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23,351 results for “Comparative”
Extending Refactoring Detection to Kotlin: A Dataset and Comparative Study
<p><span>This page serves as supplementary material for the article </span><span>Extending Refactoring Detection to Kotlin: A Dataset and Comparative Study</span><span>. In detail, we offer a downloadable dataset in JSON format, comprising 2,043 instances of refactoring instances covering 21 distinct refactoring types. These refactorings are applied within 200 commits across 10 Kotlin repositories and are manually validated by the authors of the paper.</span><span> </span></p> <p><span>Results.json: The results as </span><span>a single</span><span> JSON file.</span></p> <ul> <li> <p><span>Overview of JSON Template: Each entry in this file provides details </span><span>about</span><span> commits, including </span><span>their </span><span>SHA-1 hash, GitHub URL, and an exhaustive list of refactorings </span><span>identified</span><span> </span><span>in </span><span>that specific commit. Refactorings are defined by their type (e.g., 'RenameClass') and are accompanied by detailed descriptions of the </span><span>refactoring</span><span>. Additionally, the entry specifies the tools that </span><span>detected</span><span> the refactoring, such as 'RefDetect' and 'KotlinRMiner.' The validation field indicates whether the refactoring was confirmed, using 'TP' for true positive and 'FP' for false positive. Optional comments and validator information may be also included</span><span>.</span></p> </li> </ul> <p><span>AllCommits.zip: The Results for each repository in a single JSON file.</span></p> <p><span>Times.xlsx: The Excel file containing the time taken by each tool (RefDetect and KotlinMiner) to identify refactoring in each commit.</span></p> <p><span>Results.xlsx: T</span><span>he Excel file contains precision, recall, and F-score metrics for all identified refactoring types.</span></p>
Data from: Comparative assessment of a novel fan box trap for collecting Anopheles farauti and culicine mosquitoes alive in tropical north Queensland, Australia
<p>During preliminary mosquito surveys at Cowley Beach Training Area in north Queensland, Australia, it was found that the utility of the standard encephalitis virus surveillance (EVS) trap for collecting the malaria vector <em>Anopheles farauti</em> (Laveran) adults was compromised by the harsh tropical conditions. With the aim of increasing the survival rate of mosquitoes, we designed a downdraft fan box trap (FBT) that incorporated a screened fan at the bottom of the trap, so mosquitoes did not have to pass through a fan. The FBT was tested against the EVS and Centers for Disease Control (CDC) light traps, where mosquitoes do pass through a fan, and a nonpowered passive box trap (PBT). We conducted four trials to compare the quantity and survival of <em>An. farauti</em> and culicine mosquitoes were collected in these traps. Although not significant, the FBT collected more <em>An</em>. <em>farauti</em> than the EVS trap and PBT and significantly less <em>An. farauti</em> than the CDC light trap. However, the FBT improved on the CDC light trap in terms of the survival of <em>An</em>. <em>farauti</em> adults collected, with a significantly higher percentage alive in the FBT (74.6%) than in the CDC light trap (27.5%). Thus, although the FBT did not collect as many anophelines as the CDC, it proved to be superior to current trap systems for collecting large numbers of live and relatively undamaged mosquitoes. Therefore, it is recommended that FBTs be used for collecting <em>An. farauti</em> adults in northern Australia, especially when high survival and sample quality are important.</p>
Just another copy and paste? Comparing the security vulnerabilities of ChatGPT generated code and StackOverflow answers
<div>Supplemental material for the paper "Just another copy and paste? Comparing the security vulnerabilities of ChatGPT generated code and StackOverflow answers" published in DLSP 2024.</div> <div> <div> </div> </div>
Enhancing comparative T-cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice
<p>All data files used to generate the figures in the paper are shared in this project.</p> <p>Scripts are available on <a href="https://github.com/i3-unit/CRM_24" target="_blank" rel="noopener">GitHub</a>.</p>
Data required for "Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences"
<p>In the early 1900s,mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of NGS technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using next-generation sequencing (NGS) to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.</p>
The comparative effects of landscape-level forest fragmentation, forest area and local habitat measures on Connecticut bird communities
<p>I studied how breeding and wintering forest bird communities across Connecticut responded to variation in habitat characteristics and particularly such landscape attributes as forest fragmentation. I surveyed birds at 1,815 points along 121 transects that traversed ca. 400 km of forest. I also made 12705 habitat measurements at survey points and computed areas of forest, non-forest, core forest and perimeter/area ratios of forest for 31,550 ha of study area. I computed sampled species richness and community density as well as individual species' population densities for each transect. Moreover, I classified species encountered as to their nest site selection, macrohabitat use, microhabitat use, migratory strategy and trophic affiliation. Based on observations of 36,702 summering individuals of 123 species and 13,742 wintering individuals of 63 species, declines in community density occurred with increasing fragmentation although species richness was often more closely associated with habitat measures. Among landscape measures, forest fragmentation had the closest association with summer community measures 67% of the time, strongly suggesting that fragmentation effects were the predominant driver of such community patterns. However, short-distance migrant density and richness, foraging generalist density and richness, edge/successional species density and richness, habitat generalist density, and Brown-headed Cowbird density showed little relationship to landscape measures. The effects of fragmentation appeared to predominate over those of simply forest extent in predicting summer and winter bird community characteristics even in the comparatively extensive forests of southern New England. Despite the importance of fragmentation effects, community and individual species measures often tended to be more closely associated with habitat measures than with those of fragmentation. In addition, few summer or winter community measures or species patterns showed any significant relationship to natural forest breaks. Winter community and species density patterns showed little relationship to any landscape measures, with particularly elevation appearing to be a principal driver of winter patterns.</p>
Data from: Temperature has an overriding role compared to photoperiod in regulating the seasonal timing of winter moth egg hatching
<p>To accurately predict species' phenology under climate change, we need to gain a detailed mechanistic understanding of how different environmental cues interact to produce the seasonal timing response. In the winter moth (<em>Operophtera brumata</em>), seasonal timing of egg hatching is strongly affected by ambient temperature and has been under strong climate change-induced selection over the past 25 years. However, it is unclear whether photoperiod received at the egg stage also influences timing of egg hatching. Here, we investigated the relative contribution of photoperiod and temperature in regulating winter moth egg development using two split-brood experiments. We experimentally shifted the photoperiod eggs received by 2-4 weeks compared to the actual calendar date and measured the timing of egg hatching, both at a constant temperature and in combination with two naturally changing temperature treatments – mimicking a cold and a warm year. We found an eight-fold larger effect of temperature compared to photoperiod on egg development time. Moreover, the very small photoperiod effects we found were outweighed by both between- and within-clutch variation in egg development time. Thus, we conclude that photoperiod received at the egg stage does likely not play a substantial role in regulating the seasonal timing of egg hatching in the winter moth. These insights into the regulatory mechanism of seasonal timing could have important implications for predicting insect climate change adaptation, as we might expect different targets of selection depending on the relative contribution of different environmental cues.</p>
Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
<p>Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (<em>Fragum sueziense</em>) and a closely related non-symbiotic species (<em>Trigoniocardia granifera</em>) under different light conditions to detect potential molecular pathways involved in mollusk photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared to those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologs in <em>T. granifera</em> transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as mollusks and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in driving host-symbiont adaptations in diverse organisms.</p>
FIGURE 1 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)
FIGURE 1 (Continued)
HRRR Convective Objects for "Comparing Distributions of Overshooting Convection in HRRR Forecasts to Observations"
<p>Data files for all convective objects identified from High-Resolution Rapid Refresh (HRRR) model forecasts for the Contiguous United States initialized at 06 UTC every day of May and July 2021. Convection was defined in the following two ways, one corresponding to each file uploaded here:</p> <ul> <li>Meeting the criteria for convection defined by the Storm Labelling in Three-Dimensions (SL3D; Starzec et al. 2017) algorithm</li> <li>Satisfying two vertical velocity thresholds (2 m/s at 4 km altitude and 5 m/s at 8 km altitude)</li> </ul>
Lower baseline immunity in invasive Egyptian Goose compared to sympatric native waterfowls
<p>Successful invasive species out-compete native species for vital resources. To increase their spreading success, invasive species need to trade off nutritional and metabolic resources allocated to reproduction and range expansion with other costly body functions. One proposed mechanism for the reallocation of resources is a trade-off with the immune function. According to the evolution of the increased competitive ability hypothesis, a reduced investment in immunity would be favoured by parasite loss in colonised habitats. It is also suggested that invaders would reallocate resources among different immune effectors depending on the new pathogens they encounter in the new habitat. Reallocation of resources may also involve the regulation of oxidative status given its fundamental link with the immune system. Relying on a panel of blood-based markers of immune function and oxidative status quantified in an invasive species (Egyptian Goose) and two native competing species (Mallard and Mute Swan) in Germany, we tested the hypothesis that the invasive species would have a lower investment in immune function compared to the native species. We predicted lower levels of baseline immune markers associated with systemic inflammatory response, and higher levels of certain low-cost immunological effectors (e.g. humoral effectors) in the invasive species compared to the two native species. If Egyptian Geese reduced their investment in immune function, we would also expect that geese generated less oxidative damage and had a lower expression of antioxidant defences than native species. We found lower levels of several immune markers associated either with inflammatory response or humoral innate and adaptive immunity in the invasive species compared to the two native species. The bacteria-killing ability of plasma was the only immune marker that was upregulated in Egyptian Geese. Markers of oxidative status were higher in Mallards compared to the other species. The results of our study point to an overall reduced investment in immune function in the invasive species as a possible energy-saving immunological strategy due to the loss of parasites in the newly colonised habitats, as observed in a previous study. Thus, a lower investment in immune function may benefit other energy-demanding activities, such as reproduction, dispersal, and territoriality.</p>
Parameterized Task Graph Scheduling Algorithm for Comparing Algorithmic Components - All Figures and Datasets
<p>Figures and Datasets for "Parameterized Task Graph Scheduling Algorithm for Comparing Algorithmic Components"</p> <ul> <li>dataset.zip: All datasets evaluated</li> <li>figures.zip: All plots (1080) for all results for our paper</li> </ul>
Evaluation of comparative Efficacy of two routes of administration of Carathmus Tinctorius (Medicated Enema and Nasal Administration) as an Adjuvant Therapy with Standard Care With Physiotherapy in the Rehabilitation of Thrombolytic Stroke (Pakshaghat): A Randomized Controlled Trial Protocol
Open the record for dataset details and reuse information.
Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities
<p><span>Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (<em>Cuon alpinus</em>), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density). We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale. Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors including individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.</span></p>
Evaluation of comparative efficacy of Trayodashang Guggul versus Asitaka Churna Vati in the management of Katigraha (Stiffness in Lumbar Region): A randomized controlled trial protocol
Open the record for dataset details and reuse information.
Analyse comparative du positionnement de HEPIA vis-à-vis des autres HES du domaine Ingénierie et Architecture concernant la gestion des publications scientifiques en accès ouvert
<p>The dataset includes a series of Excel files containing data relevant for a Master project " <span>Analyse comparative du positionnement de HEPIA vis-à-vis des autres HES du domaine Ingénierie et Architecture concernant la gestion des publications scientifiques en accès ouvert</span>" carried out by Valentina Caracuta at the Haute Ecole de Gestion (HEG) de Géneve a.a. 2022-2024 under the supervion of Patrick Ruch and Emilie Pasche. </p> <p>The data in this dataset allows for a comparison of the practices and strategies of different universities of applied sciences (HES) in the field of engineering and architecture, especially with regard to open access to scientific publications. </p> <p>It includes the following informations: </p> <p>List of scientific publications: Detailed data on the publications issued by the different institutions, including type of publication, year, co-authors and academic or industrial partnerships.</p> <p>Open access data: Information specific to open access publications, such as the journals and platforms used, the type of access (green, gold, etc.), and the access policy of each institution.</p> <p>Comparative publication strategies: Analysis of the strategies adopted different HES in terms of managing open access publications, including possible institutional guidelines, incentives to publish in open access, and logistical support.</p> <p>Performance and visibility indicators: Data on the visibility of publications (citations, impact of journals) and the share of articles in open access in each institution.</p>
Plasticizer Content by TGA datasets - Comparative TGA curves for samples before and after SE.
<p>Datasets obtained for the Plasticizer Content by TGA analysis, from the paper "An Integrated Characterization Strategy on Board for Recycling of poly(vinyl butyral) (PVB) from Laminated Glass Wastes"</p>
Optimal IoT Sensor Deployment in the WUI: A Comparative Analysis of Strategies
<p>Included here are individual burn maps used for evaluating algorithm results in the paper: Optimal IoT Sensor Deployment in the WUI: A Comparative Analysis of Strategies. This paper was accepted for presentation at IEEE HONET 2024, the 21st IEEE International Conference on Smart Communities. (For financial/travel reasons the paper has since been withdrawn)</p> <p>Also included are maps of fuel load and elevation (geotifs) and the daily weather (in .csv format) for the region of interest used in the burn probability simulator Burn-P3+ to generate the individual burn maps.</p> <p>This paper investigates optimized IoT sensor deployment strategies within the Wildland-Urban Interface (WUI), a key component of smart communities. It presents a comparative analysis of a novel dynamic grid approach against traditional random and greedy algorithms. By employing the Burn-P3+ simulator, detailed burn probability maps are generated for two Canadian geographically distinct areas: the Halifax Regional Municipality and Kelowna. Our analysis reveals that the dynamic grid method significantly enhances fire detection capabilities by strategically distributing IoT sensors in alignment with calculated burn probability. This approach shows a marked improvement of as much as 35% in burn detection over traditional deployment methods. The paper highlights the advantages of structured IoT sensor placement in supporting smart communities, offering more efficient and effective wildfire management strategies in the WUI through real-time data available to both fire mitigation teams and AI.</p> <p>Partial code for the sensor deployment algorithms discussed in the above mentioned paper is <a href="https://github.com/richardjpurcell/sensor-deployment-algorithms">available on GitHub</a>.</p>
Thesis data: Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels
<p>Starting dataset used within the thesis; Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels.</p> <p>Results of manual annotation of and extract of nonPatchTaggedCommitLinks within the NVD CVE dataset.</p>
Challenges in adjusting scoring matrices when comparing functional motifs with non-standard compositions
<p>This research was funded by the National Science Centre in Poland (grant number 2021/41/N/ST6/01919)</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.