Miracle-dz/UniFAR-FTUs huggingface dataset:
Object Oriented Software Clustering Based on Community Structure

Software comprehension plays a critical role in software maintenance. Understanding a software system is not an easy task because in most cases documentation of software design is outdated, incomplete or absent. Therefore support of tools and algorithms are necessary for software developers to understand software quicker and easier. Clustering algorithms have been widely used for software architecture recovery. Their performance depends not only on the algorithm itself but also on the nature of the software system. For example, an algorithm that is successful for a procedural program or a small software system or might be unsuccessful for a large system developed in object-oriented paradigm. In this paper, we propose the adaption of the fast community detection algorithm for object-oriented software clustering and evaluate its performance with other clustering algorithms in the literature. It is an agglomerative hierarchical clustering algorithm that has been introduced to find communities in networks. The algorithm can operate on directed weighted graphs and it has a considerable speed advantage over other algorithms. Experimental results show that the algorithm also performs well for clustering object-oriented systems.
Selective Genomic Copy Number Imbalances and Probability of Recurrence in Early-Stage Breast Cancer

A number of studies of copy number imbalances (CNIs) in breast tumors support associations between individual CNIs and patient outcomes. However, no pattern or signature of CNIs has emerged for clinical use. We determined copy number (CN) gains and losses using high-density molecular inversion probe (MIP) arrays for 971 stage I/II breast tumors and applied a boosting strategy to fit hazards models for CN and recurrence, treating chromosomal segments in a dose-specific fashion (-1 [loss], 0 [no change] and +1 [gain]). The concordance index (C-Index) was used to compare prognostic accuracy between a training (n = 728) and test (n = 243) set and across models. Twelve novel prognostic CNIs were identified: losses at 1p12, 12q13.13, 13q12.3, 22q11, and Xp21, and gains at 2p11.1, 3q13.12, 10p11.21, 10q23.1, 11p15, 14q13.2-q13.3, and 17q21.33. In addition, seven CNIs previously implicated as prognostic markers were selected: losses at 8p22 and 16p11.2 and gains at 10p13, 11q13.5, 12p13, 20q13, and Xq28. For all breast cancers combined, the final full model including 19 CNIs, clinical covariates, and tumor marker-approximated subtypes (estrogen receptor [ER], progesterone receptor, ERBB2 amplification, and Ki67) significantly outperformed a model containing only clinical covariates and tumor subtypes (C-Index full model, train[test] = 0.72[0.71] ± 0.02 vs. C-Index clinical + subtype model, train[test] = 0.62[0.62] ± 0.02; p<10−6). In addition, the full model containing 19 CNIs significantly improved prognostication separately for ER–, HER2+, luminal B, and triple negative tumors over clinical variables alone. In summary, we show that a set of 19 CNIs discriminates risk of recurrence among early-stage breast tumors, independent of ER status. Further, our data suggest the presence of specific CNIs that promote and, in some cases, limit tumor spread.
Regulation of freA, acoA, lysF, and cycA Expression by Iron Availability in Aspergillus nidulans

ABSTRACT In the filamentous fungus Aspergillus nidulans, iron homeostasis is regulated at the transcriptional level by the negative-acting GATA factor SREA. In this study the expression of a putative heme-containing metalloreductase-encoding gene, freA, was found to be upregulated by iron limitation independently of SREA, demonstrating the existence of an iron-regulatory mechanism which does not involve SREA. In contrast to freA, various other genes encoding proteins in need of iron-containing cofactors—acoA, lysF, and cycA—were downregulated in response to iron depletion. Remarkably, SREA deficiency led to increased expression of acoA, lysF, and cycA under iron-replete growth conditions.
Interference Exploitation in Full-Duplex Communications: Trading Interference Power for Both Uplink and Downlink Power Savings

This paper considers a multiuser full-duplex (FD) wireless communication system, where an FD radio base station (BS) serves multiple single-antenna half-duplex uplink and downlink users simultaneously. Unlike conventional interference mitigation approaches, we propose using knowledge of the data symbols and the channel state information (CSI) at the FD radio BS to exploit the multi-user interference constructively rather than to suppress it. We propose a multi-objective optimization problem (MOOP) via the weighted Tchebycheff method to study the tradeoff between the two desirable system design objectives, namely the total downlink transmit power and the total uplink transmit power, at the same time ensuring the required quality-of-service (QoS) for all users. In the proposed MOOP, we adapt the QoS constraints for the downlink users to accommodate constructive interference for both generic phase shift keying modulated signals and for quadrature amplitude modulated signals. We also extended our work to a robust design to study the system with imperfect uplink and downlink CSI. The simulation results and analysis show that significant power savings can be obtained. More importantly, however, the MOOP approach here allows for the power saved to be traded off for both uplink and downlink power savings, leading to an overall energy efficiency improvement in the wireless link.
Prevalence of Vitamin B12 deficiency in patients of type 2 diabetes mellitus on metformin: A case control study from Pakistan

Introduction Diabetes Mellitus is the most common endocrine disorder and metformin is the most commonly prescribed oral hypoglycemic agent. Metformin is well known to cause viamin B12 deficiency due to effect on calcium-dependent membrane action in the terminal ileum leading to malabsorption of vitamin B12. The purpose of this study is to determine prevalence and associations of Vitamin B12 deficiency in patients of type 2 diabetes mellitus treated with metformin. Methods This case control study was carried out in department of medicine, Combined Military Hospital, Kharian from 1st Jan 2012 to 30 december 2012. We enrolled 114 outdoor patients of type 2 diabetes mellitus currently on metformin for atleast 12 months, by consecutive sampling, and 105 age and sex matched patients taken as control. Patients with vitamin B12 levels of less than 150 pg/ml were said to be B12 deficient. The results were analyzed on SPSS version 16. Results Serum B12 levels were low in 35 patients (31%) on metformin as compared to only 9 patients (8.6%) among controls,(p value 0.002). Mean B12 levels were significantly low in metformin group 311 pg/ml (±194.4), p value 0.03. Dose of metformin had inverse correlation with B12 levels and the difference was statistically significant with p-value < 0.001. Conclusion Our study demonstrated significantly high prevalence of vitamin B12 deficiency in patients treated with metformin with significant effect of dose and duration of metformin use on B12 levels. Physicians must recognize this important fact and screen diabetics on metformin therapy for underlying B12 deficiency.
Ethnic Segmentation of Real Estate Agent Practice in the Urban Housing Market

Abstract This study investigated the extent to which the real estate industry is segmented along racial or ethnic lines. A 1982 survey of Anglo, black, and Hispanic real estate agents in the Denver metropolitan area showed ethnic segmentation in the structure of real estate business practice. Sellers select real estate agents at least partially on the basis of a common ethnicity, ethnicity affects the size and location of territories in which an agent obtains listings, and an agent's network of business contacts is limited by and is shaped by the ethnicity of the agent. Ethnicity therefore adds a further distortion to the spatially biased information set available to real estate agents.
Predicting Affect in Music Using Regression Methods on Low Level Features

Music has been shown to impact the aective states of the listener. The emotion in music task at the MediaEval challenge 2015 focuses on predicting the aective dimensions of valence and arousal in music using low level features. In particular, this edition of the challenge involves prediction on full length songs given a training set containing smaller 30 second clips. We approach the problem as a regression task and test several regression algorithms. We proposed these regression methods on the dataset from previous edition of the same task (Mediaeval 2014) involving prediction on 30 second clips instead of full length songs. Through evaluation on the 2015 data set, we obtain a point of reference for the model performances on longer song clips. Whereas our models perform relatively well in predicting arousal (root mean square error: .24), we do not obtain good results for valence prediction (root mean square error: .35). We analyze the results and the experimental setup and discuss plausible solutions for a better prediction.
Decay rates for solutions of a system of wave equations with memory

The purpose of this article is to study the asymptotic behavior of the solutions to a coupled system of wave equations having integral convolutions as memory terms. We prove that when the kernels of the convolutions decay exponentially, the rst and second order energy of the solutions decay exponentially. Also we show that when the kernels decay polynomially, these energies decay polynomially.
Sampling Exponentially Tilted Stable Distributions

Several algorithms for sampling exponentially tilted positive stable distributions have recently been suggested. Three of them are known as exact methods, that is, neither do they rely on approximations nor on numerically critical procedures. One of these algorithms is outperformed by another one uniformly over all parameters. The remaining two algorithms are based on different ideas and both have their advantages. After a brief overview of sampling algorithms for exponentially tilted positive stable distributions, the two algorithms are compared. A rule is derived when to apply which for sampling these distributions.
Adolescent Changes in Dopamine D1 Receptor Expression in Orbitofrontal Cortex and Piriform Cortex Accompany an Associative Learning Deficit

The orbitofrontal cortex (OFC) and piriform cortex are involved in encoding the predictive value of olfactory stimuli in rats, and neural responses to olfactory stimuli in these areas change as associations are learned. This experience-dependent plasticity mirrors task-related changes previously observed in mesocortical dopamine neurons, which have been implicated in learning the predictive value of cues. Although forms of associative learning can be found at all ages, cortical dopamine projections do not mature until after postnatal day 35 in the rat. We hypothesized that these changes in dopamine circuitry during the juvenile and adolescent periods would result in age-dependent differences in learning the predictive value of environmental cues. Using an odor-guided associative learning task, we found that adolescent rats learn the association between an odor and a palatable reward significantly more slowly than either juvenile or adult rats. Further, adolescent rats displayed greater distractibility during the task than either juvenile or adult rats. Using real-time quantitative PCR and immunohistochemical methods, we observed that the behavioral deficit in adolescence coincides with a significant increase in D1 dopamine receptor expression compared to juvenile rats in both the OFC and piriform cortex. Further, we found that both the slower learning and increased distractibility exhibited in adolescence could be alleviated by experience with the association task as a juvenile, or by an acute administration of a low dose of either the dopamine D1 receptor agonist SKF-38393 or the D2 receptor antagonist eticlopride. These results suggest that dopaminergic modulation of cortical function may be important for learning the predictive value of environmental stimuli, and that developmental changes in cortical dopaminergic circuitry may underlie age-related differences in associative learning.
GABAergic Inhibition Antagonizes Adaptive Adjustment of the Owl's Auditory Space Map during the Initial Phase of Plasticity

We studied the influence of GABA-mediated inhibition on adaptive adjustment of the owl's auditory space map during the initial phase of plasticity. Plasticity of the auditory space map was induced by subjecting owls to a chronic prismatic displacement of the visual field. In the initial stages of plasticity, inhibition suppressed responses to behaviorally appropriate, newly functional excitatory inputs. As a result, adaptive changes in excitatory input were only partially expressed as postsynaptic spike activity. This masking effect of inhibition on map plasticity did not depend on the activity of NMDA receptors at the synapses that supported the newly learned responses. On the basis of these results, we propose that the pattern of feedforward inhibition is less dynamic than the pattern of feedforward excitation at the site of plasticity. As a result, initially in the adjustment process the preexisting pattern of feedforward GABAergic inhibition opposes changes in the auditory space map and tends to preserve the established response properties of the network. The implications of this novel role of inhibition for the functional plasticity of the brain are discussed.
Addressing Health Disparities in Chronic Kidney Disease

According to the official health statistics, Taiwan has the highest prevalence of end stage renal disease (ESRD) in the world. Each year, around 60,000 ESRD patients in Taiwan consume 6% of the national insurance budget for dialysis treatment. The prevalence of chronic kidney disease (CKD) has been climbing during 2008–2012. However, the spatial disparities and clustering of CKD at the public health level have rarely been discussed. The aims of this study are to explore the possible population level risk factors and identify any clusters of CKD, using the national health insurance database. The results show that the ESRD prevalence in females is higher than that in males. ESRD medical expenditure constitutes 87% of total CKD medical expenditure. Pre-CKD and pre-ESRD disease management might slow the progression from CKD to ESRD. After applying ordinary least-squares regression, the percentages of high education status and the elderly in the townships are positively correlated with CKD prevalence. Geographically weighted regression and Local Moran’s I are used for identifying the clusters in southern Taiwan. The findings can be important evidence for earlier and targeted community interventions and reducing the health disparities of CKD.
Efavirenz and Metabolites in Cerebrospinal Fluid: Relationship with CYP2B6 c.516G→T Genotype and Perturbed Blood-Brain Barrier Due to Tuberculous Meningitis

ABSTRACT Efavirenz (EFZ) has been associated with neuropsychiatric side effects. Recently, the 8-hydroxy-EFZ (8OH-EFZ) metabolite has been shown to be a potent neurotoxin in vitro, inducing neuronal damage at concentrations of 3.3 ng/ml. EFZ induced similar neuronal damage at concentrations of 31.6 ng/ml. We investigated the effect of genotype and blood-brain barrier integrity on EFZ metabolite concentrations in cerebrospinal fluid (CSF). We measured CSF drug concentrations in subjects from two separate study populations: 47 subjects with tuberculous meningitis (TBM) coinfection in Vietnam receiving 800 mg EFZ with standard antituberculous treatment and 25 subjects from the PARTITION study in the United Kingdom without central nervous system infection receiving 600 mg EFZ. EFZ and metabolite concentrations in CSF and plasma were measured and compared with estimates of effectiveness and neurotoxicity from available published in vitro and in vivo data. The effect of the CYP2B6 c.516G→T genotype (GG genotype, fast EFV metabolizer status; GT genotype, intermediate EFV metabolizer status; TT genotype, slow EFV metabolizer status) was examined. The mean CSF concentrations of EFZ and 8OH-EFZ in the TBM group were 60.3 and 39.3 ng/ml, respectively, and those in the no-TBM group were 15.0 and 5.9 ng/ml, respectively. Plasma EFZ and 8OH-EFZ concentrations were similar between the two groups. CSF EFZ concentrations were above the in vitro toxic concentration in 76% of samples (GG genotype, 61%; GT genotype, 90%; TT genotype, 100%) in the TBM group and 13% of samples (GG genotype, 0%; GT genotype, 18%; TT genotype, 50%) in the no-TBM group. CSF 8OH-EFZ concentrations were above the in vitro toxic concentration in 98% of the TBM group and 87% of the no-TBM group; levels were independent of genotype but correlated with the CSF/plasma albumin ratio. Potentially neurotoxic concentrations of 8OH-EFZ are frequently observed in CSF independently of the CYP2B6 genotype, particularly in those with impaired blood-brain barrier integrity.
A Comparative Case Study of Architecting Practices in the Embedded Software Industry

The goal of this study is to improve the understanding of how architecting is performed within the field of software-intensive systems. Architects at six different internationally well-known companies have been interviewed to understand their way of working. This paper presents the practices that are found most successful. The context of the different companies as well as the architecting practices are compared and analyzed. Many of the architecting practices found in the study can be explained by the context of the different companies. The study shows that architects at all companies mention a general lack of understanding of software-intensive systems within industries that used to be mechanical. The architects' view of their work is very similar independently of where they work. Also the way architecting is performed is very similar, but surprisingly only one company has a defined process for architecting.
Isolation and two-step classification of normal white blood cells in peripheral blood smears

Introduction: An automated system for differential white blood cell (WBC) counting based on morphology can make manual differential leukocyte counts faster and less tedious for pathologists and laboratory professionals. We present an automated system for isolation and classification of WBCs in manually prepared, Wright stained, peripheral blood smears from whole slide images (WSI). Methods: A simple, classification scheme using color information and morphology is proposed. The performance of the algorithm was evaluated by comparing our proposed method with a hematopathologist′s visual classification. The isolation algorithm was applied to 1938 subimages of WBCs, 1804 of them were accurately isolated. Then, as the first step of a two-step classification process, WBCs were broadly classified into cells with segmented nuclei and cells with nonsegmented nuclei. The nucleus shape is one of the key factors in deciding how to classify WBCs. Ambiguities associated with connected nuclear lobes are resolved by detecting maximum curvature points and partitioning them using geometric rules. The second step is to define a set of features using the information from the cytoplasm and nuclear regions to classify WBCs using linear discriminant analysis. This two-step classification approach stratifies normal WBC types accurately from a whole slide image. Results: System evaluation is performed using a 10-fold cross-validation technique. Confusion matrix of the classifier is presented to evaluate the accuracy for each type of WBC detection. Experiments show that the two-step classification implemented achieves a 93.9% overall accuracy in the five subtype classification. Conclusion: Our methodology achieves a semiautomated system for the detection and classification of normal WBCs from scanned WSI. Further studies will be focused on detecting and segmenting abnormal WBCs, comparison of 20× and 40× data, and expanding the applications for bone marrow aspirates.
The Impact of Collective Teacher Efficacy on Student Achievement in High School Science

The Impact of Collective Teacher Efficacy on Student Achievement in High School Science. Burcham, Mark W. , 2009: Dissertation, Gardner-Webb University, Collective Teacher Efficacy/Student Achievement in High School Science/Teacher Efficacy/Roger Goddard/Albert Bandura This dissertation was designed to examine the impact of collective teacher efficacy on high school science achievement by looking at relationships among collective teacher efficacy, its two constructs, group competence and group task analysis, and high school science achievement scores at four rural high schools in Northwestern North Carolina. The researcher gathered historical test data from the testing coordinator from the school system and then administered the Collective Teacher Efficacy Instrument, developed by Goddard, Hoy, and Woolfolk Hoy (2000), to 24 science teachers from the four high schools. Using this information, the researcher conducted statistical analyses to determine the relationships among collective teacher efficacy, group competence, and group task analysis as compared with the tested science curriculum (physical science, biology, chemistry, and physics). The researcher also examined which construct was the most contributing factor and examined differences in efficacy levels and student achievement levels at each high school. Analysis of the data from this study indicated collective teacher efficacy, as well as its two constructs, group competence and group task analysis, does have a positive impact on student achievement in high school science. Analysis of the data revealed group competence is the major contributing factor for student achievement in biology and group task analysis is the major contributing factor for student achievement in physical science, chemistry, and physics. Further analysis of the data in this study, also revealed that the two high schools with the highest levels of collective teacher efficacy had the highest levels of student achievement.
Study on conductivity property of quartz based on molecular simulation

In quartz system, conductivity property, to a great extent, depends on defects, including intrinsic and extrinsic defects. In this paper, we introduce the different defects into quartz system. And then defect formation energies are calculated based on density functional theory. From the computed results, the positions and concentration of defects in quartz can be obtained. We also apply the molecular dynamics simulation to calculate dynamics properties for these different defects models. In the molecular dynamics, different forcefields are utilized to compute the dynamics property of these defects systems. Dissimilar results are obtained, however, by these different forcefields. Comparing the simulated results, we choose the most suitable forcefield for quartz system. Finally, conductivity of quartz in defects systems can be obtained accurately. From the calculated result, we can find that Na atom plays the dominant role for conductivity. The simulation results are consistent with experiment data well. And the molecular simulate research can help establish relationship between microcosmic structure and macroscopic property.