Miracle-dz/UniFAR-FTUs huggingface dataset:
Verification support for ARINC‐653‐based avionics software

Software model checking consists in applying the most powerful results in formal verification research to programming languages such as C. One general technique to implement this approach is producing a reduced model of the software in order to employ existing and efficient tools, such as SPIN. This paper focusses on the application of this approach to the avionics software constructed on top of the Application Executive Software (APEX) Interface, which is widely employed by manufacturers in the avionics industry. It presents a method to automatically extract PROMELA models from the C source code. In order to close the extracted model during verification, we built a reusable APEX‐specific environment. This APEX environment models the execution engine (i.e. an APEX compliant real‐time operating system) that implements APEX services. In particular, it explains how to deal with aspects such as real‐time and APEX scheduling. Time is modelled in such a way that the we save time and memory by avoiding the analysis of irrelevant steps. This model of time and the construction of a deterministic scheduler guarantees the scalability of our approach. The paper also presents a tool that can verify realistic applications, and that has been used as a novel testing method to ensure the correctness of our APEX environment. This testing method uses SPIN to execute official APEX test cases. Copyright © 2010 John Wiley & Sons, Ltd.
A Novel Target and Approach for Identifying Antivirals against Molluscum Contagiosum Virus

ABSTRACT The dermatological disease molluscum contagiosum (MC) presents as lesions restricted solely to the skin. The poxvirus molluscum contagiosum virus (MCV) is responsible for this skin disease that is easily transmitted through casual contact among all populations, with greater frequency in children and immunosuppressed individuals. In addition, sexual transmission of MCV in adolescents and adults is a health concern. Although the skin lesions ultimately resolve in immunocompetent individuals, they can persist for extended periods, be painful, and result in scarring. Treatment is problematic, and there is no drug that specifically targets MCV. The inability of MCV to propagate in cell culture has impeded drug development. To overcome these barriers, we integrated three new developments. First, we identified a new MCV drug target (mD4) that is essential for processive DNA synthesis in vitro. Second, we discovered a small chemical compound that binds to mD4 and prevents DNA synthesis in vitro. Third, and most significant, we engineered a hybrid vaccinia virus (mD4-VV) in which the natural vaccinia D4 (vD4) gene is replaced by the mD4 target gene. This hybrid virus is dependent on mD4 for viral growth in culture and is inhibited by the small compound. This target system provides, for the first time, a platform and approach for the discovery and evaluation of new therapeutics that can be used to treat MC.
Role of the G Protein-Coupled Receptor, mGlu1, in Melanoma Development

Melanoma remains one of the cancers for which a decline in morbidity has not been achieved with current scientific and medical advances. Mono-therapies targeting melanoma have been largely ineffective, increasing the need for identification of new drugable targets. Multiple tumor suppressors and oncogenes that impart genetic predisposition to melanoma have been identified and are being studied in an attempt to provide insight on the development of anti-melanoma therapies. Metabotropic Glutamate Receptor I (GRM1) has recently been implicated as a novel oncogene involved in melanomagenesis. GRM1 (mGlu1, protein) belongs to the G protein coupled receptor (GPCR) super family and is normally functional in the central nervous system. Our group showed in a transgenic mouse model system that ectopic expression of Grm1 in melanocytes is sufficient to induce spontaneous melanoma development in vivo. GPCRs are some of the most important therapeutic drug targets discovered to date and they make up a significant proportion of existing therapies. This super family of transmembrane receptors has wide spread expression and interacts with a diverse array of ligands. Diverse physiological responses can be induced by stimulator(s) or suppressor(s) of GPCRs, which contributes to their attractiveness in existing and emerging therapies. GPCR targeting therapies are employed against a variety of human disorders including those of the central nervous system, cardiovascular, metabolic, urogenital and respiratory systems. In the current review, we will discuss how the identification of the oncogenic properties of GRM1 opens up new strategies for the design of potential novel therapies for the treatment of melanoma.
Performance-driven processor allocation

In current multiprogrammed multiprocessor systems, to take into account the performance of parallel applications is critical to decide an efficient processor allocation. In this paper, we present the performance-driven processor allocation policy (PDPA). PDPA is a new scheduling policy that implements a processor allocation policy and a multiprogramming-level policy, in a coordinated way, based on the measured application performance. With regard to the processor allocation, PDPA is a dynamic policy that allocates to applications the maximum number of processors to reach a given target efficiency. With regard to the multiprogramming level, PDPA allows the execution of a new application when free processors are available and the allocation of all the running applications is stable, or if some applications show bad performance. Results demonstrate that PDPA automatically adjusts the processor allocation of parallel applications to reach the specified target efficiency, and that it adjusts the multiprogramming level to the workload characteristics. PDPA is able to adjust the processor allocation and the multiprogramming level without human intervention, which is a desirable property for self-configurable systems, resulting in a better individual application response time.
Determination of rule weights of fuzzy association rules

In this paper, first we extend two basic measures of association rules in data mining (i.e, confidence and support) to the case of fuzzy association rules. The main difference between standard and fuzzy association rules is the discretization of continuous variables. While continuous variables are divided into intervals for generating standard association rules, they are divided into linguistic values in the case of fuzzy association rules. Next we examine two specifications of rule weights of fuzzy association rules for pattern classification problems. One is the direct use of the confidence as a rule weight. The other is based on a slightly complicated formulation where the rule weight of each fuzzy association role is discounted by the confidence or other rules with the same antecedent conditions and different consequent classes. Through computer simulations on a pattern classification problem with many continuous attributes, we compare these two definitions with each other. Simulation results show that the direct use of the confidence is inferior to the other definition of rule weights. Then we examine three rule selection criteria (i.e., confidence, support, and their product). It is shown that good fuzzy association rules are extracted from numerical data using the product criterion. Finally we compare the performance of fuzzy association rules with that of standard association rules.
Global hydrobelts and hydroregions: improved reporting scale for water-related issues?

Global-scale water issues such as its availability, water needs or stress, or management, are mapped at various resolutions and reported at many scales, mostly along polit- ical or continental boundaries. As such, they ignore the fun- damental heterogeneity of hydroclimates and natural bound- aries of river basins. Here we describe the continental land- masses at two levels: eight hydrobelts strictly limited by river basins, defined at a 30 0 (0.5 ) resolution, which are decom- posed on continents as 26 hydroregions. The belts were de- fined and delineated, based primarily on the annual average temperature (T ) and run-off (q), to maximise inter-belt dif- ferences and minimise intra-belt variability. This new global puzzle defines homogeneous and near- contiguous entities with similar hydrological and thermal regimes, glacial and postglacial basin histories, endorheism distribution and sensitivity to climate variations. The mid- latitude, dry and subtropical belts have northern and southern analogues and a general symmetry can be observed forT and q between them. The boreal and equatorial belts are unique. Population density between belts and between the continents varies greatly, resulting in pronounced differences between the belts with analogues in both hemispheres. Hydroregions (median size 4.7 M km 2 ) are highly con- trasted, with the average q ranging between 6 and 1393 mm yr 1 and the average T between 9.7 and +26.3 C, and a population density ranging from 0.7 to 0.8 p km 2 for the North American boreal region and some Australian hydroregions to 280 p km 2 for some Asian hy- droregions. The population/run-off ratio, normalised to a reference pristine region, is used to map and quantify the global population at risk of severe water quality degradation. Our initial tests suggest that hydrobelt and hydroregion divi- sions are often more appropriate than conventional continen- tal or political divisions for the global analysis of river basins within the Earth system and of water resources. The GIS files of the hydrobelts and hydroregions are available at the supplement of this article and at doi:10.1594/PANGAEA.806957 as well as geotypes.net.
Financial incentives for patients in the treatment of psychosis

Poor medication adherence in patients with a psychosis is associated with relapse. It has been proposed that outcomes might be improved by using financial incentives for treatment adherence (FITA). However, a strong moral intuition against this practice has been found. This paper examines the ethics of FITA. Three arguments are presented, which if accepted would severely restrict or even prohibit the practice. These are based on (1) “incommensurable values”, where FITA denigrates an aspect of “respect for the person”, (2) “exploitation”, where unfair advantage is taken of the patient, and (3) “fairness”, where it is difficult to draw a line between those who should and should not be offered payment. A number of practical impediments are also considered.
A new species of Pestalotiopsis from leaf spots of Licuala grandis from Hainan, China

A new species, Pestalotiopsis licualacola, was isolated from grey leafspots of Licuala grandis (ruffled fan palm). It is morphologically distinct in having relatively small, greyish brown conidia (16–20 × 3–5 μm), and 1–3 short apical appendages without knobs. Phylogenetic analysis based on combination of ITS, β-tubulin and tef1 gene sequence data clearly distinguishes P. licualacola from other species in this genus, with ex-type sequence data in GenBank. Based on morphology and molecular phylogeny we describe it as a new species.
Age-dependent effect of Alzheimer’s risk variant of CLU on EEG alpha rhythm in non-demented adults

Polymorphism in the genomic region harboring the CLU gene (rs11136000) has been associated with the risk for Alzheimer’s disease (AD). CLU C allele is assumed to confer risk for AD and the allele T may have a protective effect. We investigated the influence of the AD-associated CLU genotype on a common neurophysiological trait of brain activity (resting-state alpha-rhythm activity) in non-demented adults and elucidated whether this influence is modified over the course of aging. We examined quantitative electroencephalography (EEG) in a cohort of non-demented individuals (age range 20–80) divided into young (age range 20–50) and old (age range 51–80) cohorts and stratified by CLU polymorphism. To rule out the effect of the apolipoprotein E (ApoE) genotype on EEG characteristics, only subjects without the ApoE ε4 allele were included in the study. The homozygous presence of the AD risk variant CLU CC in non-demented subjects was associated with an increase of alpha3 absolute power. Moreover, the influence of CLU genotype on alpha3 was found to be higher in the subjects older than 50 years of age. The study also showed age-dependent alterations of alpha topographic distribution that occur independently of the CLU genotype. The increase of upper alpha power has been associated with hippocampal atrophy in patients with mild cognitive impairment (Moretti etal., 2012a). In our study, the CLU CC-dependent increase in upper alpha rhythm, particularly enhanced in elderly non-demented individuals, may imply that the genotype is related to preclinical dysregulation of hippocampal neurophysiology in aging and that this factor may contribute to the pathogenesis of AD.
Changes in antioxidant enzyme activities of European mistletoe (Viscum album L. subsp. album) leaves as a response to environmental stress caused by pollution of the atmosphere by nitrogen dioxide

In the present study we investigated the seasonal pattern of activity of antioxidant enzymes such as superoxide dismutase (SOD) catalase (CAT) ascorbate peroxidase (APX), guaiacol peroxidase (POD) and syringaldazine peroxidase (SPOD) as well as the total protein concentration in the European mistletoe (Viscum album L. subsp. album). We studied mistletoe leaves that grew on the selected tree species in different parts the city of Lodz, exposed to a greater or lesser extent to the nitrogen dioxide. Sampling campaigns were conducted during the growing season 2013 in early May (at the beginning of the growing season) and in November (at the end of the growing season). We showed considerable seasonal variations of antioxidant enzymatic activity and total protein concentrations for all the samples studied. The test parameters varied depending on the host plants exposition to pollution with nitrogen dioxide. The changes in enzymatic activity did not depend on the host plants. In mistletoe leaves greater changes of SOD activity and total protein concentration were observed in autumn. There is correlation between the level of nitrogen dioxide in atmosphere and activities the enzymes. SOD activity was signifi cantly higher in autumn when the host plants were defoliated. Increased CAT activity was observed in late spring. We demonstrated the positive correlation between changes in enzyme activities and the progress of growing season. Increased activities of POD, CAT and APX to a limited extent depended on the place of growing and exposition to air pollution. In late spring activity of the enzymes did not signifi cant grow because of the protective umbrella from host plant leaves preventing the access of nitrogen dioxide to mistletoe. The higher SOD activity in mistletoe is a consequence of oxidative stress causes by nitrogen dioxides evidently observed in the city center. The test parameters, mainly the activity of SOD, can be used in the future as markers of the *e-mail: jacpat@biol.uni. lodz.pl DOI: 10.15244/pjoes/60720 726 Patykowski J.G. , Kołodziejek J.
A User Study on the Automated Assessment of Reviews

Reviews are text-based feedback provided by a reviewer to the author of a submission. Reviews play a crucial role in providing feedback to people who make assessment decisions (e.g. deciding a student’s grade, purchase decision of a product). It is therefore important to ensure that reviews are of a good quality. In our work we focus on the study of academic reviews. A review is considered to be of a good quality if it can help the author identify mistakes in their work, and help them learn possible ways of fixing them. Metareviewing is the process of evaluating reviews. An automated metareviewing process could provide quick and reliable feedback to reviewers on their assessment of authors’ submissions. Timely feedback on reviews could help reviewers correct their assessments and provide more useful and effective feedback to authors. In this paper we investigate the usefulness of metrics such as review relevance, content type, tone, quantity and plagiarism in determining the quality of reviews. We conducted a study on 24 participants, who used the automated assessment feature on Expertiza, a collaborative peer-reviewing system. The aim of the study is to identify reviewers’ perception of the usefulness of the automated assessment feature and its different metrics. Results suggest that participants find relevance to be the most important and quantity to be the least important in determining a review’s quality. Participants also found the system’s feedback from metrics such as content type and plagiarism to be most useful and informative.
Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal

ABSTRACT To date Borrelia lusitaniae is the only genospecies ofBorrelia burgdorferi sensu lato isolated from Ixodes ricinus ticks collected in Portugal and Tunisia. This suggests that the genospecies diversity of B. burgdorferi sensu lato decreases toward the southwestern margin of its Old World subtropical range. In order to further explore the genetic diversity of B. burgdorferi sensu lato from this region, 55 I. ricinus and 27 Hyalomma marginatum questing adults, collected during the spring of 1998 from a sylvatic habitat south of Lisbon, Portugal, were analyzed. Infection prevalences of 75% inI. ricinus ticks and 7% in H. marginatum ticks were detected by a nested PCR that targets the rrf(5S)-rrl (23S) spacer of B. burgdorferi sensu lato. Restriction fragment length polymorphism (RFLP) analysis of theI. ricinus-derived amplicons showed that the sequences in the majority of samples were similar to those of B. lusitaniae type strains (76% for strain PotiB1, 5% for strain PotiB3). Two novel RFLP patterns were obtained from 12% of the samples. The remaining 7% of samples gave mixed RFLP patterns. Phylogenetic analysis of rrf-rrl spacer sequences revealed a diverse population of B. lusitaniae in questing adultI. ricinus ticks (the sequences did not cluster with those of any other genospecies). This population consisted of 10 distinct sequence types, suggesting that multiple strains of B. lusitaniae were present in the local I. ricinuspopulation. We hypothesize that B. lusitaniae has a narrow ecological niche that involves host species restricted to the Mediterranean Basin.
Some time-space relationships for crustal melting and granitic intrusion at various depths

Abstract Crustal melting occurs at the higher grades of metamorphism. Migmatites reflect crustal anatexis without necessary additional heat supply. Granites usually result from crustal melting resulting from ‘hot’ geotherms, or reflect an external heat supply. The commonest mechanisms of crustal melting are: (i) decompression of crust thickened into mantle in convergent orogens; (ii) asthenosphere upwelled beneth the crust in extensional orogens; (iii) massive invasion or underplating of crust by mantle magma generated by mantle decompression. This paper considers some of the processes governing timescales and lengthscales of these various magmatic events with particular view to determining the intensity and duration of crustal melting, and relationships between the rates of melt extraction, ascent and emplacement.
Permeability and calcium signaling in lung endothelium: unpack the box…

This brief review assesses the role of Ca2+ signaling in lung endothelium in regulation of endothelial permeability. The disconnect between experimental and clinical outcomes to date may be due, in part, to the use of tools which yield information about aggregate permeability or Ca2+ responses in lung or in endothelial monolayers. The teaching point of this review is to “unpack the box,” i.e. consider the many potential issues which could impact interpretation of outcomes. These include phenotypic heterogeneity and resultant segment-specific permeability responses, methodologic issues related to permeability measures, contributions from Ca2+ channels in cells other than endothelium—such as alveolar macrophages or blood leukocytes), Ca2+ dynamic patterns, rather than averaged Ca2+ responses to channel activation, and the background context, such as changes in endothelial bioenergetics with sepsis. Any or all of these issues might color interpretation of permeability and Ca2+ signaling in lung.
Extending the Algebraic Framework of Query Processing to Handle Outerjoins

A crucial part of relational query optimization is the reordering of query processing for more efficient query evaluation. The reordering may be explicit or implicit. Our major goal in this paper is to describe manipulation rules for queries that include outerjoins, and views or nested subqueries. By expressing queries and processing Strategies in terms of relational algebra, one can use the ordinary mechanisms of query optimization and view substitution with a minimum of disrupt ion. We also aggregate operators, universal sorting.
Selective export of human GPI-anchored proteins from the endoplasmic reticulum

Selective export of transmembrane proteins from the endoplasmic reticulum (ER) relies on recognition of cytosolic-domain-localized transport signals by the Sec24 subunit of the COPII vesicle coat. Human cells express four Sec24 isoforms, termed Sec24A, Sec24B, Sec24C and Sec24D that are differentially required for selective, signal-mediated ER export of transmembrane proteins. By contrast, luminally exposed glycosylphosphatidylinositol (GPI)-anchored membrane proteins cannot bind directly to Sec24 and must either use membrane-spanning cargo receptors or alternative mechanisms for ER export. Little is known about the mechanism underlying export of GPI-anchored proteins from the ER in higher eukaryotes. Using siRNA-based silencing, we identified that ER-to-Golgi transport of the human GPI-anchored protein CD59 requires Sec24, with preference for the Sec24C and Sec24D isoforms, and the recycling transmembrane protein complex p24-p23 that exhibited the same Sec24C-Sec24D isoform preference for ER export. Co-immunoprecipitation indicated unprecedented physical interaction of CD59 as well as a GFP-folate-receptor-GPI-anchor hybrid with a p24-p23 complex. Density gradient centrifugation revealed co-partitioning of CD59 and p24-p23 into biosynthetically early lipid raft fractions, and CD59 transport to the Golgi was cholesterol dependent. The results suggest that the 24p-23p complex acts as a cargo receptor for GPI-anchored proteins by facilitating their export from the ER in a Sec24-isoform-selective manner involving lipid rafts as early sorting platforms.
History of medical mycology in the united states

INTRODUCTION 237 THE ERA OF DISCOVERY, 1894 TO 1919 237 Overview, 1894 to 1900 237 Scientific Contributions, 1894 to 1900 237 Blastomycosis 237 Coccidioidomycosis 239 Sporotrichosis 239 Mycotic mycetoma 239 Dermatophytosis 239 Overview, 1900 to 1919 239 Scientific Contributions, 1900 to 1919 239 Coccidioidomycosis 239 Sporotrichosis 240 Blastomycosis 240 Histoplasmosis 240 Chromoblastomycosis 240 Zygomycosis 241 THE FORMATIVE YEARS, 1920 TO 1949 241 Overview, 1920 to 1929 241 Scientific Contributions, 1920 to 1929 241 Mycotic mycetoma 241 Cryptococcosis 241 Histoplasmosis 241 Sporotrichosis, an occupational disease 241 Laboratory diagnosis 242 Skin test development 242 First training and research center 242 Overview, 1930 to 1939 242 Scientific Contributions, 1930 to 1939 242 Coccidioidomycosis 242 Meningeal infections 243 Histoplasmosis 243 Chromoblastomycosis 243 Taxonomy and classification 243 Fungal endotoxins 244 Training and research centers 244 Overview, 1940 to 1949 244 Scientific Contributions, 1940 to 1949 244 Systemic candidiasis 244 Zygomycosis 244 Mycotic mycetoma 244 Pseudallescheriasis 244 Epidemiology and ecology 245 Laboratory diagnosis 245 Antifungal agents 245 Training and research centers 245 THE ADVENT OF ANTIFUNGAL AND IMMUNOSUPPRESSIVE THERAPIES, 1950 TO 1969 246 Overview, 1950 to 1959 246 Scientific Contributions, 1950 to 1959 246 Opportunistic fungal infections in compromised patients 246