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3,947 results for “Requirements”
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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>
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation
<p>This includes</p> <p>1- the data set collected at 100mW = 0.04 kW/cm^2 for the Cy3-Cy5 dye pair that is reported in the paper in Figure 2c and SI Figure 14ab (Supplementary Additional Data 1)</p> <p>2- Matlab script (zetacorrect.m) to do the simplified zeta correction and a Mathematica notebook (TestingSimplifiedZeta.nb) to show the derivation of simplified zeta correction</p> <p>3- the raw data corresponding to Figure 2c (Supplementary Additional Data 2)</p> <p>4- Main Text and Supplementary Figures Source Data</p> <p>----<br>## Citations</p> <p>If you use any of these shared materials, please use the relevant citatations:</p> <p> ```<br> * Avik K. Pati^{*}, Zeliha Kilic^{*}, Maxwell I. Martin^{#}, Daniel S. Terry^{#}, Alessandro Borgia, Sukanta Bar,<br> Steffen Jockusch, Roman Kiselev, Roger B. Altman, Scott C. Blanchard,<br> Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation,2024,Nature Methods<br> ```</p> <p>----<br>## Relevant Publications</p> <p>In our smFRET data analysis, we used SPARTAN<br>* Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond scale:<br> [paper](https://www.nature.com/articles/nmeth.3769)</p>
Model Generation from Requirements with LLMs: an Exploratory Study - Replication Package
<p>This is a replication package for the paper "<span>Model Generation from Requirements </span><span>with LLMs: an Exploratory Study</span>", by Sallam Abualhaija, Chetan Arora, and Alessio Ferrari.</p> <p><strong>Abstract: </strong>Complementing natural language (NL) requirements with graphical models can improve stakeholders’ communication and provide directions for system design. However, creating models from requirements involves manual effort. The advent of generative large language models (LLMs), ChatGPT being a notable example, offers promising avenues for automated assistance in model generation. This paper investigates the reliability of ChatGPT in generating sequence diagrams from NL requirements. Specifically, we conduct a qualitative study examining the sequence diagrams generated by ChatGPT for 28 requirements documents of various types and from different domains. Our study aims to uncover potential issues that emerge in the models generated by ChatGPT, thereby hindering its applicability in practice. Observations have systematically been captured through evaluation logs, and categorized through thematic analysis. Our results indicate that, although the models generally conform to the standard and exhibit a reasonable level of understandability, their correctness with respect to the specified requirements often presents challenges. This issue is particularly pronounced in the presence of requirements smells, such as ambiguity and inconsistency. The insights derived from this study can influence the practical utilization of LLMs in the RE process, and open the door to novel RE-specific prompting strategies targeting effective model generation.</p> <p>The replication package consists of the following folders:</p> <p><strong>logs:</strong> includes the evaluation logs produced by each evaluator</p> <p><strong>original-documents: </strong>includes the original requirements documents used for the evaluation</p> <p><strong>RQ1 - quantitative analysis:</strong> includes the analysis made on the scores given to each model and model variant. It includes five files:</p> <p>- results.csv: numerical results of the evaluation for each criterion<br>- analysis-results.Rmd: R file used to perform the quantitative analysis (requires R Studio to be executed)<br>- analysis-results.html: html file produced by analysis-results.Rmd<br>- cross-check.csv: file with the cross-checking of the two assessors applied to a subset of the models<br>- symmary_results.xlsx: final output of the quantitative results in terms of Wilcoxon signed rank tests</p> <p><strong>RQ2 - thematic analysis: </strong>includes the codebook produced by the thematic analysis of the issues in generating models with ChatGPT</p>
Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment
<p><strong>When using any of this data, please cite the corresponding manuscript</strong></p> <div> <div> <p><a title="Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.Sci. Adv.10,eadl1710(2024).DOI:10.1126/sciadv.adl1710" href="https://doi.org/10.1126/sciadv.adl1710">Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. Sci. Adv. 10, eadl1710 (2024). DOI:10.1126/sciadv.adl1710</a></p> </div> </div> <p><strong>Original Data</strong></p> <p>The following files contain all count data for the original data of this manuscript:</p> <p>sepsis1_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis1 sequencing<br>sepsis1_velocyto.loom -> velocyto matrices for sepsis1<br>sepsis2_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis2 sequencing<br>sepsis2_velocyto.loom -> velocyto matrices for sepsis2</p> <p>sepsis_seurat.rds -> processed Seurat object containing original data cells. (Upd.: the meta.data-column "cellnames" contains the cell type annotation given in Figure 1B)</p> <p><strong>Original Data Scripts</strong></p> <p>process.R -> main analysis script<br>functions.R -> helper functions for main analysis script<br>enrichmentAnalysis.R -> script running the enrichment analysis<br>process_wgcna.R -> script performing the wgcna analysis<br>velocities_step1.R -> script performing velocity analysis (from seurat to data matrices)<br>velocities_step2.py -> actual velocity analysis<br><br><strong>GSE137539 Re-Analysis</strong></p> <p>gse137539_processed.Rds -> processed seurat object<br>gse137539_process.R -> analysis script</p> <p><strong>Bulk Analysis</strong></p> <p>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-> Raw UMI counts (intronic+exonic from zUMIs) and DE genes<br>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -> Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process</p>
INTELLIMAN_WP2_Application Requirements and Integration_T2.4_Fresh food handling use case analysis, integration and validation_Apple 6D pose estimation dataset_v0
<p>The dataset contains the data generated for the training of the 6D pose estimation neural network<br>DOPE related to the publication:<br>M. Costanzo, M. De Simone, S. Federico, C. Natale and S. Pirozzi, "Enhanced 6D Pose Estimation for<br>Robotic Fruit Picking," 2023 9th International Conference on Control, Decision and Information<br>Technologies (CoDIT), Rome, Italy, 2023, pp. 901-906, doi: 10.1109/CoDIT58514.2023.10284072.</p>
Data required for "Redefining awn development in rice through the breeding history of Japanese awn reduction"
<p>The study challenges the conventional understanding of awn loss as a domestication syndrome, showing instead that many awned varieties continued to be widely grown in Japan until the early twentieth century and that selection for awn reduction was active at that time, demonstrating that awn loss is not a domestication syndrome but “a trait that emerged during crop improvement”. Although selection for awnless mutants was carried out independently using different types of awned cultivars in the early twentieth century in Japan, awn loss was caused by the mutation in <em>OsEPFL1</em>. This suggests that a single mutant haplotype of <em>OsEPFL1</em> was conserved in the genomes of different cultivars and subsequently selected within each line to meet the demand for awnless varieties. The study also conducts phylogenetic analyses of EPFL1 in 48 grass plants, revealing its unique involvement in awn formation in rice while potentially playing a different role in the domestication of other grass plants. Finally, an attempt is made to isolate an awn-forming gene that has not been identified from the awned rice cultivar “Omachi”, which is still cultivated in Japan. The results presented in this paper provide a new perspective on domestication against the conventional understanding of awn development, shedding light on its potential as a useful organ for breeding to mitigate environmental stress.</p>
Data for: Evaluation of Methods for Eliciting and Specifying Usability Requirements using User Stories: A Controlled Experiment
<p>Este projeto contém os materiais utilizados na pesquisa intitulada Evaluation of Methods for Eliciting and Specifying Usability Requirements using User Stories: A Controlled Experiment: TCLE, Formulário de Caracterização, Cenário, Oráculo, User Stories, Protótipo, Storyboards, Avaliação de ferramentas em escala de Likert e Dados coletados do formulário.</p>
SimRE: A Requirements Similarity Tool for Software Product Lines - Dataset
<p>The <strong>RequirementsPairs</strong> file consists of 34 pairs of software requirements related to GIS (Geographic Information Systems), each paired with a corresponding similarity degree. It was introduced in the paper <em>"SimRE: A Requirements Similarity Tool for Software Product Lines."</em></p> <p><strong>GISv1</strong> and <strong>GISv2</strong> refer to version 1 and version 2 of the GIS dataset, respectively. These datasets are composed of 173 requirements that represent the functionality of a web-based GIS product line.</p>
Ethical Requirements in the Age of Artificial Intelligence - Supplementary material
<p><strong>Context:</strong> Software developers and users are growing concerned about the ethical use of software, especially with Artificial Intelligence (AI). In this context, we investigated how ethical requirements can be elicited and incorporated into software development. <strong>Problem</strong>: The challenge is identifying and defining effective methods for eliciting and managing ethical requirements in software development. <strong>Solution</strong>: We conducted a Systematic Literature Review (SLR) to identify techniques, methods, processes, frameworks, and tools for eliciting, analyzing, and specifying ethical requirements. <strong>IS Theory</strong>: We explore the application of theories related to requirements engineering, ethics in technology, and data governance. It focuses, in particular, on ensuring that information systems comply with ethical and legal principles from the beginning of the development cycle. <strong>Method</strong>: Following the Kitchenham and Charters protocol, we conducted an SLR with stages of planning, conducting, and reporting the results. <strong>Summarization of Results</strong>: We have identified 47 primary studies. These studies address different approaches to eliciting ethical requirements, including techniques based on user stories, analysis of ethical guidelines, specific frameworks such as ECCOLA, and methods such as interviews and modeling. <strong>Contributions and Impact on the IS area</strong>: The report contributes to the field by consolidating existing practices in the literature regarding ethical requirements. It provides a comprehensive overview of the techniques and tools available for integrating ethical considerations into software systems and identifies gaps and opportunities for future research. The study significantly impacts the IS field by providing practical and theoretical guidelines for eliciting ethical requirements in information systems.</p> <p>Supplementary material of SLR.</p>
A Comprehensive Review of Techniques, Methods, Processes, Frameworks, and Tools for Privacy Requirements
<p> Context: Requirements Engineering (RE) relies on the collaboration of various roles—such as requirements engineers, stakeholders, and developers—and various techniques, methods, processes, frameworks, and tools. This makes RE a highly human-dependent process that benefits greatly from tool support. Understanding how these techniques, methods, processes, frameworks, and tools are applied across RE phases could provide valuable insights into ways to enhance the RE process, contributing to more successful outcomes. Objective: The primary objective of this study is to identify the techniques, methods, processes, frameworks, and tools applied across different requirements engineering phases—such as elicitation, analysis, specification, validation, and management—to address privacy requirements. Method: We conducted a systematic literature review (SLR) and identified 125 primary studies, and we also conducted a survey with 37 practitioners. Results: Our review identified a range of techniques, methods, processes, frameworks, and tools for addressing privacy requirements. Most studies were conducted in academic contexts, with the most frequently used tools being: PriS Method, Secure Tropos, LINDDUN, i* (i-star), STRAP (Structured Analysis for Privacy), Privacy by Design (PbD), and SQUARE. Additionally, over 75% of the studies applied these tools in the privacy requirements elicitation phase. In the industry, most of the techniques identified in the literature are not known or used by practitioners. Conclusion: This study provides a comprehensive analysis of techniques and tools for privacy requirements in RE, revealing a strong focus on academic contexts with limited industry application. Future research should explore the scalability and effectiveness of these tools in real-world environments, as well as the reasons why practitioners do not use them.</p>
Does the System of Radiological Protection Require Science to the Nth Degree to be Fit For Purpose?
<p>The objective of the of the System is "to contribute to an appropriate level of protection for people and the environment" according to ICRP 103. This may be broadly accepted as the purpose of the System. An inherent requirement for protection is an understanding of the risk, where the System burdens Radiation Protection Practitioners with an assumption; a theory. Adoption of LNT has made it mandatory to wear 7 kg of PPE during for a long surgery with a short X-ray exam in the middle, adding a risk of musculoskeletal injuries. In a practical, holistic approach to safety accepting the risk of life long debilitating injury to avoid 0.0025% risk of cancer at some uncertain time is difficult to justify. The discussion paper acknowledges the uncertainty of the LNT Hypothesis. However, despite the uncertainty proposes its continuation at all radiation levels.</p> <p>Is the purpose of the System the pursuit of pure science, or is the purpose to provide practitioners with the ability to protect people?</p>
Thermal requirements for egg development of two endemic Wiseana pest species (Lepidoptera: Hepialidae) of economic importance
<p>Raw and analyzed data for our paper title "Thermal requirements for egg development of two endemic <em>Wiseana</em> pest species (Lepidoptera: Hepialidae) of economic importance". </p>
Supplementary Material on "Early timing analysis based on scenario requirements and platform models"
<p>This dataset provides supplementary material on the submission “Early timing analysis based on scenario requirements and platform models” to the SoSyM theme issue on Model-Driven Requirements Engineering. It provides software and models for illustrating the paper's example application results as well as more detailed evaluation data.</p> <p>MSD-CCSL-TimingAnalysis.zip contains our approach and encompasses the following artifacts (Java 8 and not later required; if needed modify the GemocStudio.ini and point the vm to a corresponding Java version via "-vm <PathToJava8>\jre\bin"):</p> <ul> <li>Development workspace: <ul> <li>ECL specification under /de.fraunhofer.iem.swt.msd.tam.dse/ecl/MSDLanguage.ecl</li> <li>MoCCML constraints under /de.fraunhofer.iem.swt.msd.tam.mocc/mocc/MSDLanguageComplete.moccml</li> <li>TAM profile under /de.fraunhofer.iem.swt.msd.tam.tamProfile/model/tam.profile.uml</li> </ul> </li> <li>Runtime workspace: <ul> <li>Models under "01_ExampleModels"</li> <li>Exemplary traces under "02_ExampleTraces"</li> <li>QVT-O Transformations (e.g., Preprocessing) needed when modifying the models</li> </ul> </li> </ul> <p>Papyrus-CCSLEditor-Measurement.zip contains the plugins and artifacts that we used for measuring the particular modeling operations for the evaluation of the hypothesis H2 (see further documents below). It requires Java 11; if needed modify the eclipse.ini and point the vm to a corresponding Java version via "-vm <PathToJava11>\jre\bin". Contained plugins and artifacts:</p> <ul> <li>Development workspace: <ul> <li>is.ru.cs.PapyrusActivityLogger: Our adapted version of ModRec, particularly extended by an Xtext document listener</li> <li>org.eclipse.gemoc.moccml.*: MoCCML editor prerequisites for the CCSL runtime model</li> <li>org.scenariotools.msd.profile and de.fraunhofer.iem.swt.msd.tam.tamProfile: Profiles that we partially use in the Papyrus runtime model</li> </ul> </li> <li>Runtime workspace: <ul> <li>CCSL Measuring Project: Measuring project for CCSL models</li> <li>Papyrus Measuring Project: Measuring project for Papyrus models</li> </ul> </li> </ul> <p>Further documents:</p> <ul> <li>MSD-CCSL-TimingAnalysisTutorial.pdf: Tutorial on starting the simulative timing analysis</li> <li>EvaluationData_H1_TimingEffectTestResults: Test results for the particular timing effects based on several models for hypothesis H1</li> <li>Files for hypothesis H2: <ul> <li>EvaluationData_H2.xlsx: Spreadsheet containing the particular model element amounts of MSD-spec-1--4 and CCSL-model-1--4, the measurements for the categorized atomic model operation kinds, the multiplication scheme for predicting the raw overall effort, and the measured transformation execution times</li> <li>EvaluationData_H2_MSD-specification-effort.pdf: PDF extract of the spreadsheet contents for the MSD specification effort and computation</li> <li>EvaluationData_H2_CCSL-model-effort.pdf: PDF extract of the spreadsheet contents for the CCSL model effort and computation</li> <li>EvaluationData_H2_transformationExecTimes.pdf: PDF extract of the spreadsheet contents for the transformation execution times</li> <li>EvaluationData_H2_MSD-specification_measurement-timestamps.txt: Raw timestamp logs for the conducted measurements for model operations on MSD specifications</li> <li>EvaluationData_H2_CCSL-model_measurement-timestamps.txt: Raw timestamp logs for the conducted measurements for model operations on CCSL models</li> </ul> </li> </ul>
mCRL2 models, requirements and test logs for the EULYNX Point interface case study
<p>mCRL2 models and mu-calculus formulas for the EULYNX Point Interface. Models and requirements are made in the context of the FormaSig project. Data is made available for replication purposes.</p> <p>REQ_P_001, REQ_P_001_1 and REQ_P_002 are requirements for the point specific mCRL2 model point_spec.mcrl2</p> <p>Remaining .mcf files are requirements for the generic PDI interface pdi_spec.mcrl2</p> <p>Artifacts relating to testing are:</p> <ul> <li>An mCRL2 model, mbt.mcrl2</li> <li>A rename file to rename internal actions to tau, rename_file.re</li> <li>Partial state space associated to mbt.mcrl2, partial_state_space.aut</li> <li>The weak-trace bisim reduced version of the state space, partial_state_space_reduced.aut</li> <li>Testing logs, test-logs.zip</li> <li>The source code of the simulator and the testing tools, Simulator code.zip</li> </ul>
Supplementary data to publication "Growth efficiency, intestinal biology, and nutrient utilization and requirements of black soldier fly (Hermetia illucens) larvae compared to monogastric livestock species: a review"
<p>The datasets provided in the excel file were used to generate Table 2 and Fig. 2 in the publication entitled "Growth efficiency, intestinal biology, and nutrient utilization and requirements of black soldier fly (Hermetia illucens) larvae compared to monogastric livestock species: a review" by Seyedalmoosavi et al., 2022 published in Journal of Animal Science and Biotechnology. https://doi.org/10.1186/s40104-022-00682-7</p>
Modelling and Enforcing Access Control Requirements for Smart Contracts - Data Set
<p>This data set contains all artifacts for the master thesis of Jan-Philipp Töberg at the Karlsruher Institute of Technology. This includes the Eclipse project for the metamodel and the generator, the extension of the Slither framework and the use case instances employed during the evaluation. Additionally, extensive instructions regarding the installation and usage are provided.</p>
Dataset and additional files/softwares required for the paper "LeSICiN: A Heterogeneous Graph-based Approach for Automatic Legal Statute Identification from Indian Legal Documents"
<p>This dump contains all files and softwares required for running the codes for the paper "LeSICiN: A Heterogeneous Graph-based Approach for Automatic Legal Statute Identification from Indian Legal Documents". Specifically, these codes are available at https://github.com/Law-AI/LeSICiN.</p> <p>LeSICiN is a deep neural network for the task of Legal Statute Identification which also uses graphical properties of the document-statute citation network for training and predictions.</p> <p>We have three datasets --- train, dev and test. These are all .jsonl files with each instance dict per line; each instance dict contains the unique id, list of sentences and cited labels of the particular instance. Also, there is a fourth file --- secs.jsonl, which stores the text of all the statutes in similar format.</p> <p>schemas.json list out the metapath schemas for fact and section type nodes, while type_map.json maps the id of each node to its type (Act/Chapter/Topic/Section/Fact). </p> <p>label_tree.json and citation_network.json list out the edges for the two parts of the network in the format of a 3-tuple ('source id', 'relationship type', 'target id')</p> <p>"ils2v.bin" is the pretrained sent2vec vectorizer that can generate a 200-dim vector for each sentence</p>
Data from: Partial mycoheterotrophy in green plants forming Paris-type arbuscular mycorrhiza requires a thorough investigation
<p>Recently, many green plants forming <em>Paris</em>-type arbuscular mycorrhiza (AM) have been suggested to receive fungal carbon (Giesemann <em>et al.</em> 2020b, 2021). Whereas the enrichment of natural abundance of heavy stable isotopes (particularly <sup>13</sup>C) has been considered as strong evidence for this 'partial mycoheterotrophy,' we show our own data on isotopic abundances and mycorrhizal colonization in Japanese plants and argue that the <sup>13</sup>C-enrichment may not always be the result of acquiring carbon from AM fungi.</p>
Dataset of the paper "A Mixed-Criticality Approach to Fault Tolerance: Integrating Schedulability and Failure Requirements"
<p>Dataset for the paper "A Mixed-Criticality Approach to Fault Tolerance: Integrating Schedulability and Failure Requirements" published in RTAS'22 conference</p>
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