Miracle-dz/UniFAR-FTUs huggingface dataset:
On the correlation between testing effort and software complexity metrics

Software complexity metrics, such as code size and cyclomatic complexity, have been used in the software engineering community for predicting quality metrics such as maintainability, bug proneness and robustness. However, not many studies have addressed the relationship between complexity metrics and software testing and there is little experimental evidence to support the use of these code metrics in the estimation of test effort. We have investigated and evaluated the relationship between test effort (i.e, number of test cases and test execution time) and software complexity metrics for industrial control software used in an embedded system. We show how to measure different software complexity metrics such as number of elements, cyclomatic complexity, and information flow for a popular programming language named FBD used in the safety critical domain. In addition, we use test data and test suites created by experienced test engineers working at Bombardier Transportation Sweden AB to evaluate the correlation between several complexity measures and the testing effort. We found that there is a moderate correlation between software complexity metrics and test effort. In addition, the results show that the software size (i.e., number of elements in the FBD program) provides the highest correlation level with the number of test cases created and test execution time. Our results suggest that software size and structure metrics, while useful for identifying parts of the system that are more complicated, should not be solely used for identifying parts of the system for which test engineers might need to create more test cases. A potential explanation of this result concerns the nature of testing, since other attributes such as the level of thorough testing required and the size of the specifications can influence the creation of test cases. In addition, we used a linear regression model to estimate the test effort using the software complexity measurement results.
JDriver: Automatic Driver Class Generation for AFL-Based Java Fuzzing Tools

AFL (American Fuzzy Lop) is a powerful fuzzing tool that has discovered hundreds of real-world vulnerabilities. Recent efforts are seen to port AFL to a fuzzing Java program and have shown to be effective in Java testing. However, these tools require humans to write driver classes, which is not plausible for testing large-scale software. In addition, AFL generates files as input, making it limited for testing methods that process files. In this paper, we present JDriver, an automatic driver class generation framework for AFL-based fuzzing tools, which can build driver code for methods’ processing files as well as ordinary methods not processing files. Our approach consists of three parts: a dependency-analysis based method to generate method sequences that are able to change the instance’s status so as to exercise more paths, a knowledge assisted method to make instance for the method sequences, and an input-file oriented driver class assembling method to handle the method parameters for ordinary methods. We evaluate JDriver on commons-imaging, a widely used image library provided by the Apache organization. JDriver has successfully generated 149 helper methods which can be used to make instances for 110 classes. Moreover, 99 driver classes are built to cover 422 methods.
The interdependence of gene-regulatory elements and the 3D genome

&NA; Imaging studies, high‐resolution chromatin conformation maps, and genome‐wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross‐talk between gene‐regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause‐consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer‐promoter contacts in gene regulation. &NA; Vermunt et al. discuss the relationship between gene‐regulatory elements and nuclear architectural features in transcription.
The Effect of Boron Nitride on the Thermal and Mechanical Properties of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)

The thermal and mechanical properties of poly(3-hydroxybutyrate-co-3-hydroxyvalerate, PHBV) composites filled with boron nitride (BN) particles with two different sizes and shapes were studied by scanning electron microscopy (SEM), differential scanning calorimetry (DSC), X-ray diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), thermal gravimetric analysis (TGA) and mechanical testing. The biocomposites were produced by melt extrusion of PHBV with untreated BN and surface-treated BN particles. Thermogravimetric analysis (TGA) showed that the thermal stability of the composites was higher than that of neat PHBV while the effect of the different shapes and sizes of the particles on the thermal stability was insignificant. DSC analysis showed that the crystallinity of the PHBV was not affected significantly by the change in filler concentration and the type of the BN nanoparticle but decreasing of the crystallinity of PHBV/BN composites was observed at higher loadings. BN particles treated with silane coupling agent yielded nanocomposites characterized by good mechanical performance. The results demonstrate that mechanical properties of the composites were found to increase more for the silanized flake type BN (OSFBN) compared to silanized hexagonal disk type BN (OSBN). The highest Young’s modulus was obtained for the nanocomposite sample containing 1 wt. % OSFBN, for which increase of Young’s modulus up to 19% was observed in comparison to the neat PHBV. The Halpin–Tsai and Hui–Shia models were used to evaluate the effect of reinforcement by BN particles on the elastic modulus of the composites. Micromechanical models for initial composite stiffness showed good correlation with experimental values.
Population-Level Analysis to Determine Parameters That Drive Variation in the Plasma Metabolite Profiles

The plasma metabolome is associated with multiple phenotypes and diseases. However, a systematic study investigating clinical determinants that control the metabolome has not yet been conducted. In the present study, therefore, we aimed to identify the major determinants of the plasma metabolite profile. We used ultra-high performance liquid chromatography (UHPLC) coupled to quadrupole time of flight mass spectrometry (QTOF-MS) to determine 106 metabolites in plasma samples from 2503 subjects in a cross-sectional study. We investigated the correlation structure of the metabolite profiles and generated uncorrelated metabolite factors using principal component analysis (PCA) and varimax rotation. Finally, we investigated associations between these factors and 34 clinical covariates. Our results suggest that liver function, followed by kidney function and insulin resistance show the strongest associations with the plasma metabolite profile. The association of specific phenotypes with several components may suggest multiple independent metabolic mechanisms, which is further supported by the composition of the associated factors.
Mitochondrial energetics is impaired in very long-chain acyl-CoA dehydrogenase deficiency and can be rescued by treatment with mitochondria-targeted electron scavengers

Abstract Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency is the most common defect of mitochondrial long-chain fatty acid β-oxidation. Patients present with heterogeneous clinical phenotypes affecting heart, liver and skeletal muscle predominantly. The full pathophysiology of the disease is unclear and patient response to current therapeutic regimens is incomplete. To identify additional cellular alterations and explore more effective therapies, mitochondrial bioenergetics and redox homeostasis were assessed in VLCAD-deficient fibroblasts, and several protective compounds were evaluated. The results revealed cellular and tissue changes, including decreased respiratory chain (RC) function, increased reactive oxygen species (ROS) production and altered mitochondrial function and signaling pathways in a variety of VLCAD-deficient fibroblasts. The mitochondrially enriched electron and free radical scavengers JP4-039 and XJB-5-131 improved RC function and decreased ROS production significantly, suggesting that they are viable candidate compounds to further develop to treat VLCAD-deficient patients.
Patulin in Apples and Apple-Based Food Products: The Burdens and the Mitigation Strategies

Apples and apple-based products are among the most popular foods around the world for their delightful flavors and health benefits. However, the commonly found mold, Penicillium expansum invades wounded apples, causing the blue mold decay and ensuing the production of patulin, a mycotoxin that negatively affects human health. Patulin contamination in apple products has been a worldwide problem without a satisfactory solution yet. A comprehensive understanding of the factors and challenges associated with patulin accumulation in apples is essential for finding such a solution. This review will discuss the effects of the pathogenicity of Penicillium species, quality traits of apple cultivars, and environmental conditions on the severity of apple blue mold and patulin contamination. Moreover, beyond the complicated interactions of the three aforementioned factors, patulin control is also challenged by the lack of reliable detection methods in food matrices, as well as unclear degradation mechanisms and limited knowledge about the toxicities of the metabolites resulting from the degradations. As apple-based products are mainly produced with stored apples, pre- and post-harvest strategies are equally important for patulin mitigation. Before storage, disease-resistance breeding, orchard-management, and elicitor(s) application help control the patulin level by improving the storage qualities of apples and lowering fruit rot severity. From storage to processing, patulin mitigation strategies could benefit from the optimization of apple storage conditions, the elimination of rotten apples, and the safe and effective detoxification or biodegradation of patulin.
Test Sequence Reduction of Wireless Protocol Conformance Testing to Internet of Things

Wireless communication protocols are indispensable in Internet of Things (IoT), which refer to rules and conventions that must be followed by both entities to complete wireless communication or service. Wireless protocol conformance testing concerns an effective way to judge whether a wireless protocol is carried out as expected. Starting from existing test sequence generation methods in conformance testing, an improved method based on overlapping by invertibility and multiple unique input/output (UIO) sequences is proposed in this paper. The method is accomplished in two steps: first, maximum-length invertibility-dependent overlapping sequences (IDOSs) are constructed, then a minimum-length rural postman tour covering the just constructed set of maximum-length IDOSs is generated and a test sequence is extracted from the tour. The soundness and effectiveness of the method are analyzed. Theory and experiment show that desirable test sequences can be yielded by the proposed method to reveal violations of wireless communication protocols in IoT.
GTRD: a database on gene transcription regulation—2019 update

Abstract The current version of the Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org) contains information about: (i) transcription factor binding sites (TFBSs) and transcription coactivators identified by ChIP-seq experiments for Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Arabidopsis thaliana; (ii) regions of open chromatin and TFBSs (DNase footprints) identified by DNase-seq; (iii) unmappable regions where TFBSs cannot be identified due to repeats; (iv) potential TFBSs for both human and mouse using position weight matrices from the HOCOMOCO database. Raw ChIP-seq and DNase-seq data were obtained from ENCODE and SRA, and uniformly processed. ChIP-seq peaks were called using four different methods: MACS, SISSRs, GEM and PICS. Moreover, peaks for the same factor and peak calling method, albeit using different experiment conditions (cell line, treatment, etc.), were merged into clusters. To reduce noise, such clusters for different peak calling methods were merged into meta-clusters; these were considered to be non-redundant TFBS sets. Moreover, extended quality control was applied to all ChIP-seq data. Web interface to access GTRD was developed using the BioUML platform. It provides browsing and displaying information, advanced search possibilities and an integrated genome browser.
Neuromuscular organization of the Ctenophore Pleurobrachia bachei

Ctenophores are descendants of one of the earliest branching metazoan lineage with enigmatic nervous systems. The lack of convenient neurogenic molecules and neurotransmitters suggests an extensive parallel evolution and independent origins of neurons and synapses. However, the field lags due to the lack of microanatomical data about the neuro‐muscular systems in this group of animals. Here, using immunohistochemistry and scanning electron microscopy, we describe the organization of both muscular and nervous systems in the sea gooseberry, Pleurobrachia bachei, from North Pacific. The diffuse neural system of Pleurobrachia consists of two subsystems: the subepithelial neural network and the mesogleal net with about 5,000–7,000 neurons combined. Our data revealed the unexpected complexity of neuromuscular organization in this basal metazoan lineage. The anatomical diversity of cell types includes at least nine broad categories of neurons, five families of surface receptors and more than two dozen types of muscle cells as well as regional concentrations of neuronal elements to support ctenophore feeding, complex swimming, escape, and prey capture behaviors. In summary, we recognize more than 80 total morphological cell types. Thus, in terms of cell‐type specification and diversity, ctenophores significantly exceed what we currently know about other prebilaterian groups (placozoan, sponges, and cnidarians), and some basal bilaterians.
The involvement of microglia in Alzheimer's disease: a new dog in the fight

First described clinically in 1906, Alzheimer's disease (AD) is the most common neurodegenerative disease and form of dementia worldwide. Despite its prevalence, only five therapies are currently approved for AD, all dealing with the symptoms rather than the underlying causes of the disease. A multitude of experimental evidence has suggested that the once thought inconsequential process of neuroinflammation does, in fact, contribute to the AD pathogenesis. One such CNS cell type critical to this process are microglia. Plastic in nature with varied roles, microglia are emerging as key contributors to AD pathology. This review will focus on the role of microglia in the neuroinflammatory response in AD, highlighting recent studies implicating aberrant changes in microglial function in disease progression. Of critical note is that with these advances, a reconceptualization of the framework in which we view microglia is required.
Vestibular Testing: Patient Perceptions, Morbidity, and Opportunity Costs.

OBJECTIVE To characterize patient tolerance and nonmonetary cost burdens of vestibular testing. Rigorously acquired data are essential for patient counseling and to determine if proposed additions/modifications to current protocols improve quality, experience, and efficiencies of care. STUDY DESIGN Prospective observational study. SETTING Tertiary center. PATIENTS 130 adults (67% women, mean age 55 yr), referred to audiology clinic for vestibular testing. INTERVENTION(S) Surveys administered to patients and audiologists immediately and 1 week following videonystagmography (VNG) with caloric and/or rotary chair (RC) testing. MAIN OUTCOME MEASURE(S) Symptoms, visual analog scale ratings of dizziness, distress, and nausea during testing; test completion; and opportunity costs (time, missed work). RESULTS Seventy-five patients (58%) experienced undesirable symptoms during testing, including nausea (50%), vomiting (5%), and headaches (12%). Distress and nausea ratings during testing were low (<3/10), with RC ratings lower than VNG. Nineteen patients (15%) discontinued testing early, rating distress and nausea two to three times higher than those who completed testing (p < 0.05). Greater dizziness was associated with younger age and female sex, not migraine and total eye speed. Women had increased distress. Test times were 71 [23] and 26 [13] minutes for VNG with calorics and RC, respectively. Testing required 48% to miss work (range 2-120 h) and 78% obtained assistance to/from testing. Posttest symptoms included drowsiness/fatigue (44%), nausea (31%), and headache (33%). CONCLUSIONS This work provides baseline patient tolerance data for vestibular testing. While eliciting distress ratings comparable to other in-office otolaryngology procedures, there are high frequencies of undesirable symptoms, posttest morbidity, and opportunity costs.
How Would Americans' Out-of-Pocket Costs Change If Insurance Plans Were Allowed to Exclude Coverage for Preexisting Conditions?

Issue A current Republican legislative proposal would permit insurers to offer plans that exclude coverage of treatment for preexisting health conditions, even while the bill would maintain the Affordable Care Act’s rule prohibiting denial of coverage to people with a preexisting condition. Goal Estimate patients’ out-of-pocket costs for five common preexisting conditions if the bill were to become law and assess any additional impact on out-of-pocket expenditures if spending on care for preexisting conditions no longer counted against plan deductibles. Methods Analysis of 2014–2016 Medical Expenditure Panel Survey data for the privately insured adult population under age 65; and the proposed Ensuring Coverage for Patients with Pre-Existing Conditions Act (S. 3388). Findings and Conclusion If preexisting conditions were excluded from coverage, nearly all people with these conditions would see increased out-of-pocket costs. Average out-of-pocket costs for those with cancer or diabetes would triple, while costs for arthritis, asthma, and hypertension care would rise by 27 percent to 39 percent. Some individuals would see much larger increases: for example, 10 percent of diabetes patients could expect to incur over $9,200 annually in out-of-pocket costs. Many with preexisting conditions also would spend more on conditions that are not excluded, since out-of-pocket spending on their preexisting conditions would no longer count toward the deductible and out-of-pocket maximum.
Reporter‐based forward genetic screen to identify bundle sheath anatomy mutants in A. thaliana

Summary The evolution of C4 photosynthesis proceeded stepwise with each small step increasing the fitness of the plant. An important pre‐condition for the introduction of a functional C4 cycle is the photosynthetic activation of the C3 bundle sheath by increasing its volume and organelle number. Therefore, to engineer C4 photosynthesis into existing C3 crops, information about genes that control the bundle sheath cell size and organelle content is needed. However, very little information is known about the genes that could be manipulated to create a more C4–like bundle sheath. To this end, an ethylmethanesulfonate (EMS)‐based forward genetic screen was established in the Brassicaceae C3 species Arabidopsis thaliana. To ensure a high‐throughput primary screen, the bundle sheath cells of A. thaliana were labeled using a luciferase (LUC68) or by a chloroplast‐targeted green fluorescent protein (sGFP) reporter using a bundle sheath specific promoter. The signal strengths of the reporter genes were used as a proxy to search for mutants with altered bundle sheath anatomy. Here, we show that our genetic screen predominantly identified mutants that were primarily affected in the architecture of the vascular bundle, and led to an increase in bundle sheath volume. By using a mapping‐by‐sequencing approach the genomic segments that contained mutated candidate genes were identified.
The Differences in Antibiotic Decision-making Between Acute Surgical and Acute Medical Teams: An Ethnographic Study of Culture and Team Dynamics

Abstract Background Cultural and social determinants influence antibiotic decision-making in hospitals. We investigated and compared cultural determinants of antibiotic decision-making in acute medical and surgical specialties. Methods An ethnographic observational study of antibiotic decision-making in acute medical and surgical teams at a London teaching hospital was conducted (August 2015–May 2017). Data collection included 500 hours of direct observations, and face-to-face interviews with 23 key informants. A grounded theory approach, aided by Nvivo 11 software, analyzed the emerging themes. An iterative and recursive process of analysis ensured saturation of the themes. The multiple modes of enquiry enabled cross-validation and triangulation of the findings. Results In medicine, accepted norms of the decision-making process are characterized as collectivist (input from pharmacists, infectious disease, and medical microbiology teams), rationalized, and policy-informed, with emphasis on de-escalation of therapy. The gaps in antibiotic decision-making in acute medicine occur chiefly in the transition between the emergency department and inpatient teams, where ownership of the antibiotic prescription is lost. In surgery, team priorities are split between 3 settings: operating room, outpatient clinic, and ward. Senior surgeons are often absent from the ward, leaving junior staff to make complex medical decisions. This results in defensive antibiotic decision-making, leading to prolonged and inappropriate antibiotic use. Conclusions In medicine, the legacy of infection diagnosis made in the emergency department determines antibiotic decision-making. In surgery, antibiotic decision-making is perceived as a nonsurgical intervention that can be delegated to junior staff or other specialties. Different, bespoke approaches to optimize antibiotic prescribing are therefore needed to address these specific challenges.