Miracle-dz/UniFAR-FTUs huggingface dataset:
Demystifying maintainability

Due to its economic impact "maintainability" is broadly accepted as an important quality attribute of software systems. But in contrast to attributes such as performance and correctness, there is no common understanding of what maintainability actually is, how it can be achieved, measured, or assessed. In fact, every software organization of significant size seems to have its own definition of maintainability. We address this problem by defining an unique two-dimensional quality model that associates maintenance activities with system properties including the capabilities of the organization. The separation of activities and properties facilitates the identification of sound quality criteria and allows to reason about their interdependencies. The resulting quality controlling process enforces these criteria through tool-supported measurements as well as manual inspections. We report on our experiences with the incremental development of the quality model and its application to large scale commercial software projects. Among the positive effects are a slowdown of decay and a significantly increased awareness for long-term quality aspects.
A Serious Game for Training in Emotion Regulation : From Design to Evaluation

Games are often used as training devices in various tasks, but proper biofeedback is more seldom used. Within an EU project it was explored how biofeedback games can target emotion regulation and be evaluated meaningfully. While many use games and biofeedback separately, here the focus was to combine them. This was explored through how the games were perceived and played while players were punished in-game, based on their physiological activity. By implementing games and study the interaction patterns in experimental settings, primarily correlational data was acquired. The results suggest that targeting cognitive constructs has to be validated for each specific game, since game strategies can influence the activation of the cognitive constructs.
Conserved sequence elements involved in regulation of ribosomal protein gene expression in halophilic archaea

A region of the Haloferax volcanii genome encoding ribosomal proteins L11e, L1e, L10e, and L12e was cloned and sequenced, and the transcripts derived from the cluster were characterized. Flanking and noncoding regions of the sequence were analyzed phylogenetically by comparison with the homologous sequences from two other halophilic archaea, i.e., Halobacterium cutirubrum and Haloarcula marismortui. Motifs, identified by high-level sequence conservation, include both transcriptional and translational regulatory elements and other elements of unknown function.
The Gate of the Influenza Virus M2 Proton Channel Is Formed by a Single Tryptophan Residue*

The influenza virus M2proton-selective ion channel is known to be essential for acidifying the interior of virions during virus uncoating in the lumen of endosomes. The M2 protein is a homotetramer that contains four 19-residue transmembrane (TM) domains. These TM domains are multifunctional, because they contain the channel pore and also anchor the protein in membranes. The M2 protein is gated by pH, and thus we have measured pH-gated currents, the accessibility of the pore to Cu2+, and the effect of a protein-modifying reagent for a series of TM domain mutant M2 proteins. The results indicate that gating of the M2 ion channel is governed by a single side chain at residue 41 of the TM domain and that this property is mediated by an indole moiety. Unlike many ion channels where the gate is formed by a whole segment of a protein, our data suggest a model of striking simplicity for the M2 ion channel protein, with the side chain of Trp41 blocking the pore of the M2 channel when pHout is high and with this side chain leaving the pore when pHout is low. Thus, the Trp41 side chain acts as the gate that opens and closes the pore.
Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis

In the Cancer Genome Atlas (TCGA) project, gene expression of the same set of samples is measured multiple times on different microarray platforms. There are two main advantages to combining these measurements. First, we have the opportunity to obtain a more precise and accurate estimate of expression levels than using the individual platforms alone. Second, the combined measure simplifies downstream analysis by eliminating the need to work with three sets of expression measures and to consolidate results from the three platforms. We propose to use factor analysis (FA) to obtain a unified gene expression measure (UE) from multiple platforms. The UE is a weighted average of the three platforms, and is shown to perform well in terms of accuracy and precision. In addition, the FA model produces parameter estimates that allow the assessment of the model fit. The R code is provided in File S2. Gene-level FA measurements for the TCGA data sets are available from http://tcga-data.nci. nih.gov/docs/publications/unified_expression/.
HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1)-infected persons who maintain plasma viral loads of <50 copies RNA/ml without treatment have been termed elite controllers (EC). Factors contributing to durable control of HIV in EC are unknown, but an HLA-dependent mechanism is suggested by overrepresentation of “protective” class I alleles, such as B*27, B*51, and B*57. Here we investigated the relative replication capacity of viruses (VRC) obtained from EC (n = 54) compared to those from chronic progressors (CP; n = 41) by constructing chimeric viruses using patient-derived gag-protease sequences amplified from plasma HIV RNA and inserted into an NL4-3 backbone. The chimeric viruses generated from EC displayed lower VRC than did viruses from CP (P < 0.0001). HLA-B*57 was associated with lower VRC (P = 0.0002) than were other alleles in both EC and CP groups. Chimeric viruses from B*57+ EC (n = 18) demonstrated lower VRC than did viruses from B*57+ CP (n = 8, P = 0.0245). Differences in VRC between EC and CP were also observed for viruses obtained from individuals expressing no described “protective” alleles (P = 0.0065). Intriguingly, two common HLA alleles, A*02 and B*07, were associated with higher VRC (P = 0.0140 and 0.0097, respectively), and there was no difference in VRC between EC and CP sharing these common HLA alleles. These findings indicate that cytotoxic T-lymphocyte (CTL) selection pressure on gag-protease alters VRC, and HIV-specific CTLs inducing escape mutations with fitness costs in this region may be important for strict viremia control in EC of HIV.
An analysis of relapse prevention factors and their ability to predict sustained abstinence following treatment completion.

BACKGROUND & OBJECTIVES This study assessed the role of 14 specific relapse-prevention activities and their underlying factors in maintaining abstinence among subjects (N = 302) completing outpatient treatment for stimulant dependence. METHODS We examined what broader dimensions might subsume the 14 items constituting the Drug Avoidance Activities checklist (Farabee et al. J Subst Abuse Treat 2002;23:343-350), and how well these derived factors predicted concurrent drug use at baseline and again 3 and 12 months later. RESULTS Although four factors were identified consistently for the three time points, only avoidance strategies had sufficient internal consistency to be retained for further analysis. Controlling for age, gender, and ethnicity, the avoidance subscale was a significant predictor of UA results at all time periods: a one-point increase in the avoidance strategies scale was associated with an 86% increase in odds of a negative UA at baseline (OR = 1.86, 95% CI = 1.37-2.53, p < .001), a 77% increase at 3-month follow-up (OR = 1.77, CI = 1.37-2.29, p < .001), and a 37% increase at 12-month follow-up (OR = 1.37, CI = 1.04-1.81, p = .026). CONCLUSIONS Although correlations of individual items with UA results showed statistically significant (p < .05) results for 8 of 14 items at one or more observation points, avoidance-related behaviors showed the strongest associations with sustained abstinence.
A Stronger Consistency for Soft Global Constraints in Weighted Constraint Satisfaction

Weighted Constraint Satisfaction is made practical by powerful consistency techniques, such as AC*, FDAC* and EDAC*, which reduce search space effectively and efficiently during search, but they are designed for only binary and ternary constraints. To allow soft global constraints, usually of high arity, to enjoy the same benefits, Lee and Leung give polynomial time algorithms to enforce generalized AC* (GAC*) and FDAC* (FDGAC*) for projection-safe soft non-binary constraints. Generalizing the stronger EDAC* is less straightforward. In this paper, we first reveal the oscillation problem when enforcing EDAC* on constraints sharing more than one variable. To avoid oscillation, we propose a weak version of EDAC* and generalize it to weak EDGAC* for non-binary constraints. Weak EDGAC* is stronger than FDGAC* and GAC*, but weaker than VAC and soft k-consistency for k > 2. We also show that weak EDGAC* can be enforced in polynomial time for projection-safe constraints. Extensive experimentation confirms the efficiency of our proposal.
Modeling Relationships between Various Domains of Hearing Aid Provision

Various inventories have been developed to quantify the success of hearing aid provision. Though numerous parameters including initial measures (hearing disability, handicap) or ‘outcome measures’ (e.g. benefit, satisfaction and usage) are recorded, relationships and interactions among them are still unclear. A study applying a questionnaire addressing 11 domains relevant to amplification was conducted in order to generate different psychometric models with the AMOS© software package for structural equation modeling. The models expose easily interpretable interactions and are helpful in understanding effects occurring with commonly used outcome measures: benefit reflects the difference between the aided and unaided condition but additionally comprises the importance of the hearing aid within a specific situation. Satisfaction is highly reliant on benefit. Usage is strongly dependent on the severity of hearing problems and therefore not appropriate in assessing the success of amplification. Moreover, the models help to predict the outcome of clinically used inventories (i.e. the Glasgow Hearing Aid Benefit Profile).
A Dose-Response Relation of Headers and Concussions With Cognitive Impairment in Professional Soccer Players

The purpose of this study was to determine the effects of headers and concussions on cognitive impairment in professional soccer players. A group of 84 active professional soccer players from several premier league soccer clubs underwent neuropsychological evaluations. The dose-response relation between the number of headers in one professional season and the number of soccer-related concussions on cognitive functioning was investigated. It was found that the number of headers in one season was related to poorer results on tests measuring focused attention and visual/verbal memory. Soccer-related concussions were related to poorer results on tests measuring sustained attention and visuoperceptual processing. The findings suggest that headers as well as concussions separately contribute to cognitive impairment.
Late deaths and survival after childhood cancer: implications for cure

Abstract Objectives: To investigate causes of death and survival in subjects who had survived at least five years after diagnosis of childhood cancer; to compare observed mortality with that expected in the general population; and to compare results with a corresponding cohort diagnosed earlier. Design : Retrospective cohort study. Setting : Population based National Register of Childhood Tumours. Subjects : 9080 five year survivors of childhood cancer diagnosed in Britain during 1971-85, of whom 793 had died. Comparison with corresponding cohort diagnosed during 1940-70. Main outcome measures : Cause of death established from all available sources of information (including hospital and general practitioner records and postmortem reports) and underlying cause of death coded on death certificate. Results : Of the 781 deaths for which sufficient information was available, death was attributed to recurrent tumour in 578 (74%) cases, treatment related effect in 121 (15%), second primary tumour in 52 (7%), and other causes in 30 (4%). Comparison of observed mortality with that expected in the general population indicated a fourfold excess of deaths from non-neoplasic causes. The risk of dying of recurrent tumour in the next 10 years after surviving five years from diagnosis during 1940-70 and 1971-85 fell from 12% to 8%. The risk of dying from a treatment related effect increased slightly from 1% to 2%. Conclusion : Improvements in five year survival after childhood cancer have been accompanied by a reduction in risk of dying from recurrent tumour during the subsequent 10 years and by a slight increase in risk of dying from treatment related effects. The results provide information relevant to decisions concerning balance between effective treatments and their potentially harmful effects.
Overexpression of the Epidermis-Specific Homeodomain-Leucine Zipper IV Transcription Factor OUTER CELL LAYER1 in Maize Identifies Target Genes Involved in Lipid Metabolism and Cuticle Biosynthesis1[C][W]

Transcription factors of the homeodomain-leucine zipper IV (HD-ZIP IV) family play crucial roles in epidermis-related processes. To gain further insight into the molecular function of OUTER CELL LAYER1 (OCL1), 14 target genes up- or down-regulated in transgenic maize (Zea mays) plants overexpressing OCL1 were identified. The 14 genes all showed partial coexpression with OCL1 in maize organs, and several of them shared preferential expression in the epidermis with OCL1. They encoded proteins involved in lipid metabolism, defense, envelope-related functions, or cuticle biosynthesis and include ZmWBC11a (for white brown complex 11a), an ortholog of AtWBC11 involved in the transport of wax and cutin molecules. In support of the annotations, OCL1-overexpressing plants showed quantitative and qualitative changes of cuticular wax compounds in comparison with wild-type plants. An increase in C24 to C28 alcohols was correlated with the transcriptional up-regulation of ZmFAR1, coding for a fatty acyl-coenzyme A reductase. Transcriptional activation of ZmWBC11a by OCL1 was likely direct, since transactivation in transiently transformed maize kernels was abolished by a deletion of the activation domain in OCL1 or mutations in the L1 box, a cis-element bound by HD-ZIP IV transcription factors. Our data demonstrate that, in addition to AP2/EREBP and MYB-type transcription factors, members of the HD-ZIP IV family contribute to the transcriptional regulation of genes involved in cuticle biosynthesis.
Evaluation of corrosion resistance and surface characteristics of orthodontic wires immersed in different mouthwashes.

BACKGROUND Patients use mouthwashes in addition to mechanical cleaning during orthodontic treatment. The effects of mouthwashes on the archwires have not been examined yet. OBJECTIVE To compare the corrosion resistance of four different arch wires and corrosion effects of different mouthwashes to formulate a biocompatible and mechanically useful arch wire and mouthwash combination. METHODS Each group comprised of 4 wire samples of 2 cm 0.016 × 0.022 inch. 1st group: ion implanted nickel titanium (INT), 2nd group: nickel titanium, without ion implantation (NT), 3rd group: micro layered esthetic nickel titanium (ENT), 4th group: stainless steel (SS) wires. They were immersed inside 2 ml of artificial saliva solutions (AS) for the control, or AS (9%) combined with 1 of the 3 mouthwashes (91%) for study groups, for 24 hours. These mouthwashes were essential oil (EO), chlorhexidine (CHX), sodium-fluoride (NaF). An electrochemical analyzer was used for electrochemical impedance spectroscopy measurements. RESULTS High corrosion resistance was obtained for ENT than the other wires. The corrosion potentials are 0.007, -0.042, 0.074 and -0.015 V (Ag/AgCl) for ENT, INT, SS and NT in the artificial salivary, respectively. In NaF containing mouthwash Rp value of ENT is significantly high in comparison to others. The impedance responses of all materials increased significantly in the presence of NaF mouthwash as well as in the CHX mouthwash. Low frequencies are seen at all materials in EO mouthwash. Diameters of loops are 22, 5.9, 5.9 and 3.7 MΩ at ENT, INT, SS and NT. CONCLUSIONS In this study, micro layered esthetic nickel titanium wires are found biocompatible among other wires and NaF and CHX mouthwashes can be recommend for their good corrosion resistance during fixed orthodontic therapy.
Multidetector CT of the liver and hepatic neoplasms: effect of multiphasic imaging on tumor conspicuity and vascular enhancement.

OBJECTIVE Our aim was to determine which of three contrast-enhanced phases (early arterial, late arterial, or portal venous) was optimal for achieving maximal enhancement of the celiac artery, portal vein, and hepatic parenchyma. We also wanted to learn which phase provided the maximal tumor-to-parenchyma difference when using multidetector CT (MDCT) with fixed timing delays. MATERIALS AND METHODS Fifty-two patients with suspected or known hepatic tumors underwent multiphasic contrast-enhanced MDCT using double arterial (early and late arterial) and venous phase acquisitions with fixed timing delays. All patients were administered 150 mL of IV contrast material at an injection rate of 4 mL/sec. Images were acquired at 20 sec for the early arterial phase, 35 sec for the late arterial phase, and 60 sec for the portal venous phase. Attenuation measurements of the celiac artery, portal vein, normal hepatic parenchyma, and the hepatic tumor were compared. Three reviewers independently and subjectively rated tumor conspicuity for each of the three phases. Ratings were compared using kappa statistics. RESULTS Late arterial phase images showed maximal celiac axis attenuation, whereas portal venous phase images revealed the highest portal vein and normal hepatic parenchymal attenuation. Maximal tumor-to-parenchyma differences for hypovascular tumors was superior in the portal venous phase, but we found no significant differences in maximal tumor-to-parenchyma differences for hypervascular tumors among the evaluated phases. On subjective analysis, interobserver agreement was moderate to very good for the three phases. All three reviewers graded both hypovascular and hypervascular tumor conspicuity as superior in either the late arterial phase or the portal venous phase in most patients. In only one patient was the early arterial phase graded as superior to the late arterial and portal venous phases (by two of the three reviewers). CONCLUSION When MDCT of the liver is performed using fixed timing delays, maximal vascular and hepatic parenchymal enhancement is achieved on either late arterial phase or portal venous phase imaging. In most patients, early arterial phase imaging does not improve tumor conspicuity by either quantitative or subjective analysis.
Systematic G-protein-coupled Receptor Analysis inDrosophila melanogaster Identifies a Leucokinin Receptor with Novel Roles*

Leucokinins are insect neuropeptides that stimulate hindgut motility and renal fluid secretion.Drosophila has a single leucokinin gene, pp, encoding the longest known leucokinin, Drosokinin. To identify its receptor, a genome-wide scan for G-protein-coupled receptors was performed in silico and candidate receptors identified by similarity to known tachykinin receptors. The deduced peptides were expressed, with a transgene for the calcium reporter aequorin, in S2 cells and only one gene (CG10626) encoded a protein that responded to Drosokinin. The properties of the heterologously expressed receptor (action through intracellular calcium with an EC50of 4 × 10−11 m and at 1 2 <1 s) match closely those reported for the action of Drosokinin on Malpighian (renal) tubules. Antibodies raised against the receptor identified known sites of leucokinin action: stellate cells of the Malpighian tubule, two triplets of cells in thepars intercerebralis of the adult central nervous system, and additional cells in larval central nervous system. Western blots and reverse transcription-PCR confirmed these locations, but also identified expression in male and female gonads. These tissues also displayed elevated calcium in response to Drosokinin, demonstrating novel roles for leucokinin. A functional genomic approach has thus yielded the first complete characterization of a leucokinin receptor in an insect.
Electronic Communications of the EASST Volume 10 ( 2008 ) Proceedings of the Seventh International Workshop on Graph Transformation and Visual Modeling Techniques ( GT-VMT 2008 ) The GP Programming System

We describe the programming system for the graph-transform ation language GP, focusing on the implementation of its compiler and abstract machine. We also compare the system’s performance with other graph-tra nsformation systems. The GP language is based on conditional rule schemata and com es with a simple formal semantics which maps input graphs to sets of output gr aphs. The implementation faithfully matches the semantics by using backtr ing and allowing to compute all possible results for a given input.
Alcohol Intake, Type of Beverage, and the Risk of Cerebral Infarction in Young Women

Background and Purpose— The relationship between alcohol consumption and cerebral infarction remains uncertain, and few studies have investigated whether the relationship varies by alcohol type or is present in young adults. We examined the relationship between alcohol consumption, beverage type, and ischemic stroke in the Stroke Prevention in Young Women Study. Methods— All 59 hospitals in the greater Baltimore-Washington area participated in a population-based case-control study of stroke in young women. Case patients (n=224) were aged 15 to 44 years with a first cerebral infarction, and control subjects (n=392), identified by random-digit dialing, were frequency matched by age and region of residence. The interview assessed lifetime alcohol consumption and consumption and beverage type in the previous year, week, and day. ORs were obtained from logistic regression models controlling for age, race, education, and smoking status, with never drinkers as the referent. Results— Alcohol consumption, up to 24 g/d, in the past year was associated with fewer ischemic strokes (<12 g/d: OR 0.57, 95% CI 0.38 to 0.86; 12 to 24 g/d: OR 0.38, 95% CI 0.17 to 0.86; >24 g/d: OR 0.95, 95% CI 0.43 to 2.10) in comparison to never drinking. Analyses of beverage type (beer, wine, liquor) indicated a protective effect for wine consumption in the previous year (<12 g/wk: OR 0.58, 95% CI 0.35 to 0.97; 12 g/wk to <12 g/d: OR 0.55, 95% CI 0.28 to 1.10; ≥12 g/d: OR 0.92, 95% CI 0.23 to 3.64). Conclusions— Light to moderate alcohol consumption appears to be associated with a reduced risk of ischemic stroke in young women.