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Systematic Mapping Study on Domain-Specific Language Development Tools - Data Repository

Domain-specific languages (DSL) are programming or modeling languages devoted to a given application domain. There are many tools used to support the implementation of a DSL, making hard the decision-making process for one or another. In this sense, identifying and mapping their features is relevant for decision-making by academic and industrial initiative on DSL development.  Objective: The goal of this work is to identify and map the tools, Language Workbenches (LW), or frameworks that were proposed to develop DSLs discussed and referenced in publications between 2012 and 2019.  Method: A Systematic Mapping Study (SMS) of the literature scoping tools for DSL development.  Results: We identified 59 tools, including 9 under a commercial license and 41 with non-commercial licenses, and analyzed their features from 230 papers.  Conclusion: There is a substantial amount of tools that cover a large number of features. Furthermore, we observed that usually, the developer adopts one type of notation to implement the DSL: textual or graphical. We also discussed research gaps, such as a lack of tools that allow meta-meta model transformations and that support modeling tools interoperability.

Gene expression counts from fibroblast, strand-specific, BCM UDN

File description: <ol> <li> Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> URL: <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a>   Title: BCM UDN Fibroblast Number of samples: 139 Tissue: Fibroblast Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): : D17: 1, D84: 12, E34: 2, G82: 1, H57: 3, K92: 3, M25: 18, NONE: 35, Q02: 1, Q20: 5, Q33: 2, Q89: 12, R62: 44 Strand specific: TRUE Paired end: TRUE Protocol: poly(A) enrichment Dataset contact: David Murdock, <a href="mailto:david.murdock@bcm.edu">david.murdock@bcm.edu</a> Citation: Cite both the resource using Zenodo's citation and the publication under References

Data sets v.1.1 for Perspective: SARS-CoV-2 may regulate cellular responses through depletion of specific host miRNAs

The list of potential (bioinformatic predictions) interactions of human miRNA with 7 coronavirus genomes that include 3 pathogenic and 4 non-pathogenic coronaviruses. (Data Set 1). The HCoVs' RNA genomes of pathogenic strains were SARS-CoV-2 (NC_045512.2), SARS-CoV (NC_004718.3), MERS-CoV (NC_019843.3). The non-pathogenic strains were HCoV-OC43 (KU131570.1), HCoV-229E (NC_002645.1), HCoV-HKU1 (KF686346.1), and HCoV-NL63 (NC_005831.2). These coronaviruses were tested against the set of 896 confident mature human miRNA sequences that were obtained from the miRBbase v2.21 using the RNA22 v2 microRNA target discovery tool web-server. In order to reduce the false discovery rate of the MTS predictions, the most strict parameters were applied to the default computation workflow using a specificity of 92% versus a sensitivity of 22%. Data set 2.  The potential targets of miRNA that could be bound to either the pathogenic, the non-pathogenic or both groups of HCoVs. Predicted base on miRDIP database (with only top 1% of the most probable targets considered), Data set 3.  Pre-miRNA sequences in the SARS-CoV-2 RNA sequence that could potentially enter the human RNAi pathway, base on miRNAFold webserver.

Gene expression counts from blood, strand-specific, BCM UDN

File description: <ol> <li> Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> URL: <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a>   Title: BCM UDN Whole Blood Number of samples: 125 Tissue: Peripheral blood Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): : 1, D84: 10, E34: 2, H57: 1, K92: 4, M25: 17, NONE: 53, Q20: 3, Q33: 2, Q89: 6, R62: 26 Strand specific: TRUE Paired end: TRUE Protocol: poly(A) enrichment, no globin depletion Dataset contact: David Murdock, <a href="mailto:david.murdock@bcm.edu">david.murdock@bcm.edu</a> Citation: Cite both the resource using Zenodo's citation and the publication under References

opencc-by-4.0Mar 2020View details →

Artifacts: An Efficient Approach for Reviewing Security-Related Aspects in Agile Requirements Specifications of Web Applications

Abstract: Defects in requirements specifications can have severe consequences during the software development lifecycle. Some of them result in time and cost overruns due to incorrect or missing quality characteristics, such as security. This characteristic requires special attention in web applications because they have become a target for manipulating sensible data. Several concerns make security difficult to deal with. For instance, (1) when stakeholders discuss general requirements they are often unaware that they should also discuss security-related aspects, because (2) they typically do not have enough expertise in security. This often leads to unspecified or ill-defined security requirements. These concerns become even more challenging in agile contexts, where lightweight documentation is typically produced. To tackle this problem, we designed an approach for reviewing security-related aspects in agile requirements specifications of web applications. Our proposal considers user stories and security specifications as inputs and relates those user stories to security properties via Natural Language Processing. Based on the related security properties, our approach identifies high-level security requirements from the Open Web Application Security Project (OWASP) to be verified, and generates a reading technique to support reviewers in detecting defects. We evaluate our approach via three experiment trials conducted with 56 novice software engineers, measuring effectiveness, efficiency, usefulness, and ease of use. We compare our approach against using: (1) the OWASP high-level security requirements, and (2) a perspective-based approach as proposed in contemporary state of the art. The results strengthen our confidence that using our approach has a positive impact (with large effect size) on the performance of inspectors in terms of effectiveness and efficiency. The files below contains the following data: 1) Consent form.docx: This document provides to the research subjects information to decide whether to participate in a research study or not based on an explanation of the proposed research and the nature of the participation that is requested of them. 2) Characterization_Questionnaire.docx:  This document shows the questions used to characterize the working experience and knowledge of the participants of the controlled experiment. The answers obtained through this questionnaire allowed us to identify some key characteristics about three knowledge areas: Agile Software Development, Software Security and Software Inspection. 3) Experiment_Results.xlsx: This Excel document shows a summary of the results of the experiments by participant ID, trial and technique. It also synthesizes the defects found by the reviewers and the characterization, follow up and TAM questionnaire.       4) FollowUp_Questionnaire_AdHoc_Technique.docx: This document shows the questions used to acquire information about the review conducted by inspectors who used the ad hoc technique. 5) FollowUp_Questionnaire_Reading_Technique.docx: This document shows the questions used to acquire information about the review conducted by inspectors who used the proposed reading technique.  6)  Repository of Keywords.docx: This document shows the keywords used by our proposed approach and that indicate some security concern.  7) Task_description_AdHoc_A.docx: This document shows textual instructions on how to follow the ad hoc review for a set of user stories.  8) Task_description_AdHoc_B.docx: This document shows textual instructions on how to follow the ad hoc review for another set of user stories. 9) Task_description_RT_A.docx: This document shows textual instructions on how to follow the proposed reading technique for a set of user stories. 10) Task_description_RT_B.docx: This document shows textual instructions on how to follow the proposed reading technique for another set of user stories.  11) Training_Experiment.pptx: This document contains the material used to explain the topics involved in the experiment. It was used to train the subjects.

opencc-zeroAug 2020View details →

Data from: A quantitative inventory of yeast P body proteins reveals principles of composition and specificity

P bodies are archetypal biomolecular condensates that concentrate proteins and RNA without a surrounding membrane. While dozens of P body proteins are known, the concentrations of components in the compartment have not been measured. We used live cell imaging to generate a quantitative inventory of the major proteins in yeast P bodies. Only 7 proteins are highly concentrated in P bodies (5.1-15 uM); the 24 others examined are appreciably lower (most ≤ 2.6 uM). P body concentration correlates inversely with cytoplasmic exchange rate. Sequence elements driving Dcp2 concentration into P bodies are distributed across the protein and act cooperatively. Our data indicate that P bodies, and probably other condensates, are biochemically simpler than suggested by proteomic analyses, with implications for specificity, reconstitution and evolution.

opencc-by-4.0Aug 2020View details →

Limited host-specificity of eukaryotic virome in Hymenoptera

Additional datafiles for Bee_Euvir repository.

opencc-zeroAug 2020View details →

Host plant defense produces species-specific alterations to flight muscle protein structure and flight-related fitness traits of two armyworms

Insects manifest phenotypic plasticity in their development and behavior in response to plant defenses, via molecular mechanisms that produce tissue-specific changes. Phenotypic changes might vary between species that differ in their preferred hosts and these effects could extend beyond larval stages. To test this, we manipulated the diet of southern armyworm (SAW; Spodoptera eridania) and fall armyworm (FAW; Spodoptera frugiperda) using a tomatomutant for jasmonic acid plant defense pathway (def1), and wild-type plants, and then quantified gene expression of Troponin t (Tnt) and flight muscle metabolism of the adult insects. Differences in Tnt spliceform ratios in insect flight muscles correlate with changes to flight muscle metabolism and flight muscle output. We found that SAW adults reared on induced def1 plants had a higher relative abundance (RA) of the A isoform of Troponin t (Tnt A) in their flight muscles; in contrast, FAW adults reared on induced def1 plants had a lower RA of Tnt A in their flight muscles compared with adults reared on def1 and controls. Although massadjusted flightmetabolic rate showed no independent host plant effects in either species, higher flight metabolic rates in SAW correlated with increased RA of Tnt A. Flight muscle metabolism also showed an interaction of host plants with Tnt A in both species, suggesting that host plants might be influencing flight muscle metabolic output by altering Tnt. This study illustrates how insects respond to variation in host plant chemical defense by phenotypic modifications to their flight muscle proteins, with possible implications for dispersal.

opencc-by-4.0Aug 2020View details →

Data 2 for "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (Merops apiaster)"

Data related to the article "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (Merops apiaster)" in the format .fas. FASTA file contains sequences cytochrome b which were assigned to haemosporidian lineages with the R script (see 10.5281/zenodo.3968360).

opencc-zeroSep 2020View details →

Code and data from: A mobile sex-determining region, male-specific haplotypes, and rearing environment influence age at maturity in Chinook salmon.

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males governed by large (up to 20Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex-linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex-determination in this species and Pacific salmon in general.

opencc-zeroSep 2020View details →

Patterns of Thermal Sensitivity and Sex-Specificity of Courtship Behavior Differs Between Two Sympatric Species of Enchenopa Treehopper

Predicting how insects will react to future thermal conditions requires understanding how temperature currently affects insect behavior, from performance traits to those involved in mating and reproduction. Many reproductive behaviors are thermally-sensitive, but little is known how temperature affects the behaviors used to find mates and coordinate mating. Here, we investigate how temperature influences courtship activity in two sympatric species of Enchenopa treehoppers (Hemiptera: Membracidae). Enchenopa use substrate-borne vibrational signals exchanged in male-female duets to facilitate pair formation prior to mating. In a controlled laboratory setting, we assessed the likelihood of males and females to produce courtship signals across a range of ecologically relevant temperatures. We found that changes in courtship activity across temperatures differed between the two species. We also found sex differences within species: in one species males were more likely to signal at higher temperatures, while in the other species females were more likely to signal at higher temperatures. Our results suggest that sex-specific responses to temperature may constrain mating to narrower ranges of temperatures. Furthermore, sympatric species may respond differently to changes in thermal variation despite sharing similar climactic history.

opencc-zeroSep 2020View details →

Age specific reproduction in female pied flycatcher: evidence for asynchronous aging

Age-related variation in demographic performance is central for the understanding of population dynamics and evolutionary processes. Our understanding of age-trajectories in vital rates has long been limited by the lack of distinction between patterns occurring at the population and the individual levels, and by the lack of comparative studies of age trajectories among traits. Thus, we poorly know how sets of demographic traits change within individuals according to the age. Based on a 40 years monitoring, we investigated age-related variation in five reproductive traits in females pied flycatcher. We disentangled within from between individual processes and assessed the relative contribution of within-individual age-related changes and selective appearance and disappearance. Finally, we compared the aging pattern among these five reproductive traits. We found strong evidence for age-specific performance including both early-life improvement and late-life decline in four of the five reproductive traits. Furthermore, the aging patterns varied substantially according to reproductive trait both for the age of peak performance and for the rates of early-life improvement and late life decline. The results show that age-trajectories observed at population level may substantially differ from those occurring at the individual level and illustrate the complexity of variation in ageing patterns across traits.

Development and uncertainty assessment of pedotransfer functions for predicting water contents at specific pressure heads

There has been much effort to improve the performance of pedotransfer functions (PTFs) using intelligent algorithms, but the issue of covariate shift, i.e. different probability distributions in training and testing datasets, and its impact on prediction uncertainty of PTFs has been rarely addressed. The common practice in PTF generation is to randomly separate the dataset in training and testing subsets, and outcomes of this random selection may be different if the process is subject to covariate shift. We evaluated the impact of covariate shift generated by data shuffling and detected by Kolmogorov-Smirnov test for prediction of water contents using soil databases from Denmark and Brazil. The soil water contents at different pressure heads were predicted by developing linear and stepwise regression besides machine learning based PTFs including Gaussian regression process and ensemble method. Regression based PTFs for the Brazilian dataset resulted in better predictions compared to machine learning methods that estimated high water contents in Danish soils more accurately. One hundred PTFs were developed for water content at specific pressure heads by data shuffling generating covariate shift. From these, a hundred sets of fitted van Genuchten parameters were obtained representing the generated uncertainty. Data shuffling led to covariate shift, resulting in uncertainty in water content prediction by the PTFs. Inherent variability of data may lead to increased prediction uncertainty. For correlated data, simple regression models performed as good as sophisticated machine learning methods. Using PTF-predicted water contents for van Genuchten retention parameter fitting may lead to a high uncertainty.

opencc-by-4.0Oct 2020View details →

Data Augmentation at the LHC through Analysis-specific Fast Simulation with Deep Learning: W+jet training/test dataset

W+jet events at generator and reconstruction level, used to train analysis-specific generative models. Events are represented as an array of relevant high-level features. Reco objects are matched to Gen objects and a minimal selection is applied to define the generator support in the N-dim space identified by the input features. About 2M events, used for training/validation/testing Details in https://arxiv.org/abs/2010.01835

opencc-zeroDec 2019View details →

Pathways linking female personality with reproductive success are trait and year-specific

Personality (i.e. among-individual variation in average behavior) often covaries with fitness, but how such personality-fitness relationships come about is poorly understood. Here, we explore potential mechanisms by which two female personality traits (female-female aggression and female nest defense as manifested by hissing behavior) were linked with annual reproductive success in a population of great tits (Parus major), a socially monogamous species with biparental care. We hypothesized that personality-related differences in reproductive success result from variation in reproductive decision (lay date, brood size) and/or parental provisioning rates. Relative support for these mechanisms was evaluated using path-analysis on data collected in two successive years. We reveal that larger broods were provisioned at a higher rate by both parents and that female, but not male, provisioning rate was involved in the trade-off between offspring number (brood size) and fledgling mass. Among-individual variation in female aggression, via its association with female provisioning rate, was negatively linked to fledgling mass (i.e. indirect effect), yet only in one of the study years. Male provisioning rate did not influence these relationships. In contrast, among-individual variation in hissing behavior was directly and negatively linked with fledgling mass in both years, via an underlying mechanism that remains to be identified (i.e. direct effect). Together, our findings emphasize that personality-fitness relationships may come about via different mechanisms across personality traits and/or years, thereby illustrating additional complexity in how selection might act on and maintain among-individual variation in behavioral phenotypes in the wild.

Data from: Preserved single muscle fiber specific force in facioscapulohumeral muscular dystrophy

Objective: To investigate single muscle fiber contractile performance in muscle biopsies from patients with facioscapulohumeral muscular dystrophy, one of the most common hereditary muscle disorders. Methods: we collected 26 vastus lateralis and 24 tibialis anterior muscle biopsies from 14 genetically confirmed FSHD patients and 12 healthy controls. Single muscle fibers (N = 547) were isolated for contractile measurements. Titin content and PEVK phosphorylation were examined in vastus lateralis muscle biopsies. Results: Single muscle fiber specific force is intact at saturating and physiological calcium concentrations in all FSHD biopsies, with (FSHDFAT) and without (FSHDNORMAL) fatty infiltration. Myofilament calcium sensitivity of force is increased in single muscle fibers obtained from FSHD muscle biopsies with increased fatty infiltration, but not in FSHD muscle biopsies without fatty infiltration (pCa50: 5.77-5.80 in healthy control, 5.74-5.83 in FSHDNORMAL and 5.86-5.90 in FSHDFAT single muscle fibers). Cross-bridge cycling kinetics at saturating calcium concentrations and myofilament cooperativity did not differ from healthy controls. Passive force was increased in all FSHD muscle fibers, resulting in increased fiber stiffness. Titin content was increased in FSHD biopsies, however titin phosphorylation did not differ from healthy controls. Conclusion: Muscle weakness in patients with FSHD is not caused by reduced specific force of individual muscle fibers, even in severely affected tissue. Muscle fiber calcium sensitivity of force was increased in severely affected tissue and probably is a compensatory mechanism to maintain specific force. Fiber stiffness was increased in FSHD muscle with and without fatty infiltration, suggesting an early event in disease pathology.

Sex-specific effects of cooperative breeding and colonial nesting on prosociality in corvids

The investigation of prosocial behavior is of particular interest from an evolutionary perspective. Comparisons of prosociality across non-human animal species have, however, so far largely focused on primates, and their interpretation is hampered by the diversity of paradigms and procedures used. Here we present the first systematic comparison of prosocial behavior across multiple species in a taxonomic group outside the primate order, namely the bird family Corvidae. We measured prosociality in 8 corvid species, which vary in the expression of cooperative breeding and colonial nesting. We show that cooperative breeding is positively associated with prosocial behavior across species. Also colonial nesting is associated with a stronger propensity for prosocial behavior, but only in males. The combined results of our study strongly suggest that both cooperative breeding and colonial nesting, which may both rely on heightened social tolerance at the nest, are likely evolutionary pathways to prosocial behavior in corvids.

opencc-by-4.0Feb 2020View details →

Effect of Acute Sleep Hygiene on Salivary Cortisol Level Following A Late Night Soccer-Specific Training Session

Letter to the editor with data, no abstract available

Sex‐specific effects of predation risk on parental care in a sexually dichromatic Neotropical songbird

Predation risk affects a broad range of bird behaviours, especially parental care. The adaptive behavioural changes presented by both parents, however, may differ according to different levels of predation risk suffered by each sex. This is especially prominent in sexually dichromatic species, where one of the sexes is more visually conspicuous and hence vulnerable to increased nest predation risk during nest visits. Here, we experimentally investigated how predation risk affects the parental behaviour of a sexually dichromatic Neotropical passerine, the blue-black grassquit (Volatinia jacarina). We used playbacks of known predators and non-predatorial control sympatric species near nesting pairs in the field. Results show that grassquits modify their behaviour according to predation risk and that this behavioural response is sexdependent. Males decrease their nest visit times, become more discreet when moving towards the nest, and stop performing sexual displays after leaving the nest. In contrast, females tend to decrease latency to visit the nest and increase the duration of brooding bouts. These different sex responses reduce nest visual and acoustic detectability, since conspicuous males are readily spotted on nests and cryptic females camouflage nestlings and suppress begging calls. Although these behavioural changes might reduce predation risk, there might be a cost of reduced food load to nestlings and increased brood starvation risk. These changes in nesting activities illustrate the behavioural adaptability of passerines to ensure offspring survival in tropical high predation risk environments.