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1,944 results for “Class I”
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
<p>Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation PCR) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the <em>Rhizobacter</em> genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.</p>
MammalBase — Database of traits, measurements and diets of the species in class Mammalia
<p><strong>MammalBase is a database of traits, measurements and diets of the species in class Mammalia. It also provides Proximate Analysis data for several diet items.</strong></p> <p><strong>MammalBase aims to provide general information on mammals for broad-scale analyses in Macroecology, Palaeontology and mammalian Community structures.</strong></p> <p><strong>The database is maintained at the Natural Sciences Unit of the Finnish Museum of Natural History LUOMUS — a research institution under the University of Helsinki in Finland.</strong></p>
Trans-specific polymorphism and the convergent evolution of supertypes in MHC class II genes in Darters (Etheostoma)
<p>Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans-specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study we used deep-sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.</p>
CottonWeedDet12: a 12-class weed dataset of cotton production systems for benchmarking AI models for weed detection
<p>The dataset <strong>CottonWeedDet12</strong> consists of 5648 RGB images of 12-class weeds that are common in cotton fields in the southern U.S. states, with a total of 9370 bounding boxes. These images were acquired by either smartphones or hand-held digital cameras, under natural field light condition and throughout June to September of 2021. The images were manually labeled by qualified personnel for weed identification, and the labeling process was done using the VGG Image Annotator (version 2.10).</p> <p>The dataset, at the time of publication, is the largest publicly available multi-class dataset dedicated to weed detection. It expects to facilitate communicate efforts to exploit state-of-the-art deep learning method to push weed recognition to the next level. With the WeedDet12 dataset, a performance benchmark of a suite of YOLO object detectors has been built for weed detection. Detailed documentation of the dataset, model benchmarking and performance results is given in an accompanying journal paper: <a href="https://www.sciencedirect.com/science/article/pii/S0168169923000431">Dang, F., Chen, D., Lu, Y., Li, Z., 2023. YOLOWeeds: A novel benchmark of YOLO object detectors for multi-class weed detection in cotton production systems. Computers and Electronics in Agriculture 205, 107655. https://doi.org/10.1016/j.compag.2023.107655</a><a href="https://doi.org/10.1016/j.compag.2023.107655"> </a></p> <p>If you use the dataset on a published publication, please cite the dataset or the <a href="https://doi.org/10.1016/j.compag.2023.107655">journal article</a> above.</p>
Data from: Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways
<p>The pericarp is the predominant tissue determining the structural characteristics of most fruits. However, the molecular and genetic mechanisms controlling pericarp development remain only partially understood. Previous studies have identified that CLASS-II KNOX genes regulate fruit size, shape, and maturation in Arabidopsis thaliana and Solanum lycopersicum. Here we characterized the roles of the Solanum lycopersicum CLASS-II KNOX (TKN-II) genes in pericarp development via a detailed histological, anatomical, and karyotype analysis of the TKN-II knockdown (35S:amiR-TKN-II) fruits. We identify that 35S:amiR-TKN-II pericarps contain more cells around their equatorial perimeter and fewer cell layers than the control. In addition, the cell sizes but not the ploidy levels of these pericarps were dramatically reduced.</p> <p>Further, we demonstrate that fruit shape and pericarp layer number phenotypes of the 35S:amiR-TKN-II fruits can be overridden by the procera mutant, known to induce a constitutive response to the plant hormone gibberellin. However, neither the procera mutation nor exogenous gibberellin application can fully rescue the reduced pericarp width and cell size phenotype of 35S:amiR-TKN-II pericarps. Our findings establish that TKN-II genes regulate tomato fruit anatomy, acting via gibberellin to control fruit shape but utilizing a gibberellin-independent pathway to control the size of pericarp cells.</p>
Data for: Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes
<p>The extreme polymorphisms of HLA-I proteins enable the presentation of diverse peptides to cytotoxic T lymphocytes (CTL). The canonical endoplasmic reticulum (ER) HLA-I assembly pathway enables presentation of cytosolic peptides, but effective intracellular surveillance requires multi-compartmental antigen sampling. Endo-lysosomes are generally sites of HLA class II assembly, but human monocytes and monocyte-derived dendritic cells (moDCs) also contain significant reserves of endo-lysosomal HLA-I molecules. We hypothesized variable influences of HLA-I polymorphisms upon outcomes of endo-lysosomal trafficking, as the stabilities and peptide occupancies of cell surface HLA-I are variable. Consistent with this model, when the endo-lysosomal pH of moDCs is disrupted, HLA-B allotypes display varying propensities for reductions in surface expression, with HLA-B*08:01 or HLA-B*35:01 being among the most resistant or sensitive respectively, among eight tested HLA-B allotypes. Perturbations of moDC endo-lysosomal pH result in redistribution of HLA-B*35:01, but not HLA-B*08:01, to LAMP1+ compartments and increase HLA-B*35:01 peptide receptivity. These findings reveal the intersection of the vacuolar cross-presentation pathway with a constitutive assembly pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes derived from two soluble antigens was also more efficient for B*35:01 compared to B*08:01, even when matched for T cell response sensitivity, and more affected by cathepsin inhibition. Thus, HLA-I polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement ER assembly for constitutive HLA-I expression and increase the efficiency of cross-presentation.</p>
Modest dust settling in the IRAS04302+2247 Class I protoplanetary disk
<p>Continuum VLA images of IRAS04302+2247, from projects 21B-183 and 21B-100. For the Q and Ka observations, we also include images after correction for free-free emission.</p>
Time series of phytoplankton size classes at LTER-MC in the Gulf of Naples (1984-2015)
<p>This database contains the abundance data of four phytoplankton size classes from the Long Term Ecological Research Station MareChiara (st. LTER-MC, 40°48.5’ N, 14°15’ E) over the years 1984-2015. Samples were collected with a Niskin bottle in surface waters, fixed with neutralized formaldehyde (0.8-1.6% final concentration), and counted at the inverted microscope. Linear measurements were taken on a number of phytoplankton specimens for each species and biovolumes were calculated based on species-specific shapes. The species were grouped in size classes (< 5 µm, 5-15 µm, 15-30 µm, > 30 µm) based on their equivalent spherical diameter (ESD).</p>
A Catalogue Of Sounds For UML Class Diagrams - Experimental Study
<p>This experiment was developed within the scope of the thesis "Constructing An Auditory Notation In Software Engineering - Understanding UML Models with voice and sound", and aims to determine if the construction of a catalogue of sounds that follows a more methodical approach is more effective for comprehension, when compared to a catalogue where the choice for sounds is purely arbitrary.</p> <p> </p> <p>Here are contained the results, along with the sounds used and the form that was presented to the participants.</p>
Comparative evaluation of the forces produced by tongue on circummaxillary sutures in skeletal Class III malocclusion with maxillary hypoplasia using tongue crib with that of facemask therapy - A FEM study
<p>Data sheet showing stimulation result</p>
Correlation between body size and longevity: new analysis and data covering six taxonomic classes of vertebrates
<p class="MsoNormal"><span>Large bodied species are known to live longer than small bodied species. However, it is less clear whether the positive correlation varies across taxa. In this short communication, we combine data entries from literature and databases on body mass and maximum life span for 3722 species covering </span><span>taxonomic Classes <span><em><span>Chondrichthyes</span></em><span>, <em>Teleostei, Amphibia</em>, <em>Reptilia, Aves</em><span>, and</span><em> Mammalia</em>.</span> </span>We then analyze the log(maximum life span) – log(body mass) relationship using generalized linear model with nested random intercepts and slopes for Class/Order/Family. Our analyses generally demonstrate the positive longevity – body mass relationship but also reveal that slopes and intercepts differ slightly among all Classes except <em>Reptilia</em> and <em>Amphibia</em>. Highest slopes can be found in Classes <em>Aves</em> and <em>Chondrichthyes</em>. Differences between the smallest and largest Family-level slopes was more than threefold. While these preliminary analyses provide a brief overview of body size – longevity relationships across taxa, the dataset collated in the present study could serve as a start point for in-depth phylogenetic analyses to uncover complex pathways through which body size and its correlates might have evolved. </span></p>
An Evaluation Framework for Mapping News Headlines to Event Classes in a Knowledge Graph
<p>News headline to event classes corpus derived from Wikidata.</p> <p>Github: https://github.com/mbouadeus/news-headline-event-linking</p>
Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
<p><span>Declining biodiversity is a global challenge to sustainability and resilience of ecosystems facing multiple novel stressors, including climate change and invasive pests-pathogens. Northern hardwood forests (NHF) of the Great Lakes region have experienced declines in canopy tree diversity since European colonization, with current tree regeneration patterns in some areas suggesting perpetuation of this trend. However, regional (10<sup>6</sup> ha) patterns and possible causes are underexplored. To address this information gap, we used data from 141 managed NHF stands, Michigan, USA to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand-level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6 – 7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (<em>Fraxinus americana </em>and<em> Fagus grandifolia</em>, insect/pathogen limited; <em>Ostrya virginiana, </em>small maximum size). For the 11 most common species, conspecific canopy density (+, significant for 11 seedlings, 11 species) and stand basal area (-, saplings, 3 species) were the most consistent drivers of density, with less consistent effects for deer use, site quality, and substrate. Patterns of relative density by size class among the 18 species present on > 10 % of sites were consistent with theories of establishment or recruitment limitations due to deer browsing, deep shade, or limited suitable substrate. For seven species (including e.g., <em>Tsuga canadensis</em><span>, </span><em>Betula alleghaniensis, Populus grandidentata, Tilia americana</em><span>)</span>, relative abundance was lowest in the seedling layer and increased in larger size classes, <span>suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (<em>Acer saccharum, Quercus rubra.</em>), patterns of reduced sapling relative abundance compared to seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., <em>F</em></span><em>agu<span>s grandifolia, Ostrya virginiana, Pinus strobus</span></em><span>) had highest relative density for saplings suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most abundant for </span><em>Acer rubrum </em><span>and </span><em>Prunus </em><span>spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. Americana, consistent with recent pest-related canopy mortality. Our results</span> suggest sustained low diversity and shifting composition are being driven by limited local seed availability, deep shading, limited seedling establishment substrate, and abundant deer. Management aimed at overcoming these specific limitations may be necessary to promote future NHF resilience.</span></p>
Database for "Estimation of the Energy Recovery and Emission Potential of Typically Incinerated Norwegian Waste Classes"
<p>A great challenge for waste-to-energy power plants is their uncertain and variable feedstock, which<br> can lead to the power plants not being run as efficiently as possible, leading to reduced energy<br> output and control of emissions. A way to describe the feedstock is to use surrogates. This is a<br> method where the hundreds or thousands of different species of a feedstock are modelled using a few<br> surrogate species, enabling the feedstock’s modelling. The surrogates also provide an estimation<br> of the HHV and the fraction of biomass, oil-based waste and inorganics.<br> This thesis formulated surrogates for waste classes typically incinerated, using a linear least-square<br> solution between available surrogate species and experimental values. Most of the species used<br> were from two existing models in the literature, but three new species were created to improve the<br> representation of some waste classes containing fossil-originated wastes, rubber and PET. These<br> were made by creating reactions based on experimental data from the literature and then testing<br> these reactions under pyrolysis conditions in a stochastic reactor model.<br> The surrogates for the waste classes were formulated by first dividing the waste into components<br> and then finding the surrogate formulation for each component. There were found surrogates<br> for 41 components, which were used to create the surrogate formulation for 30 waste classes. It<br> was found that most of the surrogates modelled the elemental composition accurately compared<br> to experimental values. A statistical overview of the experimental and model data for the waste<br> classes was also created. This overview is relevant for stakeholders in waste management and for<br> other research, such as life-cycle analysis.</p>
Mapping of aridity and its connections with climate classes and climate desertification in future scenarios – Brazilian semi-arid region
<p>This database comes from the article entitled ''Mapping of aridity and its connections with climate classes and climate desertification in future scenarios –Brazilian semi-arid region'' (https://seer.ufu.br/index.php/sociedadenatureza /article/view/67666/36193). We provide data on aridity and desertification index for the current scenario and future projections considering changes in climate.</p>
Data from: Potential of MALDI−TOF MS-based proteomic fingerprinting for species identification of Cnidaria across classes, species, regions and developmental stages
<p><span>Morphological identification of cnidarian species can be difficult throughout all life stages due to the lack of distinct morphological characters. Moreover, in some cnidarian taxa genetic markers are not fully informative, and in these cases combinations of different markers or additional morphological verifications may be required. Proteomic fingerprinting based on MALDI-TOF mass spectra was previously shown to provide reliable species identification in different metazoans including some cnidarian taxa. For the first time, we tested the method across four cnidarian classes (Staurozoa, Scyphozoa, Anthozoa, Hydrozoa) and included different scyphozoan life-history stages (polyp, ephyra, medusa) into our dataset. Our results revealed reliable species identification based on MALDI-TOF mass spectra across all taxa with species-specific clusters for all 23 analyzed species. In addition, proteomic fingerprinting was successful for distinguishing developmental stages, still by retaining a species specific signal. Furthermore, we identified the impact of different salinities in different regions (North Sea and Baltic Sea) on proteomic fingerprints to be negligible. In conclusion, the effects of environmental factors and developmental stages on proteomic fingerprints seem to be low in cnidarians. This would allow using reference libraries built up entirely of adult or cultured cnidarian specimens for the identification of their juvenile stages or specimens from different geographic regions in future biodiversity assessment studies.</span></p>
Class Diagram case Reengineering FRS web
<p>Domain model yang telah dibuat sebelumnya dapat dikembangkan lebih lanjut menjadi class diagram. Class diagram digunakan untuk menggambarkan struktur statis dari sistem, termasuk kelas-kelas yang ada, atribut-atribut mereka, serta hubungan dan interaksi antara kelas-kelas tersebut</p>
Appendix - Informative Speech Features based on Emotion Classes and Gender in Explainable Speech Emotion Recognition
<p>Appendix tables for the paper "Informative Speech Features based on Emotion Classes and Gender in Explainable Speech Emotion Recognition".</p> <p>Feature informativeness information was gathered using SHAP values.</p> <p>TABLE VIII: Table of Statistics and Individual t-Test Results Between Each Emotion vs Neutral</p> <p>TABLE IX: (continue)Table of Statistics and Individual t-Test Results Between Each Emotion vs Neutral</p> <p>TABLE X: Table of Statistics and Individual t-Test Results Between Genders</p> <p>TABLE XI: (continue) Table of Statistics and Individual t-Test Results Between Genders</p> <p>TABLE XII: Table of 5 the most informative feature for each model, according to SHAP values</p> <p>TABLE XIII: (continue)Table of 5 the most informative feature for each model, according to SHAP values</p>
Data from: Dissecting molecular evolution of class 1 integron gene cassettes and their bacterial hosts in suburban creeks via epicPCR
<p>Horizontal gene transfer (HGT) of class 1 integrons plays a key role in the dissemination of antimicrobial resistance (AMR) with clinical consequences worldwide. Class 1 integrons in clinical pathogens are commonly associated with AMR genes and embedded in mobile genetic elements. Over time, these mobile class 1 integrons have spread to diverse environmental bacterial hosts via HGT. We applied a single-cell fusion PCR-based technique to link class 1 integron gene cassette arrays to the phylogenetic markers in their bacterial hosts. Class 1 integrons and associated gene cassettes were detected in <em>Alpha</em>- and <em>Gammaproteobacteria </em>hosts from freshwater samples from two creeks in suburban Sydney. Molecular and bioinformatic characterisations of altered gene cassettes generated new insights into mechanisms that contribute to the evolution of class 1 integron gene cassettes. Here, we present experimental and bioinformatic evidence for key signatures of molecular evolution of gene cassettes, including the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of <em>attC </em>recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an insertion sequence (IS) element. Notably, our experimental testing of a new variant of the aminoglycoside adenylyltransferase encoding <em>aadA11 </em>gene cassette demonstrated that the gain of 5'-UTR contributed to a 3-fold increase in the minimum inhibitory concentration of streptomycin relative to the ancestral reference gene cassette. Understanding these signatures of molecular evolution allows us to explain their effects on AMR phenotypes and offers the potential to better predict evolutionary trajectories of class 1 integrons.</p>
Hearing aids recordings : class 1 / class 2
<pre>Sound files recorded at the output of class 1 / class 2 hearing aids with an artificial head.</pre>
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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.