Miracle-dz/UniFAR-FTUs huggingface dataset:
Employing issues and commits for in-code sentence based use case identification and remodularization

Use case driven modularization improves code comprehension and maintenance and provides another view on software alongside object-oriented modularization. However, approaches enabling use case driven modularization require to modularize code manually. In this paper, we propose an approach to employing issues and commits for in-code sentence based use case identification and remodularization. The approach aims at providing use case based perspective on the existing code. The sentences of use case steps are compared to sentences of issue descriptions, while the sentences generated from the source code of issue commits are compared to sentences generated from the corresponding methods in source code in order to quantify the similarity between use case steps and methods in source code using different similarity calculation algorithms. The resulting level of similarity is used to remodularize source code according to use cases. We conducted a study on the OpenCart open source e-shop employing 16 use cases. The approach achieved the recall of 3.37% and precision of 75%. The success of the approach strongly depends on issues and commits assigned to them. The results would be better especially for the code that natively employs use case driven modularization.
Viability of the bulk synchronous parallel model for science on cloud

In recent years, cloud computing has emerged as an alternative to classical HPC resources like supercomputers, computer clusters and grids. As cloud provides a convenient real-time access to dynamic computing resources, it appears ideal for solving large scale scientific computing problems in domains like physics, chemistry, astrophysics, climatology, etc. However, using a large number of cloud resources means that applications must be able to distribute the work between these resources in a fault tolerant manner as the commodity cloud resources are bound to fail in regular intervals. Frameworks like MapReduce can significantly simplify this by taking care of data distribution, synchronization, task parallelism, fault tolerance, etc. and only require the user to write the algorithms themselves. However, MapReduce model is not well suited for more complex iterative tasks that are commonly utilized in the field of scientific computing. This work investigates an alternative model, Bulk Synchronous Parallel (BSP), to find how suitable it and its current implementations are for running more complex scientific computing algorithms. We take a number of BSP implementations, adapt several typical scientific algorithms to them and compare the results to MPI based implementations. The goal of this work is to give an overview of the current BSP implementations, evaluate whether they are suitable for complex scientific algorithms in comparison to MPI and still provide the same advantages as MapReduce.
Cloning of a novel epidermal growth factor repeat containing gene EGFL6: expressed in tumor and fetal tissues.

The epidermal growth factor (EGF) repeat superfamily of genes often encodes proteins that govern cellular proliferative responses. Using a high-throughput screening by hybridization approach, a novel human EGF repeat superfamily member that maps to human chromosome X was identified. Termed EGFL6, the gene encodes a predicted signal peptide, suggesting that it is secreted. Other predicted features include four and one-half EGF-like repeat domains, two N-linked glycosylation sites, an integrin association motif (RGD), and a tyrosine phosphorylation site. Importantly, its transcripts are expressed in brain and lung tumor and fetal tissues, but are generally absent from normal adult tissues. Implications with respect to cell cycle regulation and oncogenesis are discussed.
Probing the Interaction of a Therapeutic Flavonoid, Pinostrobin with Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 105 M−1 at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol−1 K−1 and ΔH = −15.48 kJ mol−1) and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow’s site I, located at subdomain IIA, and was well supported by the molecular modelling data.
Social Inequalities in Mental Health and Health-Related Quality of Life in Children in Spain

OBJECTIVES: To assess mental health and health-related quality of life (HRQoL) of children and adolescents in Spain and to investigate the existence of a social gradient in mental health and HRQoL. METHODS: Within the Spanish National Health Survey (2006), the parents’ version of the Strengths and Difficulties Questionnaire was administered to a population aged 4 to 15 years, and the parents’ version of the modified KIDSCREEN-10 Index was given to a population aged 8 to 15 years. Sociodemographic data and information on family structure, socioeconomic status, health status, and discrimination were collected. Regression models were developed to analyze associations of socioeconomic status with mental health and HRQoL. RESULTS: A total of 6414 children and adolescents aged 4 to 15 years participated. Mean Strengths and Difficulties Questionnaire score was 9.38 (SD, 5.84) and mean KIDSCREEN-10 Index score (n = 4446) was 85.21 (SD, 10.73). Children whose mothers had a primary school education (odds ratio [OR]: 1.37; 95% confidence interval [CI]: 1.29–1.46) or a secondary education (OR: 1.21; 95% CI: 1.14–1.29) presented poorer mental health than those whose mothers had a university degree. Children from disadvantaged social classes (IV–V) showed slightly poorer HRQoL scores (OR: 0.98; CI: 0.97–0.99) than the remaining children. CONCLUSIONS: There is a social gradient in the mental health of children and young adolescents in Spain. No social gradient was found for HRQoL, although children from families of disadvantaged social classes had slightly worse HRQoL scores than their counterparts from more advantaged classes.
An application of GRA to analyze the credit risk in banking industry

This study proposes a new approach for analyzing the credit risks of banking industry based the modeling of Grey Relational Analysis (GRA). In order to construct a financial distress warning system for banking industry, a GRA approach is developed and applied to the real data set with 111 samples. The results of the current model are compared to those of traditional ones. The results illustrate that in the prediction of financially distress as well as financially sound banks, the proposed GRA model demonstrates better prediction accuracy than the conventional ones. The results also imply that the financial data set one year before the crisis leads to the best accuracy. It is helpful for the establishment of early warning models of financial crisis. The current results show that the proposed GRA provides a novel approach in handling financial distress warning tasks.
Impact of Alpha Particles on the Electrical Characteristics of TiO$_{2}$ Memristors

Titanium-oxide (TiO2 ) memristors exposed to 1-MeV alpha particles exhibit only minor changes in the electrical response for ion fluencies up to 1014 cm - 2. At higher fluence levels, virgin and off-state devices exhibit measurable increases in current conduction between the two platinum (Pt) electrodes. Analysis, supported by radiation transport and numerical device simulations, suggests that radiation-induced displacement damage in the TiO2 film increases the density of oxygen vacancies, thereby altering both resistivity in the bulk of the transition-metal oxide and the junction characteristics of Pt-TiO2 interface. Nevertheless, the experimental results indicate continued switching functionality of the memristors even after exposure to 1015 cm- 2 alpha particles. The high intrinsic vacancy density in the devices prior to radiation exposure is identified as the primary feature contributing to apparent radiation hardness.
Specific Inhibition of Glucocorticoid-Induced Thymocyte Apoptosis by Substance P1

Glucocorticoids (GC) are strong inducers of thymocyte apoptosis. In the present study we looked into the possibility that the neuropeptide substance P (SP) might serve as an antagonist to GC-induced apoptosis. Indeed, SP inhibited hydrocortisone (HC)-induced apoptosis of CD4+CD8+ thymocytes in mice, both in vivo and in vitro. It also inhibited HC-induced apoptosis in the T cell hybridoma line 2B4.11, which is sensitive to GC. The inhibitory effect was complete if SP was given with HC or within 1 h after it; partial inhibitory effect could be seen at 2 h and no effect at 3 h. The presence of the SP antagonist nullified SP effect. The effect was specific to both components of the system (i.e., HC as apoptosis inducer and SP as its inhibitor), as judged from comparison to three other apoptosis-inducing means (irradiation, thymic epithelial cells, or retinoic acid), and to two other neuropeptides (somatostatin and vasoactive intestinal peptide). SP/HC antagonism was further demonstrated in two relevant molecular events: 1) HC augmented GC receptor production in our cell system and this was inhibited by SP; and 2) HC reduced the expression of the transcription factor NF-κB, SP increased it and when both were present, SP effect dominated. On the other hand, the level of IκB (NF-κB inhibitory molecule) was decreased by SP, preserved at a relatively high level with HC, and when both SP and HC were present, SP effect dominated. The intensity of SP effect, both in vivo and in vitro, its specificity, its inhibition by SP antagonist, as well as the previously documented presence of SP and its receptor in the thymus suggest that SP might be a physiological antagonist of the potent thymocyte apoptosis induced by GC.
Cloning crowd motions

This paper introduces a method to clone crowd motion data. Our goal is to efficiently animate large crowds from existing examples of motions of groups of characters by applying an enhanced copy and paste technique on them. Specifically, we address spatial and temporal continuity problems to enable animation of significantly larger crowds than our initial data. We animate many characters from the few examples with no limitation on duration. Moreover, our animation technique answers the needs of real-time applications through a technique of linear complexity. Therefore, it is significantly more efficient than any existing crowd simulation-based technique, and in addition, we ensure a predictable level of realism for animations. We provide virtual population designers and animators with a powerful framework which (i) enables them to clone crowd motion examples while preserving the complexity and the aspect of group motion and (ii) is able to animate large-scale crowds in real-time. Our contribution is the formulation of the cloning problem as a double search problem. Firstly, we search for almost periodic portions of crowd motion data through the available examples. Secondly, we search for almost symmetries between the conditions at the limits of these portions in order to interconnect them. The result of our searches is a set of crowd patches that contain portions of example data that can be used to compose large and endless animations. Through several examples prepared from real crowd motion data, we demonstrate the advantageous properties of our approach as well as identify its potential for future developments.
Identification of key regulators for the migration and invasion of rheumatoid synoviocytes through a systems approach

Significance Rheumatoid arthritis (RA) is an autoimmune disorder that affects ∼1% of the population. Macrophage- and fibroblast-like synoviocytes are thought to play central roles in the pathogenesis of RA. They have shared and distinct features defining RA pathology. However, these features have not been systematically explored. Using global gene expression profiling, we identified molecular signature and biological network models underlying the pathologic features of macrophage-like vs. fibroblast-like synoviocytes. Based on the network models, we selected key regulators, including POSTN and TWIST1, responsible for synoviocyte migration/invasion causing joint destruction, and their validity was experimentally confirmed. Our findings provide a comprehensive and systematic basis for mechanisms explaining RA pathogenesis and also for identification of therapeutic targets for RA. Rheumatoid synoviocytes, which consist of fibroblast-like synoviocytes (FLSs) and synovial macrophages (SMs), are crucial for the progression of rheumatoid arthritis (RA). Particularly, FLSs of RA patients (RA-FLSs) exhibit invasive characteristics reminiscent of cancer cells, destroying cartilage and bone. RA-FLSs and SMs originate differently from mesenchymal and myeloid cells, respectively, but share many pathologic functions. However, the molecular signatures and biological networks representing the distinct and shared features of the two cell types are unknown. We performed global transcriptome profiling of FLSs and SMs obtained from RA and osteoarthritis patients. By comparing the transcriptomes, we identified distinct molecular signatures and cellular processes defining invasiveness of RA-FLSs and proinflammatory properties of RA-SMs, respectively. Interestingly, under the interleukin-1β (IL-1β)–stimulated condition, the RA-FLSs newly acquired proinflammatory signature dominant in RA-SMs without losing invasive properties. We next reconstructed a network model that delineates the shared, RA-FLS–dominant (invasive), and RA-SM–dominant (inflammatory) processes. From the network model, we selected 13 genes, including periostin, osteoblast-specific factor (POSTN) and twist basic helix–loop–helix transcription factor 1 (TWIST1), as key regulator candidates responsible for FLS invasiveness. Of note, POSTN and TWIST1 expressions were elevated in independent RA-FLSs and further instigated by IL-1β. Functional assays demonstrated the requirement of POSTN and TWIST1 for migration and invasion of RA-FLSs stimulated with IL-1β. Together, our systems approach to rheumatoid synovitis provides a basis for identifying key regulators responsible for pathological features of RA-FLSs and -SMs, demonstrating how a certain type of cells acquires functional redundancy under chronic inflammatory conditions.
Application of the Dual High-Gain Scaling Technique to Decentralized Control and Disturbance Attenuation

In this paper, we propose a dynamic high-gain scaling-based output-feedback controller for decentralized control and disturbance attenuation of interconnected large-scale systems. Each subsystem in the large-scale system has a nominal part in a general strict-feedback-like structure and appended input-to-state practically stable (ISpS) dynamics which are allowed to be driven by all the subsystem states and the subsystem input. The subsystems are interconnected through uncertain functions that appear in each of the subsystem dynamics. The bounds introduced on the uncertain functions are allowed to involve the outputs of all subsystems and also a component of the appended ISpS dynamics of all subsystems
ELECTROLYTES IN BRAIN, LIVER, DIAPHRAGM, AND BLOOD AFTER ELECTROSHOCK IN RATS

Studies of electrolyte metabolism in direct connection with electro-convulsive treatment (ECT) in human subjects are few. Astrup et al. (1955) found increased potassium in blood from the jugular vein after ECT modified with succinylcholine, whereas Posner et al. (1969) reported unchanged potassium and sodium in blood from the jugular vein and the femoral artery during and after ECT in relaxed patients. More results have emerged from animal studies. Cicardo (1945) reported increased potassium content in blood from brain of convulsing dogs, and Swingle & Swingle (1963) found significant increase of potassium and sodium in the peripheral blood after electroshock convulsions in dogs. Increased potassium and inorganic phosphate in the peripheral blood of rats several minutes after electroshock was reported by Ward & Call (1949). Spiegel-Adolf et al. (1945) measured increased sodium and inorganic phosphate in the cerebrospinal fluid of dogs within 1 hour after electroshock. Increased content of inorganic phosphate in the brain during convulsions was found by Klein & Olsen (1947) and Bain et al. (1949) in electroshock experiments in dogs and monkeys, respectively. There is a close connection between electrolyte changes and the decreased energy stores of the brain following electroshock reported by Klein & Olsen (1947), Carter & Stone (1951), King et al. (1967), and Bolwig & Rafaelsen (1972). In this study we shall report an investigation of sodium, potassium, and phosphate in brain, liver, muscle, and blood after electroshock convulsions in rats and the influence of preshock neuro-muscular blocking on serum potassium and inorganic phosphate.
Studies on the involution of the fetal cortex of the adrenal glands.

Since Thomas' 1 recognition in I9II that during the Ist year of life there is regularly a complete degeneration of the inner zone of the adrenal cortex, there have been a few papers published dealing with the histology of the process, but there has been no tabulation of the range of "normal" variation and little attempt at correlation of unusual alterations in the involuting gland with pathological changes in other organs. The present review of cases is given to show the range of variation found in the adrenal glands in 217 routine autopsies on infants and children, and to contribute to the knowledge of possible forces acting to modify the rate of involution of these glands. The adrenals at birth are relatively large structures, about onethird the size of the kidneys, and are made up of a fairly firm, yellowish gray cortex and a wide, brownish red inner portion. The gland is composed of an outer or true cortical part consisting of a narrow zone of small deeply staining cells arranged in ovoid or acinar groups, and an inner portion made up of large polyhedral cells which are frequently fat-containing, take a pale acidophilic stain and are in no definite arrangement. This inner part is the fetal cortex which is destined to disappear after birth. In the most central region a few deeply staining medullary cells may be seen. The primary inner zone, or fetal cortex, is present as a definite structure by the 4th fetal month 2 and continues with no morphological change up to the time of birth. Hyperemia is a feature of the fetal cortex at all times and is maximal at the time of birth.3 The involution of the inner or fetal zone of the adrenal cortex has been studied by Lewis and Pappenheimer 4 in ioo cases. A summary of their observations is as follows: (a) In the first few days of life the innermost cortical layer becomes increasingly hyperemic and the great filling of the capil* Received for publication March i6, 1940.
[Overcoming experiences of family members caring for elderly patients with dementia at home].

PURPOSE The purpose of the study was to understand and describe the overcoming experiences of family members caring for elderly patients with dementia at home. METHODS Data came from autobiographies on the overcoming experiences of caregiving from 31 participants, who had submitted the autobiographies to a public contest held by the Seoul Metropolitan Center for Dementia in 2012. Data were analyzed using qualitative content analysis. RESULTS Four overcoming stages emerged from the analysis: confronting stage; challenging stage; integrating stage; and transcendental stage, representing transformation of experiences from frustration and suffering to happiness and new hope in life. The confronting stage illustrates severe negative feelings and exhaustion occurring after the diagnosis of dementia. The challenging stage signifies major driving forces in taking good care of their patients. It includes tender loving memories about the patients as well as family and social supports. The integrating stage shows genuine empathy for the patients' situation and the happiness of 'here and now', while the transcendental stage represents new hope in the future. CONCLUSION Health professionals need to support caregivers to find true meaning of caring and happiness in everyday life, while providing specific information on dementia care and relieving various negative feelings.
Punching Shear Strength of Steel Fiber Reinforced Concrete Flat Plates

The primary objective of this experimental study was to determine whether addition of steel fibers to the concrete mix could significantly increase the punching shear strength of reinforced concrete slabs. Thirteen slab specimens and their companion cylinder specimens were tested. Fiber concentrations in the slabs ranged from 0 to 6.4 percent by weight of concrete. Test results of this study indicate that the addition of steel fibers to the concrete mix does significantly enhance the punching shear strength of slabs. A modification of the standard code design equation for shear punching strength of slabs is suggested to reflect the strength increase produced by the fibers. The tests also provided information on the shape and inclination of the fracture surface, and indicated that only a small, shallow region of the slab in the vicinity of the slab-column intersection is highly stressed in tension before rupture. This means that punching shear failure occurs in a progressive manner.
Bite me: Blue tails as a‘risky-decoy’defense tactic for lizards

Many lizard species use caudal autotomy to escape entrapment. Conspicuous coloration may increase the likelihood of being attacked, but if that attack can be directed towards the autotomous tail this may ultimately increase the chances of the lizard surviving a predatory attack. We tested the hypothesis that brightly-colored function to divert predatory attention away from the head and body using pairs of blue-tailed and all-brown clay model lizards. Predatory bird attacks on the 24 blue-tailed models occurred sooner (P = 0.001) than attacks on the 24 all-brown models, and over 7 days, blue-tailed models were attacked more often than all-brown models (P = 0.007). Blue-tailed models were, however, more frequently attacked on the tail than other parts of the body (P < 0.001), while all-brown models were more frequently attacked on the head and body (P = 0.019) which would be more likely to be fatal for a real lizard. Our results suggest that models with a blue tail were more conspicuous than all-brown models, attracting attacks sooner and more often, but that the attacks were predominantly directed at the tail. It is better for individuals to be attacked unsuccessfully many times, than successfully just once. Having a brightly colored tail may, therefore, act as a ‘risky decoy’. Despite increased conspicuousness, a blue tail increases the likelihood that the lizard would be able to effect escape through caudal autotomy rather than being grabbed by the head or body