Miracle-dz/UniFAR-FTUs huggingface dataset:
Variability and Complexity in Software Design: Towards a Research Agenda

Many of todayâs software systems accommodate different usage and deployment scenarios. Intentional and unintentional variability in functionality or quality attributes (e.g., performance) of software significantly increases the complexity of the problem and design space of those systems. The complexity caused by variability becomes increasingly difficult to handle due to the increasing size of software systems, new and emerging application domains, dynamic operating conditions under which software systems have to operate, fast moving and highly competitive markets, and more powerful and versatile hardware. This paper reports results of the first International Workshop on Variability and Complexity in Software Design that brought together researchers and engineers interested in the topic of complexity and variability. It also outlines directions the field might move in the future
Lessons From the Testosterone Trials

The Testosterone Trials (TTrials) were a coordinated set of seven placebo-controlled, double-blind trials in 788 men with a mean age of 72 years to determine the efficacy of increasing the testosterone levels of older men with low testosterone. Testosterone treatment increased the median testosterone level from unequivocally low at baseline to midnormal for young men after 3 months and maintained that level until month 12. In the Sexual Function Trial, testosterone increased sexual activity, sexual desire, and erectile function. In the Physical Function Trial, testosterone did not increase the distance walked in 6 minutes in men whose walk speed was slow; however, in all TTrial participants, testosterone did increase the distance walked. In the Vitality Trial, testosterone did not increase energy but slightly improved mood and depressive symptoms. In the Cognitive Function Trial, testosterone did not improve cognitive function. In the Anemia Trial, testosterone increased hemoglobin in both men who had anemia of a known cause and in men with unexplained anemia. In the Bone Trial, testosterone increased volumetric bone mineral density and the estimated strength of the spine and hip. In the Cardiovascular Trial, testosterone increased the coronary artery noncalcified plaque volume as assessed using computed tomographic angiography. Although testosterone was not associated with more cardiovascular or prostate adverse events than placebo, a trial of a much larger number of men for a much longer period would be necessary to determine whether testosterone increases cardiovascular or prostate risk.
In silico binding mechanism prediction of benzimidazole based corticotropin releasing factor-1 receptor antagonists by quantitative structure activity relationship, molecular docking and pharmacokinetic parameters calculation

Despite the various research efforts toward the treatment of stress-related disorders, the drug has not yet launched last 20 years. Corticotropin releasing factor-1 receptor antagonists have been point of great interest in stress-related disorders. In the present study, we have selected benzazole scaffold-based compounds as corticotropin releasing factor-1 antagonists and performed 2D and 3D QSAR studies to identify the structural features to elucidating the binding mechanism prediction. The best 2D QSAR model was obtained through multiple linear regression method with r 2 value of . 7390, q 2 value of . 5136 and pred_r 2 (predicted square correlation coefficient) value of . 88. The contribution of 2D descriptor, T_2_C_1 was 60% (negative contribution) and 4pathClusterCount was 40.24% (positive contribution) in enhancing the activity. Also 3D QSAR model was statistically significant with q 2 value of . 9419 and q 2_se (standard error of internal validation) value of . 19. Statistical parameters results prove the robustness and significance of both models. Further, molecular docking and pharmacokinetic analysis was performed to explore the scope of investigation. Docking results revealed that the all benzazole compounds show hydrogen bonding with residue Asn283 and having same hydrophobic pocket (Phe286, Leu213, Ile290, Leu287, Phe207, Arg165, Leu323, Tyr327, Phe284, and Met206). Compound B14 has higher activity compare to reference molecules. Most of the compounds were found within acceptable range for pharmacokinetic parameters. This work provides the extremely useful leads for structural substituents essential for benzimidazole moiety to exhibit antagonistic activity against corticotropin releasing factor-1 receptors.
Fibroblast Growth Factor 23 is Associated With Adiposity in Patients Receiving Hemodialysis: Possible Cross Talk Between Bone and Adipose Tissue.

OBJECTIVE Fibroblast growth factor 23 (FGF-23) may be involved in signaling between bone and adipose tissue in dialysis patients, but its role is uncertain. We sought to examine the association between FGF-23 and adiposity and whether this association is mediated in part by leptin. DESIGN/SETTING We performed univariate and multivariate linear regression analyses using data from 611 participants in a cohort of prevalent hemodialysis patients recruited from dialysis centers in Atlanta, GA and San Francisco, CA from 2009 to 2011. We also investigated the role of leptin in these relationships. SUBJECTS Participants were aged ≥18 years, English or Spanish speaking, and receiving hemodialysis for at least 3 months. MAIN OUTCOME MEASURES Outcome measures of adiposity included body mass index, waist circumference, and body fat measured by bioelectrical impedance spectroscopy. RESULTS Mean age was 56 ± 14 years, 39.8% were female, and median serum FGF-23 was 807 pg/mL. In fully adjusted models, FGF-23 was inversely associated with body mass index (-0.24 kg/m2 per 50% higher FGF-23, 95% confidence interval [CI]: -0.38 to -0.10), waist circumference (-0.44 cm per 50% higher FGF-23, 95% CI: -0.79 to -0.08), and percent body fat (-0.58% per 50% higher FGF-23, 95% CI: -0.79 to -0.37). Leptin was inversely associated with FGF-23. Addition of leptin to body composition models attenuated the associations between FGF-23 and measures of adiposity, but FGF-23 remained significantly associated with percent body fat (-0.17% per 50% higher FGF-23, 95% CI: -0.32 to -0.02). CONCLUSION We found a negative association between FGF-23 and adiposity that appears to be mediated in part by leptin. As adipose tissue provides a "protective energy depot" for patients with chronic illness, a decrease in adipose tissue may be one mechanism in which higher FGF-23 levels may contribute to increased mortality in dialysis patients.
Advance care planning for patients with amyotrophic lateral sclerosis

Abstract Purpose: To determine whether an advance care planning (ACP) decision-aid could improve communication about end-of-life treatment wishes between patients with amyotrophic lateral sclerosis (ALS) and their clinicians. Methods: Forty-four patients with ALS (>21, English-speaking, without dementia) engaged in ACP using an interactive computer based decision-aid. Before participants completed the intervention, and again three months later, their clinicians reviewed three clinical vignettes, and made treatment decisions (n = 18) for patients. After patients indicated their agreement with the team’s decisions, concordance was calculated. Results: The mean concordance between patient wishes and the clinical team decisions was significantly higher post-intervention (post = 91.9%, 95% CI = 87.8, 96.1, vs. pre = 52.4%, 95% CI = 41.9, 62.9; p <0.001). Clinical team members reported greater confidence that their decisions accurately represented each patient’s wishes post-intervention (mean = 6.5) compared to pre-intervention (mean = 3.3, 1 = low, 10 = high, p <0.001). Patients reported high satisfaction (mean = 26.4, SD = 3.2; 6 = low, 30 = high) and low decisional conflict (mean = 28.8, SD = 8.2; 20 = low, 80 = high) with decisions about end-of-life care, and high satisfaction with the decision-aid (mean = 52.7, SD = 5.7, 20 = low, 60 = high). Patient knowledge regarding ACP increased post-intervention (pre = 47.8% correct responses vs. post = 66.3%; p <0.001) without adversely affecting patient anxiety or self-determination. Conclusion: A computer based ACP decision-aid can significantly improve clinicians’ understanding of ALS patients’ wishes with regard to end-of-life medical care.
Molecular and Quantitative Genetic Differentiation in Sitobion avenae Populations from Both Sides of the Qinling Mountains

Quantitative trait differences are often assumed to be correlated with molecular variation, but the relationship is not certain, and empirical evidence is still scarce. To address this issue, we sampled six populations of the cereal aphid Sitobion avenae from areas north and south of the Qinling Mountains, and characterized their molecular variation at seven microsatellite loci and quantitative variation at nine life-history traits. Our results demonstrated that southern populations had slightly longer developmental times of nymphs but much higher lifetime fecundity, compared to northern populations. Of the nine tested quantitative characters, eight differed significantly among populations within regions, as well as between northern and southern regions. Genetic differentiation in neutral markers was likely to have been caused by founder events and drift. Increased subdivision for quantitative characters was found in northern populations, but reduced in southern populations. This phenomenon was not found for molecular characters, suggesting the decoupling between molecular and quantitative variation. The pattern of relationships between FST and QST indicated divergent selection and suggested that local adaptation play a role in the differentiation of life-history traits in tested S. avenae populations, particularly in those traits closely related to reproduction. The main role of natural selection over genetic drift was also supported by strong structural differences in G-matrices among S. avenae populations. However, cluster analyses did not result in two groups corresponding to northern and southern regions. Genetic differentiation between northern and southern populations in neutral markers was low, indicating considerable gene flow between them. The relationship between molecular and quantitative variation, as well as its implications for differentiation and evolution of S. avenae populations, was discussed.
Fast lesion mapping during HIFU treatment using harmonic motion imaging guided focused ultrasound (HMIgFUS) in vitro and in vivo

The successful clinical application of high intensity focused ultrasound (HIFU) ablation depends on reliable monitoring of the lesion formation. Harmonic motion imaging guided focused ultrasound (HMIgFUS) is an ultrasound-based elasticity imaging technique, which monitors HIFU ablation based on the stiffness change of the tissue instead of the echo intensity change in conventional B-mode monitoring, rendering it potentially more sensitive to lesion development. Our group has shown that predicting the lesion location based on the radiation force-excited region is feasible during HMIgFUS. In this study, the feasibility of a fast lesion mapping method is explored to directly monitor the lesion map during HIFU. The harmonic motion imaging (HMI) lesion map was generated by subtracting the reference HMI image from the present HMI peak-to-peak displacement map, as streamed on the computer display. The dimensions of the HMIgFUS lesions were compared against gross pathology. Excellent agreement was found between the lesion depth (r2 = 0.81, slope = 0.90), width (r2 = 0.85, slope = 1.12) and area (r2 = 0.58, slope = 0.75). In vivo feasibility was assessed in a mouse with a pancreatic tumor. These findings demonstrate that HMIgFUS can successfully map thermal lesions and monitor lesion development in real time in vitro and in vivo. The HMIgFUS technique may therefore constitute a novel clinical tool for HIFU treatment monitoring.
Bves, a member of the Popeye domain‐containing gene family

Bves was discovered through subtractive screens designed to identify heart‐enriched transcripts. Bves is a transmembrane protein that possesses a highly conserved structure among species of the animal kingdom. Various approaches have been used to elucidate the expression pattern of Bves mRNA and protein as well as its function in developing and mature organisms. Emerging evidence indicates that this protein is present in muscle and epithelia of developing embryos and the adult. In vitro functional studies predict a role in cell–cell interaction and/or adhesion. In vivo analysis of protein function is very limited at present, but recent work in Xenopus supports the importance of Bves in epithelial integrity. Presented in this review is a compilation of published findings concerning Bves gene and protein characteristics, expression patterns in embryos and cells, and functional significance as determined thus far. Presently, the literature supports a hypothesis that Bves is essential to the junctional architecture of muscle and epithelial cell types. Although there remain aspects of Bves structure, expression, and function that are not completely resolved, now is an appropriate time to summarize current knowledge about this protein, the remaining questions, and what its potential role in development might be. This review will serve as a departure point for others who become interested in the study of this highly conserved protein. Developmental Dynamics 235:586–593, 2006. © 2006 Wiley‐Liss, Inc.
Improving Text Categorization with Semantic Knowledge in Wikipedia

SUMMARY Text categorization, especially short text categorization, is a di ﬃ cult and challenging task since the text data is sparse and multidimensional. In traditional text classiﬁcation methods, document texts are represented with “Bag of Words (BOW)” text representation schema, which is based on word co-occurrence and has many limitations. In this paper, we mapped document texts to Wikipedia concepts and used the Wikipedia-concept-based document representation method to take the place of traditional BOW model for text classiﬁcation. In order to overcome the weakness of ignoring the semantic relationships among terms in document representation model and utilize rich semantic knowledge in Wikipedia, we constructed a semantic matrix to enrich Wikipedia-concept-based document representation. Experimental evaluation on ﬁve real datasets of long and short text shows that our approach outperforms the traditional BOW method.
RECoVar: A solution framework towards reverse engineering variability

As a Software Product Line (SPL) evolves variability specifications in problem space and variability realizations in solution space erode over time and impact productivity during development. On the one hand, the variability model tends to be incomplete and inconsistent with the core assets; on the other hand, the core assets become overly complex, which make them difficult to understand and maintain. In this paper, we present the RECoVar framework towards reverse engineering of SPL variability. The framework includes two approaches: a) code-based variability model extraction; and b) complex feature correlation mining. These two approaches help to extract various variability information, so that variability specifications and realizations can be maintained in an efficient way.
Microscopic colitis in patients with ulcerative colitis or Crohn’s disease: a retrospective observational study and review of the literature

Abstract Objectives: Onset of microscopic colitis (MC) in patients with ulcerative colitis (UC) or Crohn’s disease (CD), or vice versa, has been reported occasionally but the subject is not well described. We therefore report a retrospective observational study of such patients and review the literature. Methods: Forty-six Swedish gastroenterology clinics were contacted about patients with diagnoses of both inflammatory bowel disease (IBD) and MC. Publications were searched on PubMed. Results: We identified 31 patients with onset of MC after a median (range) of 20 (2–52) years after diagnosis of IBD, or vice versa; 21 UC patients developed collagenous colitis (CC) (n = 16) or lymphocytic colitis (LC) (n = 5); nine CD patients developed CC (n = 5) or LC (n = 4); one CC patient developed CD. Of the 21 UC patients, 18 had extensive disease, whereas no consistent phenotype occurred in CD. Literature review revealed 27 comprehensive case reports of patients with diagnoses of both IBD and MC. Thirteen MC patients developed IBD, of which four required colectomy. Fourteen IBD patients later developed MC. There were incomplete clinical data in 115 additional reported patients. Conclusions: Altogether 173 patients with occurrence of both IBD and MC were found. The most common finding in our patients was onset of CC in a patient with UC. Although these are likely random associations of two different disorders, MC should be considered in the patient with UC or CD if there is onset of chronic watery diarrhoea without endoscopic relapse of IBD.
Self-optimization of Infrastructure and Platform Resources in Cloud Computing. (Auto-optimisation des ressources des couches infrastructure et plate-forme du Cloud computing)

Elasticity is considered as an important solution to handle the performance issues in scalable distributed system. However, most of the researches of elasticity only concern the provisioning and de-provisioning resources in automatic ways, but always ignore the resource utilization of provisioned resources. This might lead to resource leaks while provisioning redundant resources, thereby causing unnecessary expenditure. To avoid the resource leaks and redundant resources, my research therefore focus on how to maximize resource utilization by self resource management. In this thesis, relevant to diverse problems of resource usage and allocation in different layers, I propose two resource management approaches corresponding to infrastructure and platform, respectively. To overcome infrastructure limitation, I propose CloudGC as middleware service which aims to free occupied resources by recycling idle VMs. In platform-layer, a self-balancing approach is introduced to adjust Hadoop configuration at runtime, thereby avoiding memory loss and dynamically optimizing Hadoop performance. Finally, this thesis concerns rapid deployment of service which is also an issue of elasticity. A new tool, named « hadoop-benchmark », applies docker to accelerate the installation of Hadoop cluster and to provide a set of docker images which contain several well-known Hadoop benchmarks. The assessments show that these approaches and tool can well achieve resource management and self-optimization in various layers, and then facilitate the elasticity of infrastructure and platform in scalable platform, such as Cloud computing.
Short‐ and long‐term effects on mAb‐producing CHO cell lines after cryopreservation

Cryopreservation provides the foundation for research, development, and manufacturing operations in the CHO‐based biopharmaceutical industry. Despite its criticality, studies are lacking that explicitly demonstrate that the routine cell banking process and the potential stress and damage during cryopreservation and recovery from thaw have no lasting detrimental effects on CHO cells. Statistics are also scarce on the decline of cell‐specific productivity (Qp) over time for recombinant CHO cells developed using the glutamine synthetase (GS)‐based methionine sulfoximine (MSX) selection system. To address these gaps, we evaluated the impact of freeze‐thaw on 24 recombinant CHO cell lines (generated by the GS/MSX selection system) using a series of production culture assays. Across the panel of cell lines expressing one of three monoclonal antibodies (mAbs), freeze‐thaw did not result in any significant impact beyond the initial post‐thaw passages. Production cultures sourced from cryopreserved cells and their non‐cryopreserved counterparts yielded similar performance (growth, viability, and productivity), product quality (size, charge, and glycosylation distributions), and flow cytometric profiles (intracellular mAb expression). However, many production cultures yielded lower Qp at increased cell age: 17 of the 24 cell lines displayed ≥20% Qp decline after ∼2–3 months of passaging, irrespective of whether the cells were previously cryopreserved. The frequency of Qp decline underscores the continued need for understanding the underlying mechanisms and for careful clone selection. Because our experiments were designed to decouple the effects of cryopreservation from those of cell age, we could conclusively rule out freeze‐thaw as a cause for Qp decline. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 34:463–477, 2018
Risk Trajectories of Readmission and Death in the First Year after Hospitalization for Chronic Obstructive Pulmonary Disease

Rationale: Characterization of the dynamic nature of posthospital risk in chronic obstructive pulmonary disease (COPD) is needed to provide counseling and plan clinical services. Objectives: To analyze risk of readmission and death after discharge for COPD among Medicare beneficiaries aged 65 years and older and to determine the association between ventilator support and risk trajectory. Methods: We computed daily absolute risks of hospital readmission and death for 1 year after discharge for COPD, stratified by ventilator support. We determined the time required for risks to decline by 50% from maximum daily values after discharge and for daily risks to plateau. We compared risks with those found in the general elderly population. Measurements and Main Results: Among 2,340,637 hospitalizations, the readmission rate at 1 year was 64.2%, including 63.5%, 66.0%, and 64.1% among those receiving invasive, noninvasive, and no ventilation, respectively. Among 1,283,069 hospitalizations, mortality at 1 year was 26.2%, including 45.7%, 41.8%, and 24.4% among those same respective groups. Daily risk of readmission declined by 50% within 28, 39, and 43 days and plateaued at 46, 54, and 61 days among those receiving invasive, noninvasive, and no ventilation, respectively. Risk of death declined by 50% by 3, 4, and 17 days and plateaued by 21, 18, and 24 days in the same respective groups. Risks of hospitalization and death were significantly higher after discharge for COPD than among the general Medicare population. Conclusions: Discharge from the hospital is associated with prolonged risks of readmission and death that vary with need for ventilator support. Interventions limited to the first month after discharge may be insufficient to improve longitudinal outcomes.
Wood density and fiber dimensions of root, stem, and branch wood of Populus ussuriensis Kom. trees

In order to determine the possibility of whole-tree wood utilization of a native tree species in Northeast China (P. ussuriensis), this study investigated the air-dried wood density and fiber dimensions for each ring in the branch, stem, and root wood of the tree species. The results showed significant differences in wood densities and fiber dimensions among tree positions (p <0.05). The root had the highest average density (0.596 g/cm3), and branch had the lowest average density (0.506 g/cm3). The root and branch wood exhibited larger fibers than that of the stem wood. The root wood had the highest average fiber wall (6.038 µm). The fiber wall of branch wood appeared thinner than the stem wood, although the difference was not statistically significant. The radial pattern of wood density and fiber dimensions indicated that branches and roots did not have juvenile wood such as was found in the stems. The study concludes that the use of branch or root wood of P. ussuriensis would be favorable for papermaking or wood-based panels.