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406 results for “API”
Diet quantity influences caste determination in honey bees (Apis mellifera)
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First observation of Tropilaelaps mercedesae (Mesostigmata: Laelapidae) on Western honey bees (Apis mellifera) exiting colonies
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Data from: Identification of two odorant receptors tuned to alarm pheromone in the honey bee <em>Apis mellifera</em>
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Data from: Investigation of the effect of temperature and colonial air on the ontogeny of circadian rhythms in young worker honey bees Apis mellifera
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Phylogeography of cavity-nesting honeybees (Apis)
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APIS ER data model
<p>ER diagram of the APIS datamodel. Please note, the diagram does only include the APIS specific data fields.</p>
Depósito publicado mediante API
<p>Depósito publicado mediante API.</p>
Dataset for "Understanding Performance Concerns in the API Documentation of Data Science Libraries"
<p>Dataset for the manuscript "Understanding Performance Concerns in the API Documentation of Data Science Libraries", including the results of knowledge classification, consistency analysis, and evolution analysis on the API documentation data.</p>
Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes
<p>While many studies have examined the effects of neonicotinoid insecticides and the parasitic mite <em>Varroa destructor</em> on honey bees (<em>Apis mellifera</em>), more information on the combined effects of such stressors on gene expression, including neural related genes, and their impact on biological pathways is needed. This study analyzed the effects of field realistic concentrations of the neonicotinoid clothianidin on adult bees infested and not infested with <em>V</em>. <em>destructor</em> over 21 consecutive days and then determined bee survivorship, weight, deformed wing virus (DWV) levels and gene expression. <em>V</em>. <em>destructor</em> parasitism with or without clothianidin exposure was significantly associated with decreased survivorship, weight loss and higher DWV levels, while clothianidin exposure was only associated with higher levels of DWV. Expression analysis of the neural genes <em>AmNlg-1</em>, <em>BlCh</em> and <em>AmAChE-2</em> showed that <em>V</em>. <em>destructor</em> caused a significant down-regulation of all of them, whereas clothianidin caused a significant down-regulation of only <em>AmNrx-1</em> and <em>BlCh</em>. An interaction was only detected for <em>AmNrx-1</em> expression. RNAseq analysis showed that clothianidin exposure resulted in 6.5 times more up-regulated differentially expressed genes (DEGs) than <em>V</em>. <em>destructor</em> alone and 123 times more than clothianidin combined with <em>V</em>. <em>destructor</em>. Similar results were obtained with down-regulated DEGs, except for a higher number of DEGs shared between <em>V</em>. <em>destructor</em> and the combined stressors. KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis of the DEGs showed that the stressor linked to the highest number of KEGG pathways was clothianidin, followed by <em>V</em>. <em>destructor</em>, and then considerably fewer number of KEGG pathways with the combined stressors. The reduced numbers of DEGs and KEGG pathways associated with the DEGs for the combined stressors compared to the stressors alone indicates that the interaction of the stressors is not additive or synergistic, but antagonistic. The possible implications of the antagonistic effect on the number of DEGs are discussed.</p>
Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites' performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.
Egg-size plasticity in Apis mellifera: honey bee queens alter egg size in response to both genetic and environmental factors
<p>Social evolution has led to distinct life-history patterns in social insects, but many colony-level and individual traits, such as egg size, are not sufficiently understood. Thus, a series of experiments was performed to study the effects of genotypes, colony size, and colony nutrition on variation in egg size produced by honey bee (<i>Apis</i> <i>mellifera</i>) queens. Queens from different genetic stocks produced significantly different egg sizes under similar environmental conditions, indicating standing genetic variation for egg size that allows for adaptive evolutionary change. Further investigations revealed that eggs produced by queens in large colonies were consistently smaller than eggs produced in small colonies, and queens dynamically adjusted egg size in relation to colony size. Similarly, queens increased egg size in response to food deprivation. These results could not be solely explained by different numbers of eggs produced in the different circumstances but instead seem to reflect an active adjustment of resource allocation by the queen in response to colony conditions. As a result, larger eggs experienced higher subsequent survival than smaller eggs, suggesting that honey bee queens might increase egg size under unfavorable conditions to enhance brood survival, and to minimize costly brood care of eggs that fail to successfully develop, and thus conserve energy at the colony level. The extensive plasticity and genetic variation of egg size in honey bees has important implications for understanding life history evolution in a social context and implies this neglected life history stage in honey bees may have trans-generational effects.</p>
Data from: Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms
Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST-based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST-based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes.
Data from: Seminal fluid of honeybees contains multiple mechanisms to combat infections of the sexually transmitted pathogen Nosema apis
The societies of ants, bees and wasps are genetically closed systems where queens only mate during a brief mating episode prior to their eusocial life and males therefore provide queens with a lifetime supply of high-quality sperm. These ejaculates also contain a number of defence proteins that have been detected in the seminal fluid but their function and efficiency have never been investigated in great detail. Here, we used the honeybee Apis mellifera and quantified whether seminal fluid is able to combat infections of the fungal pathogen Nosema apis, a widespread honeybee parasite that is also sexually transmitted. We provide the first empirical evidence that seminal fluid has a remarkable antimicrobial activity against N. apis spores and that antimicrobial seminal fluid components kill spores in multiple ways. The protein fraction of seminal fluid induces extracellular spore germination, which disrupts the life cycle of N. apis, whereas the non-protein fraction of seminal fluid induces a direct viability loss of intact spores. We conclude that males provide their ejaculates with efficient antimicrobial molecules that are able to kill N. apis spores and thereby reduce the risk of disease transmission during mating. Our findings could be of broader significance to master honeybee diseases in managed honeybee stock in the future.
[Supplementary material] Machine Learning-driven Testing of Web APIs
<p>This is the supplementary material of the paper entitled "Machine Learning-driven Testing of Web APIs".</p>
Reddit blackout announcements: 2023 API protest
<p>Starting June 12, 2023, <a href="https://www.reddit.com/r/ModCoord/comments/1401qw5/incomplete_and_growing_list_of_participating">many Reddit communities</a> (subreddits) began a protest where they "went dark" - by changing to private mode - as a protest in response to Reddit's plans to <a href="https://www.reddit.com/r/reddit/comments/12qwagm/an_update_regarding_reddits_api/">change its API access policies and fee structure</a>. Supporters of the protest criticize the planned changes for being <a href="https://www.reddit.com/r/apolloapp/comments/13ws4w3/had_a_call_with_reddit_to_discuss_pricing_bad/">prohibitively expensive for 3rd party apps</a>. Beyond 3rd party apps, there is significant concern that the API changes are a move by the platform to increase monetization, degrade the user experience, and eventually kill off other custom features such as the old.reddit.com interface, the Reddit Enhancement Suite browser extension, and more. Additionally, there are concerns that the API changes will impede the ability of subreddit moderators (who are all unpaid users) to access tools to keep their communities on-topic and free of spam.</p> <p>This dataset includes the "stickied" posts that appeared on 5,351 subreddits on June 11, 2023 and June 12, 2023 - including many subreddits announcing their plans to participate in the protest. These posts were scraped using a custom Python script that was written specifically for this purpose. Ironically, the script uses the PRAW (Python Reddit API Wrapper) library, requiring a valid Reddit API key. Accordingly, after the platform's new API pricing policy went into effect, it is no longer feasible for researchers to perform this type of web scraping without external funding support.</p>
Detecting Usage of Deprecated Web APIs via Tracing: Replication Package
<p>Replication package for "Detecting Usage of Deprecated Web APIs via Tracing", published at 21st IEEE International Conference on Software Architecture (ICSA 2024)</p> <p> </p> <p>Changes from v2 to v3:</p> <ul> <li>readme.md: The requirements are now stated and explanations are given in more detail. Some typos in commands are fixed.</li> </ul> <p> </p> <p>Changes from v1 to v2:</p> <ul> <li>DATA: In addition to the intermedia data (output.json), the overall result files (results.json) are now provided as well for all example projects.</li> <li>IMPLEMENTATION: An incomplete version of the DeprecationDetector was present in v1. The new version includes extended matching functionality for specifications and improved export formatting.</li> <li>PROJECT: The server.jar in the client-server example project has been improved.</li> </ul>
Data source for the ReMap REST API
<h2>Content</h2> <p>This Zenodo contains the ReMap BED files in <code>bgzip</code> format with the <code>TABIX</code> indexes for the 2022, 2020, 2018 and 2015 ReMap releases.</p> <p>It contains all three data types (all peaks, non-redundant peaks and CRMs), except for 2015 (only all peaks, and non-redundant peaks available). </p> <h2>Format </h2> <p>The files formats for BGZIP BED files and TABIX indexes are as follow : </p> <ul> <li><code><strong>remap2018_all_macs2_hg38_v1_2.bed.gz</strong></code></li> <li><code><strong>remap2018_all_macs2_hg38_v1_2.bed.gz.tbi</strong></code></li> </ul> <ol> <li><strong>remap2018</strong> : ReMap release number (2015, 2018, 2020 or 2022)</li> <li><strong>all</strong> : data types (all= all peaks, nr= non-redundant peaks, crm=CisRegulatoryModules)</li> <li><strong>macs2 </strong>: peak caller used (always macs2)</li> <li><strong>hg38</strong> : assembly version (hg19, hg38, mm10 etc..)</li> <li><strong>v1.2</strong> : version patches</li> </ol> <p>The versioning number (eg. v1.2, v1.0) which varies between ReMap releases have been normalized with symlinks pointing to <strong><code>*latest*</code></strong> files. e.g.</p> <ul> <li><strong>remap2018_all_macs2_hg38_<code>v1_2</code>.bed.gz --> remap2018_all_macs2_hg38_<code>latest</code>.bed.gz</strong></li> </ul> <h2>Folder architecture </h2> <p>The architecture is as follow : </p> <p><code>.</code></p> <p><code>├── 2015</code></p> <p><code>│ ├── hg19</code></p> <p><code>│ └── hg38</code></p> <p><code>├── 2018</code></p> <p><code>│ ├── hg19</code></p> <p><code>│ └── hg38</code></p> <p><code>├── 2020</code></p> <p><code>│ ├── TAIR10</code></p> <p><code>│ ├── hg19</code></p> <p><code>│ └── hg38</code></p> <p><code>└── 2022</code></p> <p><code> ├── TAIR10</code></p> <p><code> ├── dm6</code></p> <p><code> ├── hg19</code></p> <p><code> ├── hg38</code></p> <p><code> ├── mm10</code></p> <p><code> └── mm39</code></p>
API X70 crack propagation tests
<p>Databases of crack propagation tests used for the master's thesis of Alexandre Henrique Oliveira, titled "EVALUATE CRACK GROWTH BY FATIGUE AT DIFFERENT TEMPERATURES IN A WELDED JOINT OF API X70 STEEL PIPES"</p>
Processed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper
<p>Processed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper. Each directory in the archive consists of:</p> <p>- metadata.json. Metadata about a test run - tested fuzzer name, run duration, etc</p> <p>- fuzzer.json - Structured fuzzer output</p> <p>- deduplicated_cases.json - Deduplicated reported failures, when fuzzers provide it</p> <p>- sentry.json - Cleaned Sentry events for this run</p> <p>- target.json - Parsed stdout for Gitlab & Disease.sh targets that were tested without Sentry integration</p>
Detect, Fix, and Verify TensorFlow API Misuses - SANER 2022 - Experimental Data
<p>Detect, Fix, and Verify TensorFlow API Misuses - SANER 2022</p> <p>Experimental data</p>
ScienceDex guides
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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.