Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameter-Based Refactoring and the Relationship with Fan-in/Fan-out Coupling

Refactoring is an activity which, in theory, should have minimal impact on the overall structure of a system. That said, certain refactorings change the coupling profile of a system and over time those cumulative changes in coupling can have serious implications for system maintenance effort. In this paper, we analyse effect of the fan-in and fan-out metrics from the perspective of two refactorings -- namely 'Add parameter' to, and 'Remove Parameter' from, a method. We developed a bespoke pattern-matching tool to collect these two refactorings from multiple releases of the Tomcat open-source system using the Evolizer tool to extract method signature data and the JHawk metrics tool to collect the two coupling metrics. Results point to significant differences in the profiles of fan-in and fan-out between refactored and non-refactored classes. We describe how software company can take advantage from this knowledge by defining a priority list of classes which could require a refactoring. A strong over-arching theme emerged: developers seemed to focus on the refactoring of classes with relatively high fan-in and fan-out rather than classes with high values in any one. The study is the first that we know of to analyse the direct effect of a subset of Fowler's refactorings on fan-in and fan-out - relevant metrics of the overall structure of a system.
Malnutrition and some related factors in primary school children, Semnan, Iran.

BACKGROUND Malnutrition places a direct and indirect burden on individuals, especially children and communities. Malnutrition or growth failure can occur because of various reasons. This study aimed to determine the prevalence of thinness, underweight, stunting, and their related factors in students aged 6-12 years in Semnan province, central Iran. PARTICIPANTS AND METHODS Using multistage sampling, a total of 2195 primary students in Semnan province, between November 2012 and March 2013, were selected randomly and the prevalences of wasting, underweight, and stunting among the students were estimated. Students' weights were measured using a Burer digital scale (Germany), with an accuracy of 100 g. Students' heights were measured using a nonstretchable tape measure. The BMI was calculated. Using the CDC 2000 standards, values less than the fifth percentile of BMI, weight-for-age, and height-for-age were defined as thinness, underweight, and stunting, respectively. RESULTS In the total sample, 12.5, 9.2, and 9.0% of the students, respectively, were affected by thinness, underweight, and stunting. Lack of access to a computer increased the odds ratio (OR) of thinness by 1.38 times [OR=1.38, 95% confidence interval (CI): 1.06-1.78, P=0.015). Other variables (including age) did not show a significant association with the prevalence of thinness. Similarly, of all the variables studied, only access to a computer showed a significant association with the prevalence of underweight (OR=1.37, 95% CI: 1.02-1.84, P=0.036). The prevalence of stunting was associated significantly with a history of parasitic infection (OR=2.32, 95% CI: 1.53-3.51, P<0.001) and living in rural areas (OR=1.57, 95% CI: 1.15-2.16, P=0.005). CONCLUSION The prevalence of malnutrition among students is high. Hence, families and stakeholders must pay special attention to various measures including healthcare services to improve the condition. Education, health, and support programs must be strengthened and continued.
A reliability prediction method of processing plan for aircraft structural parts based on fuzzy comprehensive evaluation

Manufacturing of aircraft structural parts has the characteristics of multi-varieties, complex structure, and small batch which result in high difficulty and workload of the processing planning. When the project leader is deciding the assignment of processing planning tasks, two main factors which affect the reliability of the processing plan need to be considered: the capability of the planners and the complexity of the structural parts. This paper proposes a fuzzy comprehensive evaluation method to evaluate these two factors. The reliability of processing plans is predicted by using the two impact factors and evaluated by using the machining results both based on the fuzzy comprehensive method. A project case study is taken to demonstrate the usability of the proposed method and the test results show that the proposed prediction method is feasible and practicable.
A new Evolutionary Algorithm based on quantum statistical mechanics

A new evolutionary algorithm based on quantum statistical mechanics (QSEA) is raised in this paper. In the algorithm, the whole evolutionary system is treated as a quantum statistical system, where quantum coding is adopted to express chromosomes, and superposition of quantum bits is used to simulate the linear superposition state of the system. Quantum system entropy and statistical energy have been defined by analogy with corresponding concepts in quantum statistical mechanics. And the competition between quantum statistical energy and entropy of the system is used to simulate the conflict between dasiaselection pressurepsila and dasiadiversity of populationpsila, which helps the algorithm to keep a delicate balance between these two issues, and obtain optimal solution rapidly. Numerical experiments show that this new algorithm has high efficiency and strong ability to get global optimal solution.
Protozoan-Induced Regulation of Cyclic Lipopeptide Biosynthesis Is an Effective Predation Defense Mechanism for Pseudomonas fluorescens

ABSTRACT Environmental bacteria are exposed to a myriad of biotic interactions that influence their function and survival. The grazing activity of protozoan predators significantly impacts the dynamics, diversification, and evolution of bacterial communities in soil ecosystems. To evade protozoan predation, bacteria employ various defense strategies. Soil-dwelling Pseudomonas fluorescens strains SS101 and SBW25 produce the cyclic lipopeptide surfactants (CLPs) massetolide and viscosin, respectively, in a quorum-sensing-independent manner. In this study, CLP production was shown to protect these bacteria from protozoan predation as, compared to CLP-deficient mutants, strains SS101 and SBW25 exhibited resistance to grazing by Naegleria americana in vitro and superior persistence in soil in the presence of this bacterial predator. In the wheat rhizosphere, CLP-producing strains had a direct deleterious impact on the survival of N. americana. In vitro assays further showed that N. americana was three times more sensitive to viscosin than to massetolide and that exposure of strain SS101 or SBW25 to this protozoan resulted in upregulation of CLP biosynthesis genes. Enhanced expression of the massABC and viscABC genes did not require physical contact between the two organisms as gene expression levels were up to threefold higher in bacterial cells harvested 1 cm from feeding protozoans than in cells collected 4 cm from feeding protozoans. These findings document a new natural function of CLPs and highlight that bacterium-protozoan interactions can result in activation of an antipredator response in prey populations.
Size and UV Germicidal Irradiation Susceptibility of Serratia marcescens when Aerosolized from Different Suspending Media

ABSTRACT Experimental systems have been built in laboratories worldwide to investigate the influence of various environmental parameters on the efficacy of UV germicidal irradiation (UVGI) for deactivating airborne microorganisms. It is generally recognized that data from different laboratories might vary significantly due to differences in systems and experimental conditions. In this study we looked at the effect of the composition of the suspending medium on the size and UVGI susceptibility of Serratia marcescens in an experimental system built in our laboratory. S. marcescens was suspended in (i) distilled water, (ii) phosphate buffer, (iii) 10% fetal calf serum, (iv) phosphate-buffered saline (saline, 0.8% sodium chloride), and (v) synthetic saliva (phosphate-buffered saline with 10% fetal calf serum). At low humidity (36%), S. marcescens suspended in water-only medium was the most susceptible to UVGI, followed by those in serum-only medium. The count median diameters (CMDs) for culturable particles from water-only and serum-only media were 0.88 and 0.95 μm, respectively, with the measurements based on their aerodynamic behavior. The bacteria suspended in phosphate buffer, synthetic saliva, and phosphate-buffered saline had similar UVGI susceptibility and CMD at 1.0, 1.4, and 1.5 μm, respectively. At high humidity (68%) the CMD of the particles increased by 6 to 16%, and at the same time UVGI susceptibility decreased, with the magnitude of decrease related to the type of suspending medium. In conclusion, the choice of suspending medium influenced both size and UVGI susceptibility of S. marcescens. These data are valuable for making comparisons and deciding on the use of an appropriate medium for various applications.
The sulfur atoms of the substrate CoA and the catalytic cysteine are required for a productive mode of substrate binding in bacterial biosynthetic thiolase, a thioester‐dependent enzyme

Thioesters are more reactive than oxoesters, and thioester chemistry is important for the reaction mechanisms of many enzymes, including the members of the thiolase superfamily, which play roles in both degradative and biosynthetic pathways. In the reaction mechanism of the biosynthetic thiolase, the thioester moieties of acetyl‐CoA and the acetylated catalytic cysteine react with each other, forming the product acetoacetyl‐CoA. Although a number of studies have been carried out to elucidate the thiolase reaction mechanism at the atomic level, relatively little is known about the factors determining the affinity of thiolases towards their substrates. We have carried out crystallographic studies on the biosynthetic thiolase from Zoogloea ramigera complexed with CoA and three of its synthetic analogues to compare the binding modes of these related compounds. The results show that both the CoA terminal SH group and the side chain SH group of the catalytic Cys89 are crucial for the correct positioning of substrate in the thiolase catalytic pocket. Furthermore, calorimetric assays indicate that the mutation of Cys89 into an alanine significantly decreases the affinity of thiolase towards CoA. Thus, although the sulfur atom of the thioester moiety is important for the reaction mechanism of thioester‐dependent enzymes, its specific properties can also affect the affinity and competent mode of binding of the thioester substrates to these enzymes.
Capacity-Approaching Codes for the Magnetic Recording Channel

Digital signal processing and coding are increasingly being recognized as a cost-efficient approach in achieving substantial areal density gains while preserving the high reliability of disk drives, although historically advances in head and media technologies have been the main driving force behind areal density growth. The recent advances in capacity-approaching codes hold the promise to push the areal density to the ultimate limit. In this article the various configurations regarding the interplay between soft detection and soft decoding through an iterative process, as it applies to the magnetic recording channel, are presented. In particular, the state of the art in turbo and turbo-like coding, including LDPC coding is reviewed, and the serial concatenation of these coding schemes with inner generalized PR channels in a turbo-equalization structure is described.
Positive but not negative life events predict vulnerability to upper respiratory illness

Objectives. The primary aim of this study was to examine the role of life-events in the prediction of naturally occurring episodes of upper respiratory tract illness (mainly reported as common colds). Design. The study was prospective, involving a variable follow-up period which averaged six and a half weeks. Methods. Measures of life-events (Sarason LES), stress experience, and personality (EPQ-R) were obtained for a sample of 35 participants, who were then followed up for incidence of Upper Respiratory Tract Illness (URTI). Results. Positive but not negative life-events were shown strongly to predict subsequent incidence of URTI. Reports of recent stress experience and stress proneness were not predictive, nor were personality measures. Positive LES was shown to be predictive independent of personality measures, and health-related behaviour reports concerned with smoking, alcohol consumption and normal diet. Self-reports of URTI and symptom reporting were for the first five days of the study supplemented with objective body temperature readings. Temperature measures correlated positively and significantly with symptom and URTI reporting. Conclusions. Although some of the principal effect may reflect individual differences in exposure to infectious agents, host factors affecting symptomatic expression may also be involved, in ways that are currently not understood.
Transfection ras vH-Breast Cancer Cells following either Estrogen Stimulation or Secreted and Cellular Polypeptide Patterns of MCF-7 Human Updated

The polypeptide patterns of MCF-7 human breast cancer cells (MCF7gpt) and a stably v-H-roi-transfected subclone (MCF-7ras) have been analyzed following estradili! treatment. Since both estradili! and \-H-ras transfection increase tumorigenicity of MCF-7 cells, this study was designed to ascertain if specific changes in polypeptides were common in both treatments. Separation of cellular and secreted polypeptides was accomplished by 2-dimensional polyacrylamide gel electrophoresis, and the consequent patterns were analyzed with computer assistance. I stra dini treatment of the MCF-7gpt cells reduced the number of differences found in the polypeptide patterns between MCF-7gpt and MCF-7ras. Twelve cellular polypeptides were consistently modulated by either estradiol or v-I I-rav, with four polypeptides clearly affected in the same way by both treatments. Polypeptides Gchc-0845 (M, 54,000, pi 6.9) and Gchc-0902 (M, 52,000, pi 6.3) were suppressed by estraditi! and v-Hras, while Gchc-1240 (M, 34,000, pi 4.4) and Gchc-1396 (M, 23,000, pi 5.3) were induced by estradiol and v-I I-rav. Sixteen secreted polypeptides were altered by at least 2-fold subsequent to estradiol treatment or v-Hru.Ytransfection. Transfection with v-I I-rav had a greater effect than estradiol, stimulating the secretion of eight polypeptides and suppressing the secretion of seven polypeptides compared to estradiol which increased secretion of five polypeptides and decreased secretion of an additional three polypeptides, respectively. Synergistic effects by estradiol and vH-ras were noted for three polypeptides. The secretion of Gcls-175 (M, 50,000, pi 5.7) and Gcls-320 (M, < 14,000, pi 3.6, p-S2) was increased, while the secretion of Gcls-112 (M, 76,000, pi 6.9) was decreased. Opposing effects of estradiol and v-I l-ra.v were seen for seven polypep tides including the M, 48,000 derivative of the M, 52,000 protein (cathepsin D). These studies support the possibility that an extremely few, but specific polypeptides are regulated in association with quite diverse tumorigenic stimuli in MCF-7 human breast cancer cells.
Pathways into Irregular Status among Senegalese Migrants in Europe 1

This study examines how immigration policies construct pathways into irregular legal statuses and models three pathways: no-visa entry, overstaying, and befallen irregularity. Drawing on literature on the sociolegal production of migrant irregularity, this study hypothesizes that variation in contexts of reception and migrants’ access to forms of capital and institutional connections will produce different pathways. Retrospective MAFE-Senegal data provide legal status histories. Results show pathways that occur early in a migrant's trip-no-visa entry and overstaying-are more sensitive to both contextual variables and access to forms of capital. In contrast, befallen irregularity is less related to contextual variation.
Quality of life of family caregivers of children with autism

The purpose of this study was to explore the relationship between the quality of life (QOL) and feeling of mothers of a child with autism. The QOL instrument was also used. A total of 104 participants completed all questionnaires, which included the Taiwan version of the WHOQOL—BREF. A final robust parsimonious structural model showed a positive correlation between the four domains of QOL. Mother's feeling was positively related to the physical and psychological domains. History of chronic disease was negatively related to mother's feeling and the physical domain. Religion was negatively correlated with the psychological and environmental domains. The study provided evidence that the WHOQOL—BREF is an adequate and appropriate instrument in the assessment of caregivers of children with autism in Taiwan. Mother's feeling, history of chronic disease and religion were related to QOL in these mothers of children with autism.
Mycobacterium marinum Strains Can Be Divided into Two Distinct Types Based on Genetic Diversity and Virulence

ABSTRACT Mycobacterium marinum causes a systemic tuberculosis-like disease in a large number of poikilothermic animals and is used as a model for mycobacterial pathogenesis. In the present study, we infected zebra fish (Danio rerio) with different strains of M. marinum to determine the variation in pathogenicity. Depending on the M. marinum isolate, the fish developed an acute or chronic disease. Acute disease was characterized by uncontrolled growth of the pathogen and death of all animals within 16 days, whereas chronic disease was characterized by granuloma formation in different organs and survival of the animals for at least 4 to 8 weeks. Genetic analysis of the isolates by amplified fragment length polymorphism showed that M. marinum strains could be divided in two clusters. Cluster I contained predominantly strains isolated from humans with fish tank granuloma, whereas the majority of the cluster II strains were isolated from poikilothermic species. Acute disease progression was noted only with strains belonging to cluster I, whereas all chronic-disease-causing isolates belonged to cluster II. This difference in virulence was also observed in vitro: cluster I isolate Mma20 was able to infect and survive more efficiently in the human macrophage THP-1 and the carp leukocyte CLC cell lines than was the cluster II isolate Mma11. We conclude that strain characteristics play an important role in the pathogenicity of M. marinum. In addition, the correlation between genetic variation and host origin suggests that cluster I isolates are more pathogenic for humans.
RADIATION DETECTOR DEVELOPMENTS IN MEDICAL APPLICATIONS : INORGANIC SCINTILLATORS IN POSITRON EMISSION TOMOGRAPHY

In recent years, a number of new gamma-ray scintillators are commercially available. These scintillators are either derived from known scintillators, e.g. Lu1-xYxAlO3: Ce (LuYAP) from LuAlO3:Ce and Lu2(1-x)Y2xSiO5:Ce (LYSO) from Lu2SiO5:Ce or are the result of new discoveries, e.g. LaCl3:Ce and LaBr3:Ce. The first two materials are primarily of interest because of the relatively high detection efficiency and fast response; LYSO has found application in time-of-flight (TOF) positron-emission tomography (TOF PET) and the LuYAP–LYSO combination is used in small-animal PET. The halide scintillators have an excellent energy resolution of 3% at 662 keV and they have a relatively high light yield. LaBr3:Ce is being studied for application in TOF PET. At the same time, the search for and research on new scintillator materials are going on. For example, LuI3:Ce is a new material with a very high light yield ( 90 000 photons MeV). Other examples of new materials are (C6H13NH3)2PbI4 and (C3H7NH3)2PbBr4, organic–inorganic hybrid compounds, of which the former has a very fast sub-nanosecond response. The new scintillators show great promise for new developments in medical applications, in particular, for PET systems.
Two dimensional speckle tracking echocardiography: basic principles

Two dimensional (2D) speckle tracking echocardiography (STE) is a promising new imaging modality. Similar to tissue Doppler imaging (TDI), it permits offline calculation of myocardial velocities and deformation parameters such as strain and strain rate (SR). It is well accepted that these parameters provide important insights into systolic and diastolic function, ischaemia, myocardial mechanics and many other pathophysiological processes of the heart. So far, TDI has been the only echocardiographic methodology from which these parameters could be derived. However, TDI has many limitations. It is fairly complex to analyse and interpret, only modestly robust, and frame rate and, in particular, angle dependent. Assessment of deformation parameters by TDI is thus only feasible if the echo beam can be aligned to the vector of contraction in the respective myocardial segment. In contrast, STE uses a completely different algorithm to calculate deformation: by computing deformation from standard 2D grey scale images, it is possible to overcome many of the limitations of TDI. The clinical relevance of deformation parameters paired with an easy mode of assessment has sparked enormous interest within the echocardiographic community. This is also reflected by the increasing number of publications which focus on all aspects of STE and which test the potential clinical utility of this new modality. Some have already heralded STE as ‘the next revolution in echocardiography’. This review describes the basic principles of myocardial mechanics and strain/SR imaging which form a basis for the understanding of STE. It explains how speckle tracking works, its advantages to tissue Doppler imaging, and its limitations. ### Deformation parameters—strain and strain rate Strain is a dimensionless quantity of myocardial deformation. The so-called Langrangian strain (e) is mathematically defined as the change of myocardial fibre length during stress at end-systole compared to its original length in a relaxed state at end-diastole=(l-l)/l (figure 1). …