Miracle-dz/UniFAR-FTUs huggingface dataset:
FLASH: A Faster Optimizer for SBSE Tasks

Most problems in search-based software engineering involve balancing conflicting objectives. Prior approaches to this task have required a large number of evaluations- making them very slow to execute and very hard to comprehend. To solve these problems, this paper introduces FLASH, a decision tree based optimizer that incrementally grows one decision tree per objective. These trees are then used to select the next best sample. This paper compares FLASH to state-of-the-art algorithms from search-based SE and machine learning. This comparison uses multiple SBSE case studies for release planning, configuration control, process modeling, and sprint planning for agile development. FLASH was found to be the fastest optimizer (sometimes requiring less than 1% of the evaluations used by evolutionary algorithms). Also, measured in terms of model size, FLASH's reasoning was far more succinct and comprehensible. Further, measured in terms of finding effective optimization, FLASH's recommendations were highly competitive with other approaches. Finally, FLASH scaled to more complex models since it always terminated (while state-of-the-art algorithm did not).
Ventilation Tube Treatment

Objective. The aim of this review was to study the effectiveness of ventilation tube (VT) treatment in children with secretory otitis media (SOM), assessed by improved hearing, normalized language and quality of life (QoL), and recurrent acute otitis media (rAOM), assessed by number of episodes of AOM and QoL. Data Sources. Cochrane Library, PubMed, and Embase databases were searched for randomized and nonrandomized controlled trials and cohort studies in English, Scandinavian, German, and French languages between 1966 and April 2007. Additional literature was retrieved from reference lists in the articles. Review Methods. A total of 493 abstracts were evaluated independently by 2 members of the project group, 247 full-text versions were assessed for inclusion criteria and quality using structured evaluation forms, and 63 articles were included in the review. Results and Conclusions. This review shows that there is strong scientific evidence (grade 1) that VT treatment of SOM improves hearing for at least 9 months and that QoL is improved for up to 9 months (grade 2 scientific evidence). There was insufficient evidence to support an effect of VT treatment for rAOM. There was also insufficient evidence to determine whether the design or material of the VT or the procedure used for insertion had any influence on the effect; however, there was some evidence (grade 3) that aspiration of secretion at insertion does not prolong VT treatment. Further research is needed to address these issues.
Nonmotor manifestations of dystonia: A systematic review

Nonmotor symptoms are increasingly recognized as important determinants of quality of life and disability in a wide range of movement disorders. There is a limited body of research suggesting that many of these symptoms are also commonly associated with primary and other genetic forms of dystonia. However, the significance, etiology, pathophysiology, and treatment of these symptoms remain poorly described. The following is a review of the literature that focuses primarily on the association of these types of dystonia with psychiatric disorders, cognition, sleep, pain, and autonomic symptoms. We will also discuss potential mechanisms and approaches to treatment for nonmotor features of dystonia. © 2011 Movement Disorder Society
Exploring the Religious Life

Though religion is for most people one of the most important aspects of their lives, social scientists and other observers of human society too often misunderstand and misrepresent the nature and role of religion in history and in daily life. From the supposed decline of religious attitudes in Western Europe and the venal motivations attributed to the Christian Crusaders to the very definition of religion, personal biases and an inadequate grasp of relevant data have led to the formulation and propagation of unsupportable views on the sacred. In Exploring the Religious Life, Rodney Stark boldly overturns much received wisdom within the social sciences about religion, drawing on a wide range of sources to reassess a diverse selection of topics in the study of religion. In his first essay, Stark addresses the carelessness with which scholars use the term religion and the conviction that the belief in divinity evolved from the practice of magic in primitive cultures. In subsequent chapters, he challenges the widespread attitude among social scientists that religion is nothing more than a mask for material realities and examines the effectiveness of religious doctrines in attracting converts and influencing individuals; uncovers the surprising prevalence of upper-class asceticism in medieval Christianity; and explores the relationship between gender, piety, and criminal activity. Divine revelation is a central aspect of many religions, and Stark next applies empirical research to the phenomenon to assess its meaning in Judaism, Christianity, Islam, and Mormonism. He then turns to the confusion between faith and practice in debates over the secularization of the developed world before investigating the validity of the classic proposition within the social sciences that religion functions to sustain the moral order. He does so, examining the correlation between criminal behavior and depth of religious belief. Stark concludes with an essay on the ingenious methods he uses to unearth data about the popularity of new religions in California and northern Europe, the decline of Christian Science in America, the spread of Christianity in the Roman world, and the execution patterns during the antiwitchcraft frenzy of Enlightenment Europe. Together, the essays that constitute Exploring the Religious Life offer an engaging introduction to Rodney Stark's provocative insights and a fearless challenge to academic perceptions about religion's place in history, society, and private life.
A User-Controlled Priority Selection Strategy for Multiplayer Games

Future Quality of Service (QoS) aware networks, such as those based on the Differentiated Services (DiffServ) architecture, will provide users with the opportunity to assign a priority to the traffic they receive and generate. Different priorities will entail different per-byte or per-packet charges. To aid users operating within such an environment, a priority selection strategy is required. In this paper, we propose a priority selection strategy based on the concept of Consumer Surplus (CS), which is the positive difference between utility or the user's willingness-to-pay and cost. We then evaluate this strategy in a networking scenario where a user is involved in a multiplayer Counterstrike game, in which different priorities may be assigned to the downstream traffic. A utility curve, applicable to a First Person Shooter (FPS) game like Counterstrike, is presented. Using simulation results we show that for varied traffic loads, the CS strategy offers comparable application performance to that of always selecting the highest priority, but at a reduced cost to the user.
MET Expression and Amplification in Patients with Localized Gastric Cancer

Background: MET, the receptor for hepatocyte growth factor, has been proposed as a therapeutic target in gastric cancer. This study assessed the incidence of MET expression and gene amplification in tumors of Western patients with gastric cancer. Methods: Tumor specimens from patients enrolled on a preoperative chemotherapy study (NCI 5700) were examined for the presence of MET gene amplification by FISH, MET mRNA expression by quantitative PCR, MET overexpression by immunohistochemistry (IHC), and for evidence of MET pathway activation by phospho-MET (p-MET) IHC. Results: Although high levels of MET protein and mRNA were commonly encountered (in 63% and 50% of resected tumor specimens, respectively), none of these tumors had MET gene amplification by FISH, and only 6.6% had evidence of MET tyrosine kinase activity by p-MET IHC. Conclusions: In this cohort of patients with localized gastric cancer, the presence of high MET protein and RNA expression does not correlate with MET gene amplification or pathway activation, as evidenced by the absence of amplification by FISH and negative p-MET IHC analysis. Impact: This article shows a lack of MET amplification and pathway activation in a cohort of 38 patients with localized gastric cancer, suggesting that MET-driven gastric cancers are relatively rare in Western patients. Cancer Epidemiol Biomarkers Prev; 20(5); 1021–7. ©2011 AACR.
Authorship Attribution via Network Motifs Identification

Concepts and methods of complex networks can be used to analyse texts at their different complexity levels. Examples of natural language processing (NLP) tasks studied via topological analysis of networks are keyword identification, automatic extractive summarization and authorship attribution. Even though a myriad of network measurements have been applied to study the authorship attribution problem, the use of motifs for text analysis has been restricted to a few works. The goal of this paper is to apply the concept of motifs, recurrent interconnection patterns, in the authorship attribution task. The absolute frequencies of all thirteen directed motifs with three nodes were extracted from the co-occurrence networks and used as classification features. The effectiveness of these features was verified with four machine learning methods. The results show that motifs are able to distinguish the writing style of different authors. In our best scenario, 57.5% of the books were correctly classified. The chance baseline for this problem is 12.5%. In addition, we have found that function words play an important role in these recurrent patterns. Taken together, our findings suggest that motifs should be further explored in other related linguistic tasks.
Antioxidants ameliorate the expression of vascular endothelial growth factor mediated by protein kinase C in diabetic podocytes.

BACKGROUND The increased production of reactive oxygen species (ROS) may be involved in the onset or development of diabetic vascular complications. The release of ROS from podocytes plays a role in the pathogenesis of glomerular damage in various experimental glomerular diseases. Although it is assumed that the podocyte injury also plays an important role in diabetic nephropathy, the mechanism is still unknown. METHODS Using a differentiated mouse podocyte cell line, we investigated: (1) whether a high level of ambient glucose increases the level of ROS, (2) whether the protein kinase C (PKC) pathway is involved in a high-glucose-induced generation of ROS and vascular endothelial growth factor (VEGF) and (3) whether antioxidants ameliorate PKC-mediated VEGF expression in diabetic milieu. RESULTS Intracellular ROS generation was significantly higher in high glucose than in control conditions in cultured podocytes. High ambient glucose also increased VEGF mRNA and protein expression. The high-glucose-induced increases in ROS and VEGF mRNA and protein by podocytes were effectively inhibited by pretreatment with various antioxidants and were completely restored by PKC inhibition. The results show that cultured mouse podocytes produce ROS in response to high glucose, and that PKC is involved in high-glucose-induced ROS and VEGF production by podocyte. CONCLUSION Increased ROS in podocytes may play a role in the pathogenesis of podocyte injury in diabetic nephropathy.
Population Genetics of the Nomenspecies Enterobacter cloacae

ABSTRACT The genetic heterogeneity of the nomenspecies Enterobacter cloacae is well known. Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei, Enterobacter kobei, and Enterobacter nimipressuralis are closely related to it and are subsumed in the so-called E. cloacae complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies E. cloacae, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71R were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes hsp60, rpoB, and hemB as well as ampC, the gene of a class C β-lactamase. Based on the neighbor-joining tree of the hsp60 sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of rpoB and hemB sequences and ampC PCR-RFLPs. Sequence crowd xiii split into two groups after rpoB analysis. Only three strains formed a cluster with the type strain of E. cloacae, indicating that the minority of isolates identified as E. cloacae truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the E. cloacae complex.
A Phase-Based Self-Tuning Algorithm for Reconfigurable Cache

The performance of a given cache architecture is largely determined by the behavior of the application using the cache. Reconfigurable cache is an effective low-power technique. Using the technique, microprocessor's cache can be configured dynamically to adapt itself to the requirement of running program, and minimize the energy consumption and performance loss. We introduce a phase-based self-tuning algorithm (PBSTA), which can automatically, transparently, and dynamically manage the reconfigurable cache on a per-phase basis. In contrast with previous works, the algorithm seeks not only to lower the cache's energy consumption effectively, but also reduce the performance loss due to unnecessary reconfigurations. By simulating numerous MiBench benchmarks, the results show that the PBSTA, when applied to reconfigurable cache, saves on average 40% of total memory access energy compared with a conventional cache and the associated performance loss is close to 1.8%.
Nondegenerate Super-Anti-de Sitter Algebra and a Superstring Action

We construct an Anti-de Sitter(AdS) algebra in a nondegenerate superspace. Based on this algebra we construct a covariant kappa-symmetric superstring action, and we examine its dynamics: Although this action reduces to the usual Green-Schwarz superstring action in flat limit, the auxiliary fermionic coordinates of the nondegenerate superspace becomes dynamical in the AdS background.
DNA Immunization with Na+-K+ATPase (Sseat-6) Induces Protective Immunity to Larval Strongyloides stercoralis in Mice

ABSTRACT Strongyloides stercoralis causes chronic asymptomatic infections which can be maintained in the human host for many decades. Identification and treatment of S. stercoralis-infected individuals is required because immunosuppression can lead to fatal hyperinfection. In this study, human immunoglobulin G (IgG) that had previously been shown to transfer protective immunity to mice was used to identify potential protective antigens. Three antigens or genes from S. stercoralis larvae were identified as tropomyosin (Sstmy-1), Na+-K+ATPase (Sseat-6), and LEC-5 (Sslec-5). The genes were cloned into plasmids for DNA immunization, and mice were immunized intradermally with the three plasmids individually in combination with a plasmid containing murine granulocyte-macrophage colony-stimulating factor. Only Na+-K+ATPase induced a significant reduction in larval survival after DNA immunization. Immunization with a combination of all three plasmids, including Na+-K+ATPase, did not induce protective immunity. Serum from mice immunized with DNA encoding Na+-K+ATPase was transferred to naïve mice and resulted in partial protective immunity. Therefore, DNA immunization with Na+-K+ATPase induces protective immunity in mice, and it is the first identified vaccine candidate against infection with larval S. stercoralis.
The use of linguistic hierarchies in speech understanding

This paper describes two related systems which provide frameworks for encoding linguistic knowledge into formal rules within the context of a trainable probabilistic model. The first system, TINA [33], drives top-down from sentence level structure, terminating in either words or syllables. Its main purpose is to provide a meaning representation for the sentence. The other system, ANGIE [36], operates bottom-up from phonetic or orthographic units, characterizing the substructure of syllables/words. It provides a framework for both phonological rule modelling and letter-to-sound/sound-to-letter transformations. The two systems logically converge on the syllable or word layer. We have recently been successful in integrating their combined constraint into a recognizer search, achieving considerable improvement in understanding accuracy [9, 23]. In this paper, I will look both toward the past and the future, identifying and motivating the decisions that were made in the design of TINA and ANGIE and the associated rule formalisms, and contemplating various remaining open research issues.
A machine learning concept for DTN routing

This paper discusses the concept and architecture of a machine learning based router for delay tolerant space networks. The techniques of reinforcement learning and Bayesian learning are used to supplement the routing decisions of the popular Contact Graph Routing algorithm. An introduction to the concepts of Contact Graph Routing, Q-routing and Naïve Bayes classification are given. The development of an architecture for a cross-layer feedback framework for DTN protocols is discussed. Finally, initial simulation setup and results are given.
Physical Activity Patterns in Adults With Severe Mental Illness

Although physical inactivity is a leading cause of death and the Surgeon General recommends regular moderate physical activity, many Americans are inactive. Because of their increased burden of obesity and diabetes, people with severe mental illness (SMI) especially may benefit from physical activity, yet little is known about the prevalence and types of physical activity in people with SMI. We surveyed outpatients with schizophrenia and affective disorders at two psychiatric centers in Maryland and compared physical activity patterns to an age-gender-race-matched national sample (National Health and Nutrition Examination Survey III) of the general population. We found that people with SMI are overall less physically active than the general population, although the proportion with recommended physical activity levels was equal. The participants with SMI were more likely to walk as their sole form of physical activity. Within the SMI group, those without regular social contact and women had higher odds of being inactive.
Continuous contact simulation for smooth surfaces

Dynamics simulation of smooth surfaced rigid bodies in contact is a critical problem in physically based animation and interactive virtual environments. We describe a technique that uses reduced coordinates to evolve a single continuous contact between smooth piecewise parametric surfaces. The incorporation of friction into our algorithm is straightforward. The dynamics equations, although slightly more complex due to the reduced coordinate formulation, can be integrated easily using explicit integrators without the need for constraint stabilization. Reduced coordinates confine integration errors to the constraint manifold, thereby permitting a wide choice of step sizes with visually acceptable results. We demonstrate these results using Loop Subdivision surfaces with parametric evaluation.
Inclusive fitness in finite populations—effects of heterogeneity and synergy

I review recent results concerning the relationship between the inclusive fitness (IF) effect and standard measures of allele fitness in a finite‐population, with attention to the effect of heterogeneity in population structure and nonadditive fitness effects. In both cases, existing theoretical work is somewhat technical and I try to provide a more transparent account. In a heterogeneous population it is known that inclusive fitness will generally fail to incorporate the effects of selection on the distribution of alleles among states unless a reproductive‐value weighting is used. But even given that, recent work shows that under certain updating rules, the IF effect can fail to be equivalent to standard measures such as fixation probability. In terms of synergistic fitness effects, I review the result that in the finite population model, the IF effect can be calculated using only “additive” relatedness coefficients so that computational difficulties found in the infinite‐population model do not arise. In my own work, there is an interaction here in that my 2012 work on synergy with Maciejewski made an assumption about inclusive fitness that my 2014 work on heterogeneity with Tarnita showed to be wrong. I include (Appendix C) a corrected argument for the 2012 result.
Off-Grid Direction of Arrival Estimation Using Sparse Bayesian Inference

Direction of arrival (DOA) estimation is a classical problem in signal processing with many practical applications. Its research has recently been advanced owing to the development of methods based on sparse signal reconstruction. While these methods have shown advantages over conventional ones, there are still difficulties in practical situations where true DOAs are not on the discretized sampling grid. To deal with such an off-grid DOA estimation problem, this paper studies an off-grid model that takes into account effects of the off-grid DOAs and has a smaller modeling error. An iterative algorithm is developed based on the off-grid model from a Bayesian perspective while joint sparsity among different snapshots is exploited by assuming a Laplace prior for signals at all snapshots. The new approach applies to both single snapshot and multi-snapshot cases. Numerical simulations show that the proposed algorithm has improved accuracy in terms of mean squared estimation error. The algorithm can maintain high estimation accuracy even under a very coarse sampling grid.