: Dataset 19 of 19
<p>See supplemental materials of Kazmierczak & Van Winkle et al for more information.</p> <p>02262020_6.h5 : dataset s1-6 corresponding to a mean angle of 1.2592</p>
Data from: Behavioral elements and sensory cues involved in sexual isolation between Drosophila melanogaster strains
Sensory cues exchanged during courtship are crucial for mate choice: if they show intraspecific divergence this may cause or reinforce sexual isolation between strains, ultimately leading to speciation. There is a strong asymmetric sexual isolation between Drosophila melanogaster females from Zimbabwe (Z) and males from all other populations (M). While M and Z flies of both sexes show different cuticular pheromones, this variation is only partly responsible for the intraspecific isolation effect. Male acoustic signals are also partly involved in sexual isolation. We examined strain-specific courtship behaviour sequences to determine which body parts and sensory appendages may be involved in sexual isolation. Using two strains representative of the Z- and M-types, we manipulated sensory cues and the social context; we then measured the consequence of these manipulations on courtship and copulation. Our data suggest that Z females mated best with males whose sensory characteristics matched those of Z males in both quantity and quality. M females were less choosy and much less influenced by the sensory and social contexts. Differences in emission and reception of sensory signals seen between Z and M flies may lead to the concerted evolution of multiple sensory channel, thereby shaping a population-specific mate recognition system.
Data from: Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish
Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genes—markers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.
Data from: Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains
Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X, −Y and −Z. The resulting phylogeny provides a comprehensive view of species relatedness highlighting where the OTUs align with respect to others members of the genus. All three OTUs fall within the Eimeria clade that contains only chicken-infecting species with close affinities to E. maxima, E. brunetti and E. mitis. Mitochondrial genetic diversity was low among Australian isolates likely reflecting their recent introduction to the country post-European settlement. The lack of observed genetic diversity is a promising outcome as it suggests that the currently used live vaccines should continue to offer widespread protection against Eimeria outbreaks in all states and territories. Flocks were frequently found to host multiple strains of the same species, a factor that should be considered when studying disease epidemiology in the field.
Data from: Among-strain consistency in the pace and shape of senescence in duckweed
1.Comparative studies have demonstrated extensive variation in age-trajectories of mortality and fecundity, both within and among species, with many taxa exhibiting a general pattern of age-related demographic decline referred to as senescence. Whereas a considerable body of theory is devoted to explaining the origin and persistence of senescence, the evolutionary forces underlying variation in demographic trajectories more generally remain poorly understood. 2.Studying variation in demographic trajectories is complicated by the fact that different species (or even different populations of a given species) may live and reproduce on different time scales, which, for comparative purposes, can make it challenging to disentangle patterns of age-related demographic change (the shape of demographic age trajectories) from the time scale on which those changes happen (the pace of demographic age trajectories). 3.Here we examine variation in the pace and shape of demographic trajectories among strains of the aquatic plant Lemna turionifera Landolt from 24 sites across Alberta, Canada. Our main objectives were to describe the shape of demographic trajectories in L. turionifera, and test for among-strain variation in pace and shape. We also tested whether potential variation in pace and shape is (i) constrained by tradeoffs with other life history traits, and (ii) consistent with local adaptation to environmental characteristics at the sites of strain origin. 4.The strains we examined were overwhelmingly subject to age-related increases in mortality and declines in fecundity, with increases in mortality tending to decelerate and plateau at advanced ages. Despite substantial among-strain variation in cumulative fecundity and plant size, measures of pace and shape did not in themselves vary significantly among strains. Both within and among strains, we observed a negative relationship between plant size and the shape of fecundity trajectories, but we found no other evidence for life history tradeoffs involving pace or shape, nor for local adaptation. 5.Synthesis. Angiosperms display remarkable demographic variation. Our results suggest that the pace and shape of demographic trajectories are highly conserved within one particular angiosperm species (L. turionifera), despite substantial among-strain variation in other life history traits.
Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a susceptible Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.
Data from: Is strain elastography (IO-SE) sufficient for characterization of liver lesions before surgical resection - or is contrast enhanced ultrasound (CEUS) necessary?
Aim: To evaluate the diagnostic accuracy of IO-SE in comparison to IO-CEUS for the differentiation between malignant and benign liver lesions. Material and Methods: In a retrospective diagnostic study IO-CEUS and SE examinations of 49 liver lesions were evaluated and compared to histopathological examinations. Ultrasound was performed using a multifrequency linear probe (6–9 MHz). The loops of CEUS were evaluated up to 5 min. The qualitative characterization of IO-SE was based on a color coding system (blue = hard, red = soft). Stiffness of all lesions was quantified by a specific scaling of 0–6 (0 = low, 6 = high) using 7 ROIs (2 central, 5 peripheral). Results: All malignant lesions displayed a characteristic portal venous washout and could be diagnosed correctly by IO-CEUS. 3/5 benign lesions could not be characterized properly either by IO-CEUS or IO-SE prior to resection. Thus for IO-CEUS sensitivity, specificity, positive and negative predictive value and accuracy were 100%, 40%, 94%, 100% and 94%. Lesion sizes were between 8 and 59 mm in diameter. Regarding the IO-SE, malignant lesions showed a marked variability. In qualitative analysis, 31 of the malignant lesions were blue colored denoting overall induration. Thirteen malignant lesions showed an inhomogenous color pattern with partial indurations. Two of the benign lesions also displayed overall induration. The other benign lesions showed an inhomogenous color mapping. Calculated sensitivity of the SE was 70.5%, specificity 60%, PPV 94%, NPV 18.75%, and accuracy 69%. Conclusion: IO-CEUS is useful for localization and characterization of liver lesions prior to surgical resection whereas IO-SE provided correct characterization only for a limited number of lesions.
Data from: Morphological and molecular characterization within 26 strains of the genus Cylindrospermum (Nostocaceae, Cyanobacteria), with descriptions of three new species
Twenty-six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S rRNA gene and the 16S-23S ITS region. Phylogenetic analysis of the 16S rRNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto had all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these taxa, three species new to science in this clade were described: C. badium, C. moravicum, and C. pellucidum. Our evidence indicates that Cronbergia is a later synonym of Cylindrospermum. The phylogenetic position of Cylindrospermum within the Nostocaceae was not clearly resolved in our analyses. Cylindrospermum is unusual among cyanobacterial genera in that the morphological diversity appears to be more evident than sequence divergence. Taxa were clearly separable using morphology, but had very high percent similarity among ribosomal sequences. Given the high diversity we noted in this study, we conclude that there is likely much more diversity remaining to be described in this genus.
Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
Background: In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods: Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results: Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.
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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.