Find research datasets worth reusing

Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches (Replication Package Part 3: OpenSSL dataset)

<h1>The Replication Package of</h1> <h1>"Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches"</h1> <h3>Part 3 (OPENSSL Dataset)</h3> <div> <div>This repository includes:</div> <ol> <li>Code.zip that contains the codes to replicate some parts of this study: a. 1_generate_datasets implements our methodology to generate the datasets. b. 2_run_models runs the ML models during the evaluation. c. 3_result_replication generates charts presented in the paper from the ML evaluation results.</li> <li>Datasets.zip that contain 2 folders: a. original datasets: 1 from <a href="https://github.com/CGCL-codes/VulDeePecker" target="_blank" rel="noopener">NVD Vuldeepecker</a> and 3 extracted from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a>. <div> <div>b. OPENSSL datasets: train, validation, test sets for each time of observation extracted using our methodology from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a> dataset for project openssl.</div> </div> </li> <li>Pretrained-models.zip that we generated during our evaluation (3 test results for each time point in the timeline [2013-2019]).</li> <li>Results.zip of our evaluation, the folder ALL contains the overall results and other folders are results by model.</li> </ol> UPDATED version 5 - added a GLOBAL_README.md which contains the 3 stages and how they are connected to each other - updated LineVul.ipynb: import AdamW from torch.optim instead of transformers - updated README.md in Code2Vec with the prerequisites of Java to run gradlew for astmine UPDATED version 6 - updated CodeBert.ipynb: import AdamW from torch.optim instead of transformers Documentations <ol> <li>INSTALL.pdf : how to install the codes</li> <li>README.pdf: readme file</li> <li>REQUIREMENTS.pdf: hardware and software requirements</li> <li>STATUS.pdf : status for artifact submission</li> <li>LICENSE.pdf: the license of this artifact</li> <li>PAPER.pdf: the camera-ready version of the paper</li> </ol> </div> <div> <div>Please refer to the following repositories for the other datasets and pre-trained models:</div> <div>- Part 1 NVD Vuldeeepecker : <a href="https://doi.org/10.5281/zenodo.8207883" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.8207883</a></div> - Part 2 LINUX : <a href="https://doi.org/10.5281/zenodo.10960662" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10960662</a> <div>- Part 4 POPPLER : <a href="https://doi.org/10.5281/zenodo.14713143">https://doi.org/10.5281/zenodo.14713143</a></div> <div> </div> <div>This work was partly funded by the EU under the H2020 Program AssureMOSS (Grant n. 952647) and the Horizon Europe Program Sec4AI4Sec (Grant n. 101120393), by the Italian Ministry of University and Research (MUR) under the P.N.R.R. – NextGenerationEU grant n.\ PE00000014 (SERICS subproject COVERT), and by the Dutch Research Council (NWO) under the grant NWA.1215.18.006 (Theseus) and grant KIC1.VE01.20.004 (HEWSTI). </div> </div>

opencc-by-4.0Jan 2023View details →

Comparison of blood parameters for brachycephalic and non-brachycephalic dogs

Cranial and upper-airway anatomy of short-nosed flat-faced brachycephalic dogs predisposes brachycephalic obstructive airway syndrome (BOAS). Periodic apnoea, increased inspiratory resistance and inability to thermoregulate effectively are characteristic for BOAS, but internationally accepted objective markers of BOAS severity are missing. The objective of this study was to compare the blood parameters between non-brachycephalic (NC) and brachycephalic (BC) dogs exploring the possibility to develop a blood test for BOAS. We evaluated blood biochemistry, complete blood cell counts, red blood cell (RBC) indices, reticulocyte counts, a blood-born marker of intermittent hypoxia (glutathione, NO production), RBC hydration, deformability, and blood markers of metabolic changes and stress between BC (n = 18) and NC (meso- and dolichocephalic, n = 22) dogs.  Reticulocyte counts and the abundance of middle-fluorescence immature reticulocytes were significantly higher in BC dogs compared to NC dogs. BC dogs had significantly more NO-derived NO2-/NO3- in plasma than NC dogs. RBCs of BC dogs were shedding significantly more membrane as follows from the intensity of Eosin maleimide staining and had significantly higher mean corpuscular hemoglobin concentration than NC dogs. Intracellular reduced glutathione content in RBCs of BC dogs was significantly lower, while plasma lactate was significantly higher in BC dogs compared to NC dogs. Plasma cholesterol and triglyceride were significantly lower and cortisol was significantly higher in BC dogs compared to NC dogs. Eosinophil counts were significantly lower and the neutrophil-to-lymphocyte ratio was significantly higher in BC dogs compared to NC dogs. Taken together, our findings suggest that brachycephalic phenotype in dogs is associated with stress at the level of blood cells and systemically, with oxidation and emotional stress. The parameters identified within this study should be further investigated for their potential as objective indicators for BOAS.

opencc-by-4.0Mar 2023View details →

SARS-CoV-2 Infection and Clinical Signs in Cats and Dogs from Confirmed Positive Households in Germany

Supplemental material and raw data referring to specified publication

Dog Health Vitals Dataset

The Dog Health Vitals Dataset is a collection of recordings and vital statistics related to the health of dogs. It includes data captured during various recording sessions, providing insights into the physiological characteristics of the dogs.

Data for ms. Do people really care less about their cats than about their dogs? A comparative study in three European countries

The present dataset is based on a questionnaire which is also part of this package. The enclose questionnaire includes  identifiable and relevant variables names (yellow highlighted). Participants were recruited by Norstat, a European-based survey company, with the aim of gaining a representative sample of Austrian, Danish and UK citizens, including pet owners. The survey company administers and hosts online panels comprising citizens from many European countries. We aimed for a sample that is representative in terms of age, gender, and region. Therefore, a stratified sampling principle was set up where individuals within each stratum were randomly invited to participate. The invitations were issued through e-mail that contained a link to the online questionnaire. Data was collected from 11-25th of March 2022 in Austria, from 11-24th of March 2022 in Denmark and from 8-23rd of March 2022 in the UK. The invitation provided information about the background of the study, the participating universities, ethical approval, estimated time for questionnaire completion and further, participants were informed that the completion of the questionnaire was voluntary and anonymous, and that they could exit the survey at any point. Before participants were directed to the survey, they ensured informed consent by confirming that they are over 17 years old, and consent to participate in this survey.  Besides the questionnaire the dataset includes a csv and an Excel file consisting of the data that is used in the ms. and an rtf and a pdf file with data variable names/labels, and value labels.

openOpenJan 2020View details →

edi44/100

Gunnison's Prairie Dog Restoration Experiment (GPDREx): Population Dynamics within Grasslands at the Sevilleta National Widlife Refuge, New Mexico

Prairie dogs (Cynomys spp.) are burrowing rodents considered to be ecosystem engineers and keystone species of the central grasslands of North America. Yet, prairie dog populations have declined by an estimated 98% throughout their historic range. This dramatic decline has resulted in the widespread loss of their important ecological role throughout this grassland system. The 92,060 ha Sevilleta NWR in central New Mexico includes more than 54,000 ha of native grassland. Gunnison’s prairie dogs (C. gunnisoni) were reported to occupy ~15,000 ha of what is now the SNWR during the 1960’s, prior to their systematic eradication. In 2010, we collaborated with local agencies and conservation organizations to restore the functional role of prairie dogs to the grassland system. Gunnison’s prairie dogs were reintroduced to a site that was occupied by prairie dogs 40 years ago. This work is part of a larger, long-term study where we are studying the ecological effects of prairie dogs as they re-colonize the grassland ecosystem.

opencc-zeroJul 2020View details →

FIG. 2 in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs

FIG. 2. — Tarsal bones of Cynodictis lacustris from Aubrelong (France; Rupelian, MP21): A-E, MNHN.F.Au994, left astragalus (reversed views); A, dorsal view; B, ventral view; C, lateral view; D, distal view; E, proximal view; F-J, MNHN.F.Au2044, right calcaneus; F, dorsal view; G, lateral view; H, medial view; I, distal view; J, proximal view. Abbreviations: cf, cuboid facet; ef, ectal facet; f, foramen; ff, fibular facet; h, head; ll, lateral lip; lp, lateral process; lpt, lateral process of tuber; ml, medial lip; mpt, medial process of tuber; n, neck; ppt, proximal plantar tuberosity; plt, plantar tubercle; pp, peroneal process; ptg, plantar tendon groove; sf, sustentacular facet; sg, sagittal groove; sit, sinus of the tarsus; st, sustentaculum tali; tc, tuber calcanei; tr, trochlea. Scale bar: 1 cm.

opencc-zeroJul 2020View details →

APPENDIX 1 in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs

APPENDIX 1. — Measurements, in mm, of astragali used for the estimation of body mass. For each morphotype, only the values of the smallest and biggest specimens are provided.

opencc-zeroJul 2020View details →

FIG. 4 in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs

FIG. 4. — Calcanei of undetermined amphicyonids from the Quercy (France; Priabonian-Chattian, MP18-MP30): A-E, Morphotype A, MNHN.F.Qu9845, left calcaneus (reversed views): A, dorsal view; B, lateral view; C, medial view; D, distal view; E, proximal view; F-J, Morphotype B, KUL.PLV1542_28, left calcaneus (reversed views); F, dorsal view; G, lateral view; H, medial view; I, distal view; J, proximal view; K-O, Morphotype C, KUL.PLV1542_29, left calcaneus (reversed views): K, dorsal view; L, lateral view; M, medial view; N, distal view; O, proximal view. Abbreviations: cf, cuboid facet; ef, ectal facet; lpt, lateral process of tuber; mpt, medial process of tuber; pp, peroneal process; plt, plantar tubercle; ptg, tendinous plantar groove; sg, sagittal groove; sf, sustentacular facet; st, sustentaculum tali; tc, tuber calcanei. Scale bar: 1 cm.

dryad40/100

Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture

Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10-25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P=6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P=8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.

opencc-zeroDec 2020View details →

dryad40/100

An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion

<ol> <li>Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitive subordinates like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. </li> <li>Wild dogs in Zambia's Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors, due to spatial variation in illegal offtake.</li> <li>We used long-term data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity, and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated.</li> <li>The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, Kobus vardonii, and impala, Aepyceros melampus), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density, and intermediate in the two regions with intermediate prey density. The population growth rate (λ) was positive for the population as a whole, strongly positive in the region with the highest prey density, and strongly negative in the region with the lowest prey density.</li> <li>It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.</li> </ol>

opencc-zeroJan 2024View details →

Fig. 1 in Description Of The Nematode Dirofilaria Repens (Nematoda, Onchocercidae) Parasitic In Dogs In Ukraine

Fig. 1. Head end of DiroFIlaria repens: a — mouth opening (Mo), cuticular layer (Cl); head papillae (Hp); b — esophagus (Es).

Fig. 2 in Description Of The Nematode Dirofilaria Repens (Nematoda, Onchocercidae) Parasitic In Dogs In Ukraine

Fig. 2. Tail end of Ơ DiroFIlaria repens: a — lateral alae (Wl), longer spicule (Sl), c — shorter spicule (Ssh); b — proximal end of the spicule (Sp), distal end of the spicule (Sd), wide part (Pw), narrow part (Pn), triangular widening (Wt); c — caudal papillae.

Fig. 3 in Prairie dog responses to vector control and vaccination during an initial Yersinia pestis invasion

Fig. 3. Predicted re-encounter rates (95% confidence intervals [CIs]) over a single trapping interval (2007–2008) for adult female and male black-tailed prairie dogs inoculated at Conata Basin, South Dakota in 2007 with F1–V fusion protein vaccine or placebo on the no dust and dusted plots (the latter with flea control). Sample sizes are depicted above the 95% CIs.

Fig. 1 in Prairie dog responses to vector control and vaccination during an initial Yersinia pestis invasion

Fig. 1. Categories of flea vector control (deltamethrin dust) and F1–V fusion protein plague vaccination (V = vaccine, P = placebo, N = no inoculation) used for analyses of black-tailed prairie dog annual re-encounter rates (2007–2008 and 2008–2009) at Conata Basin, South Dakota. Annual re-encounter rates were compared for subsets of animals, here each enclosed by unique rectangles. Sample sizes are depicted in subsequent figures with results from multivariate analyses.

Fig. 5 in Prairie dog responses to vector control and vaccination during an initial Yersinia pestis invasion

Fig. 5. Predicted re-encounter rates (95% confidence intervals [CIs]) over a single trapping interval 2007–2008 for non-inoculated adult and juvenile blacktailed prairie dogs on the no dust and dusted plots (the latter with flea control) at Conata Basin, South Dakota. Sample sizes are depicted above the 95% CIs.