Find research datasets worth reusing

Data for: Temperate and tropical lizards are vulnerable to climate warming due to increased water loss and heat stress

Climate warming has imposed profound impacts on species globally. Understanding the vulnerabilities of species from different latitudinal regions to warming climates is critical for biological conservation. Using five species of Takydromus lizards as a study system, we quantified physiological and life-history responses and geography range change across latitudes under climate warming. Using integrated biophysical models and hybrid species distribution models, we found: (1) thermal safety margin is larger at high latitudes, and is predicted to decrease under climate warming for lizards at all latitudes; (2) climate warming will speed up embryonic development and increase annual activity time of adult lizards, but will exacerbate water loss of adults across all latitudes; and (3) species across latitudes are predicted to experience habitat contraction under climate warming due to different limitations: tropical and subtropical species are vulnerable due to increased extremely high temperatures, whereas temperate species are vulnerable due to both extremely high temperatures and increased water loss. This study provides a comprehensive understanding of the vulnerability of species from different latitudinal regions to climate warming in ectotherms and also highlights the importance of integrating environmental factors, behavior, physiology, and life-history responses in predicting the risk of species to climate warming.

VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability

Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.

opencc-by-4.0Nov 2022View details →

List Vulnerable Code Snippets

This database contains a list of pointers to freely available online sources containing vulnerable (non-compliant) code snippets and also non-vulnerable (compliant) code snippets for different programming languages. These code snippets can be used to train machine learning algorithms, as discussed in our publication in CYBER22 entitled "How Good is Openly Available Code Snippets Containing Software Vulnerabilities to Train Machine Learning Algorithms?". Due to potential copyright issues, the snippets are not included in the database. However, using the links provided, these can be easily obtained.

opencc-by-4.0Sep 2022View details →

Amplicon structure creates collateral therapeutic vulnerability in cancer

Raw RNA sequencing data expressed in KELLY cells with vs. without ectopic DDX1 expression AH_YB_021 DDX1, AH_YB_023 DDX1, AH_YB_025 DDX1, : DDX1 - AH_YB_022 DDX1, AH_YB_024 DDX1, AH_YB_026 DDX1, : DDX1 +

Data for: Social-ecological vulnerability of fishing communities to climate change: a U.S. West Coast case study

Climate change is already impacting coastal communities, and ongoing and future shifts in fisheries species productivity from climate change have implications for the livelihoods and cultures of coastal communities. Harvested marine species in the California Current Large Marine Ecosystem support U.S. West Coast communities economically, socially, and culturally. Ecological vulnerability assessments exist for individual species in the California Current but ecological and human vulnerability are linked and vulnerability is expected to vary by community. Here, we present automatable, reproducible methods for assessing the vulnerability of U.S. West Coast fishing-dependent communities to climate change within a social-ecological vulnerability framework. We first assessed the ecological risk of marine resources, on which fishing communities rely, to 50 years of climate change projections. We then combined this with the adaptive capacity of fishing communities, based on social indicators, to assess the potential ability of communities to cope with future changes. Specific communities (particularly in Washington state) were determined to be at risk to climate change mainly due to economic reliance on at risk marine fisheries species, like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these communities were often not found to be the most vulnerable overall. Conversely, certain communities that were not the most at risk, ecologically and economically, ranked in the category of highly vulnerable communities due to low adaptive capacity based on social indicators (particularly in Southern California). Certain communities were both ecologically at risk due to catch composition and socially vulnerable (low adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, ecological, economic, and societal data reveals that factors underlying vulnerability are variable across fishing communities on the U.S West Coast, and suggests the need to develop a variety of well-aligned strategies to adapt to the ecological impacts of climate change.

Data from: Hindcast-validated species distribution models reveal future vulnerabilities of mangroves and salt marsh species

Rapid climate change threatens biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species distribution modeling can project the potential future distributions of species under scenarios of climate change using bioclimatic data and georeferenced occurrence data. However, models projecting suitable habitat into the future are impossible to ground truth. One solution is to develop species distribution models for the present and project them to periods in the recent past where distributions are known to test model performance before making projections into the future. Here, we develop models using abiotic environmental variables to quantify the current suitable habitat available to eight Neotropical coastal species: four mangrove species and four salt marsh species. Using a novel model validation approach that leverages newly available monthly climatic data from 1960-2018, we project these niche models into two time periods in the recent past (i.e., within the past half-century) when either mangrove or salt marsh dominance was documented via other data sources. Models were hindcast-validated and then used to project the suitable habitat of all species at four time periods in the future under a model of climate change. For all future time periods, the projected suitable habitat of mangrove species decreased, and suitable habitat declined more severely in salt marsh species.

opencc-by-4.0Nov 2017View details →

Refuges_and_predator_overfishing_vulnerability

Model code and data to accompany paper: High refuge availability on coral reefs increases the vulnerability of reef-associated predators to overexploitation

opencc-by-4.0Apr 2024View details →

Exploring the Vulnerability of the Greenland Ice Sheet

Uncover the challenges of understanding Greenland’s massive ice sheet and its potential impact on sea-level rise. With unique features like surface melting and a sponge-like firn layer, the Greenland Ice Sheet holds global and local significance, contributing about 1/3rd of the total land-ice contribution to sea-level rise. The video stresses the importance of collaborative research for a better understanding of our planet’s future.

opencc-by-4.0May 2024View details →

Outliers and Missing Gait_Human, IDS, JavaScript vulnerability Datasets

Human Gait Dataset (CASIA-A) [1] is available at: http://www.cbsr.ia.ac.cn/english/Gait\%20Databases.asp, JavaScript vulnerability dataset is publicly available at [2] and KDD CUP 99 dataset is publicly available at [3].     [1] Wang L, Tan T, Ning H, Hu W. Silhouette analysis-based gait recognition for human identification. IEEE transactions on pattern analysis and machine intelligence. 2003;25(12):1505–1518 [2] Ferenc R, Heged ̋us P, Gyimesi P, Antal G, B ́an D, Gyim ́othy T. Challenging machine learning algorithms in predicting vulnerable javascript functions. In: 2019 IEEE/ACM 7th International Workshop on Realizing Artificial Intelligence Synergies in Software Engineering (RAISE). IEEE; 2019. p. 8–14. [3] Tavallaee M, Bagheri E, Lu W, Ghorbani AA. A detailed analysis of the KDD CUP 99 data set. In: 2009 IEEE symposium on computational intelligence for security and defense applications. Ieee; 2009. p. 1–6.

opencc-by-4.0May 2024View details →

Unveil the Mystery of Critical Software Vulnerabilities - Dataset

This repository contains the dataset and the scripts used to collect the dataset in our paper   Unveil the Mystery of Critical Software Vulnerabilities Shengyi Pan, Lingfeng Bao, Jiayuan Zhou, Xing Hu, Xin Xia, Shanping Li FSE 2024 (industry)   We provide a README.md that explains the usage of each file and the dataset format.

opencc-zeroJun 2024View details →

Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models

Ecological niche models (ENMs) are a powerful tool in ecological research and conservation planning. Since ENMs provide probability maps of suitable areas under environmental change, they may assist in designing conservation actions and addressing conservation priorities. However, ENMs are usually implemented by learning the species climatic preferences from their current geographic distribution, which leaves them vulnerable to the issue of niche truncation issues, as if comes with non-climatic limits to the current species distribution posed by e.g. anthropic activities and settlements, and is bound to assume that species are at equilibrium with their environments. These problems might be alleviated by the inclusion of fossil occurrences, which refer to moments during species evolution when such limits were absent, and a larger fraction of the species fundamental niche was probably explored. Here, we combined current and fossil occurrence data for 38 medium-large mammal species of conservation concern to assess the influence of the fossil record on ENM predictions under future climate change scenarios. We found that ignoring or including fossil data yields consistent trends in terms of predicted range increase/decrease. Yet, although adding fossil data invariably results in increased niche width, estimates of range change magnitude improved for just one half only of the species. These results suggest that most species might be in non-equilibrium with their environment, and that the inclusion of fossil data may be crucial to the better understanding of species climatic requirements, hence for designing effective conservation strategies.

opencc-by-4.0Jun 2024View details →

Climate change vulnerability of Arctic char across Scandinavia

Data and code for the paper "Climate change vulnerability of Arctic char across Scandinavia" by Muhlfeld et al. (2024) accepted in the journal Global Change Biology. This an extensive fish community and environmental dataset for 1,762 lakes sampled across Scandinavia (mid-1990s) that were used to model the climate vulnerability of Arctic char (Salvelinus alpinus) under baseline (1990s) and future climate warming scenarios (2050s and 2080s).

opencc-by-4.0Jun 2024View details →

Supplementary material of article Mining disaster in Brumadinho (Brazil): social vulnerability from the perspective of the fisherman community

Open the record for dataset details and reuse information.

opencc-by-4.0Jun 2024View details →

Current state of vulnerability handling from the perspective of software operators and developers: semi-structured interviews

This archive contains the transcripts of semi-structured interviews, conducted as part of the study "Leveraging Fine-grained Telemetry Data for the Detection and Prevention of Vulnerability Exploits" by Konrad Ponichtera and Sebastian Proksch. The goal of the interviews was to collect insights about the current state of vulnerability handling in the software engineering industry and identify improvement possibilities from the perspective of the system operator. The interviews have been conducted with ten software engineers with system administration/operation backgrounds, meaning that either they perform system administration/operation as part of their responsibilities, or used to do so in the past. Each participant has been assigned an identifier from P1 to P10. Their roles and industry experience have been disclosed in the attached CSV file with the questionnaire responses. <h1>Interview structure</h1> The interviews were conducted online, and transcribed to the text file, which was then reviewed and pseudonymized. Each interview took approximately one hour. During each interview, the participants were asked to look into a problem of system vulnerabilities from the perspective of a system operator, who can configure and monitor the infrastructure, as well as deploy the applications. The participants were also informed that the operator cannot modify the applications' source code and artifacts. Then the participants were asked seven open questions about the status quo of vulnerability handling in software engineering and its three aspects of awareness, impact, and mitigation. The interviewees responded in accordance with their knowledge and experience. Afterwards, the researcher guiding the session introduced the proposed system to the interviewees, by describing its goal and functionality. To avoid the moderator acceptance bias, we explained that the system was designed within the Software Engineering Research Group of Delft University of Technology. The mitigation of social desirability bias has been achieved by describing the actions taken by an imaginary operator named Albert. After going through the wireframes of the operator's dashboard interface and describing the content of each screen, the participants were asked to follow a supervised walkthrough, where they played the role of an operator. They were presented with a hypothetical situation, where a critical vulnerability, similar to the <a href="https://cve.mitre.org/cgi-bin/cvename.cgi?name=cve-2021-44228" target="_blank" rel="noopener">Log4Shell</a> appears on the dashboard. During this part, the guiding researcher was streaming the window of a wireframe editor. The interviewees were then asked to follow a think-aloud protocol, and indicate their actions as they "use" the system. Meanwhile, the researcher made changes to the wireframes to simulate the effect of the participants' actions. After the walkthrough, participants filled out a System Usability Scale (SUS) questionnaire and were asked additional questions about the impact the proposed system would have on their vulnerability awareness, impact analysis, and mitigation capability. <h1>Files</h1> The archive contains three types of artifacts from the interview: pseudonymized transcripts, the questionnaire and the wireframes. <h2>Transcripts</h2> The transcripts directory contains ten text files with pseudonymized interview transcripts. In each file, the parts spoken by the interviewing researcher have been prepended with "R:", while the parts spoken by the interviewee have been prepended by the interviewee's identifier. <h2>Questionnaire</h2> The CSV file contains the answers participants gave at the start of the interview.  Each participant was asked to provide their current job title and how many years they worked in the software engineering industry. They were also asked to specify which DevOps tools and technologies they used, and what system operator tasks they had a chance to do during their career. The goal of these questions was to estabilsh the interviewee's system operation background. Finally, after the prototype walkthrough, participants filled out SUS questionnaires, the results of which are included in the PDF. <h2>Wireframes</h2> The wireframes directory contains diagrams in DrawIO format (also exported to PDF), used during the interview. The vision GUI wireframes were used to introduce participants to what the envisioned system would look like. The walkthrough wireframes were used during the semi-supervised walkthrough scenario, where the interviewing researcher modified them following the participants' actions.

opencc-by-4.0Dec 2010View details →

Fig. 2 in Medicago Falcata L. In Estonia: Chromosomal And Morphologicalvariability, Distribution And Vulnerability Oftaxa

Fig. 2. Dendrogram of M. falcata (Ward's algorithm), measured characters

opencc-zeroJul 2024View details →

Data from: Evaluating the vulnerability of Tetracentron sinense habitats to climate-induced latitudinal shifts

Objective: Exploring the changing process of the geographical distribution pattern of Tetracentron sinense Oliv. and its main influencing factors since the last interglacial period can provide a scientific basis for the effective protection and management of the species. Methods: The MaxEnt model was used to construct the potential distribution areas of T. sinense in different periods such as the last interglacial (LIG), the last glacial maximum (LGM), the Mid-Holocene (MID), the current and future (2050s, 2070s). On the premise of discussing the influence of dominant environmental factors on its distribution model, the suitable area changes of T. sinense under different ecological climate situations were quantitatively analyzed. Results: (1) The AUC and TSS values predicted by the optimized model were 0.959 and 0.835, respectively, indicating a good predictive effect by the MaxEnt model; the potential suitable areas for T. sinense in the current period are mainly located in southwest China, which are wider compared to the actual habitats. (2) Jackknife testing showed that the lowest temperature in the coldest month (Bio6), elevation (Elev), seasonal variation coefficient of temperature (Bio4) and surface calcium carbonate content (T-CACO3) are the dominant environmental factors affecting the distribution of T. sinense. (3) From the last interglacial period to the current period, the total suitable area of T. sinense showed a decreasing trend; the distribution points of T. sinense populations in Mid-Holocene period may be the origin of the postglacial population, and Southwest China may be its glacial biological refuge. (4) Compared with the current period, the total suitable area ranges of T. sinense in China in the 2050s and 2070s decreased, and the centroid location of its total fitness area all migrated to the northwest, with the largest migration distance in 2070s under the SSPs 7.0 climate scenario. Conclusion: Temperature was the principal factor influencing the geographical distribution of T. sinense. With the global warming, the range of T. sinense suitable areas will show a shrinking trend, with a shift towards higher-latitude regions. Ex-situ conservation measures could be taken to preserve its germplasm resources.

opencc-zeroJul 2024View details →

Data from: Quantifying coextinctions and ecosystem service vulnerability in coastal ecosystems experiencing climate warming

Climate change is negatively impacting ecosystems and their contributions to human well-being, known as ecosystem services. Previous research has mainly focused on the direct effects of climate change on species and ecosystem services, leaving a gap in understanding the indirect impacts resulting from changes in species interactions within complex ecosystems. This knowledge gap is significant because the loss of a species in a food web can lead to additional species losses or "co-extinctions," particularly when the species most impacted by climate change are also the species that play critical roles in food web persistence or provide ecosystem services. Here, we present a framework to investigate the relationships among species vulnerability to climate change, their roles within the food web, their contributions to ecosystem services, and the overall persistence of these systems and services in the face of climate-induced species losses. To do this, we assess the robustness of food webs and their associated ecosystem services to climate-driven species extinctions in eight empirical rocky intertidal food webs. Across food webs, we find that highly connected species are not the most vulnerable to climate change. However, we find species that directly provide ecosystem services are more vulnerable to climate change and more connected than species that do not directly provide services, which results in ecosystem service provision collapsing before food webs. Overall, we find that food webs are more robust to climate change than the ecosystem services they provide and show that combining species roles in food webs and services with their vulnerability to climate change offer predictions about the impacts of coextinctions for future food web and ecosystem service persistence. However, these conclusions are limited by data availability and quality, underscoring the need for more comprehensive data collection on linking species roles in interaction networks and their vulnerabilities to climate change.

opencc-by-nc-4.0Mar 2018View details →

Replication Package for "On the impact of security vulnerabilities in the npm package dependency network

This is the replication package for paper "On the impact of security vulnerabilities in the npm package dependency network" accepted for publication in MSR 2018.

opencc-by-4.0Jun 2019View details →

A taxonomy for improving industry-academia communication in IoT vulnerability management. Additional Material

Research interview and Workshop Protocol from the paper "A taxonomy for improving industry-academia communication in IoT vulnerability management".