Miracle-dz/UniFAR-FTUs huggingface dataset:
Clones occurence in large object oriented software packages

Software engineers often build new procedures by cloning, copying an existing one with similar requirements, and slightly modifying it. While this may be easier than extracting the common part, and sharing it in a library, it increases the system size and often leads to higher maintenance costs. The occurrence of clones is highly dependent on the system architecture and development model, and has been studied in the past for a few large procedural systems.This paper studies the occurrence of clones in a large set of object oriented software libraries and programs (totaling 600 000 lines of code), and discusses the factors affecting the clone detection accuracy, and their frequency of occurrence.
Adaptive “Cubature and Sigma Points” Kalman Filtering Applied to MEMS IMU/GNSS Data Fusion during Measurement Outlier

In this paper, adaptive sensor fusion INS/GNSS is proposed to solve specific problem of non linear time variant state space estimation with measurement outliers, different algorithms are used to solve this specific problem generally occurs in intentional and non-intentional interferences caused by other radio navigation sources, or by the GNSS receiver’s deterioration. Non linear approximation techniques such as Extended Kalman filter EKF, Sigma Point Kalman Filters such as UKF and CDKF are computed to estimate the navigation states for UAV flight control. Several comparisons are conduced and analyzed in order to compare the accuracy and the convergence of different approaches usually applied in navigation data fusion purposes. The last non linear filter algorithm developed is the Cubature Kalman Filter CKF which provides more accurate estimation with more stability in Tracking data fusion application. In this work, CKF is compared with SPKF and EKF in ideal conditions and during GNSS outliers supposed to occur during specific interval of time, innovation based adaptive approach is selected and used to modify the covariance calculation of the non linear filters performed in this paper. Interesting results are observed, discussed with real perspectives in navigation data fusion for real time applications. Three parallel modified algorithms are simulated and compared to non-adaptive forms according to Root Mean Square Error (RMSE) criteria.
Molecular and Cellular Pathobiology HSulf-1 Modulates FGF 2-and Hypoxia-Mediated Migration and Invasion of Breast Cancer Cells

HSulf-1 modulates the sulfation states of heparan sulfate proteoglycans critical for heparin binding growth factor signaling. In the present study, we show that HSulf-1 is transcriptionally deregulated under hypoxia in breast cancer cell lines. Knockdown of HIF-1a rescued HSulf-1 downregulation imposed by hypoxia, both at the RNA and protein levels. Chromatin immunoprecipitation with HIF-1a and HIF-2a antibodies confirmed recruitment of HIF-a proteins to the two functional hypoxia-responsive elements on the native HSulf-1 promoter. HSulf-1 depletion in breast cancer cells resulted in an increased and sustained bFGF2 (basic fibroblast growth factor) signaling and promoted cell migration and invasion under hypoxic conditions. In addition, FGFR2 (fibroblast growth factor receptor 2) depletion in HSulf-1–silenced breast cancer cells attenuated hypoxia-mediated cell invasion. Immunohistochemical analysis of 53 invasive ductal carcinomas and their autologous metastatic lesions revealed an inverse correlation for the expression of HSulf-1 to CAIX in both the primary tumors (P 0.0198) andmetastatic lesions (P 0.0067), respectively, by c test. Finally, HSulf-1 expression levels in breast tumors by RNA in situ hybridization showed that high HSulf-1 expression is associated with increased disease-free and overall survival (P 0.03 and P 0.0001, respectively). Collectively, these results reveal an important link between loss of HSulf-1 under hypoxic microenvironment and increased growth factor signaling, cell migration, and invasion. Cancer Res; 71(6); 2152–61. 2011 AACR.
Movie success prediction using data mining

In this project, we developed a mathematical model to predict the success and failure of the upcoming movies based on several attributes. Some of the criteria in calculating movie success included budget, actors, director, producer, set locations, story writer, movie release day, competing movie releases at the same time, music, release location and target audience. The success prediction of a movie plays a vital role in movie industry because it involves huge investments. However, success cannot be predicted based on a particular attribute. So, we have built a model based on interesting relation between attributes. The movie industry can use this model to modify the movie criteria for obtaining likelihood of blockbusters. Also, this model can be used by movie watchers in determining a blockbuster before purchasing a ticket. Each of the criteria involved was given a weight and then the prediction was made based on these. For example, if a movies budget was below 5 million, the budget was given a lower weight. Depending on the number of actors, directors and producers past successful movies, each of these categories was given a weight. If the movie was to be released on a weekend, it was given higher weight because the chances of success were greater. If with the release of a movie, there was another high success movie released, a lower weight was given to the release time indicating that the chances of movie success were low due to the competition. The criteria were not limited just to the ones mentioned. There were be additional factors discussed in this work. We have conducted our work with simulation data.
Lack of a Pharmacokinetic Effect of Raltegravir on Midazolam: In Vitro/In Vivo Correlation

Raltegravir is a novel HIV‐1 integrase inhibitor with potent in vitro activity (95% inhibitory concentration = 33 nM in 50% human serum). In vitro characterization of raltegravir inhibition potential was assessed against a panel of cytochrome P450 (CYP) enzymes. An open‐label, 2‐period study was conducted to assess the effect of raltegravir on the pharmacokinetics of midazolam, a sensitive CYP 3A4 probe substrate: period 1, 2.0 mg of midazolam; period 2, 400 mg of raltegravir every 12 hours for 14 days with 2.0 mg of midazolam on day 14. There was no meaningful in vitro effect of raltegravir on inhibition of a panel of CYP enzymes and induction of CYP 3A4. In the presence of raltegravir, midazolam area under the curve extrapolated to infinity (AUC0‐infin) and maximum plasma concentration (Cmax) geometric mean ratios were similar (geometric mean ratios and 90% confidence intervals: 0.92 [0.82, 1.03] (P = .208) and 1.03 [0.87, 1.22] (P = .751), respectively). No substantial differences were observed in Tmax (P = .750) or apparent half‐life (P = .533) of midazolam. Plasma levels of midazolam were not substantially affected by raltegravir, which implies that raltegravir is not a clinically important inducer or inhibitor of CYP 3A4 and that raltegravir would not be expected to affect the pharmacokinetics of other drugs metabolized by CYP 3A4 to a clinically meaningful extent.
Control of Double Output Induction Machine Based stand alone Variable Speed Constant Frequency generator with nonlinear and unbalanced loads

The control algorithms proposed in the literature so far for the Double Output Induction Machine Based Variable Speed Constant Frequency (VSCF) stand alone generators suffer from the disadvantage of loss of ‘field orientation’ during sudden load disturbance at the machine terminal. As a result, undesirable transients are observed in the load voltage during such transients. This paper presents a new control strategy for such generators where the primary objective of the control scheme is to maintain constant voltage and frequency at the output of the generator irrespective of the prime mover speed and load variation. The proposed control algorithm is suitable for all types of loads such as balanced, unbalanced, linear and nonlinear. Simulation results are presented to validate the effectiveness of the proposed scheme.
Cross-National Moral Beliefs: The Influence of National Religious Context

International surveys have documented wide variation in religious beliefs and practices across nations, but does this variation in the national religious context make a difference? Building on existing theory, we explain why religion should have both micro- and macro-level effects on morality not sanctioned by the state and why the effects of religion differ from other forms of culture. Using two international surveys and hierarchical linear modeling techniques we sort out the effects of national context and personal beliefs on morality with and without legal underpinnings. We find that national religious context, the respondent's age, and religious beliefs and practices are the most consistent predictors of the sexual morality index. For morality sanctioned by the state, however, the effects for personal beliefs and practices are attenuated, and the effects of the national religious context are no longer significant.
Islam and Economic Growth

Nowadays, Muslim countries remain among the least developed countries on all levels, although they are rich in natural resources. Islam, as the common religion of these countries, can be the cause of their underdevelopment? In this context, our paper aims to investigate the impact of Islam, as a proportion of the Muslim population, on economic growth on the one hand, and to seek the factors that may influence this relationship on the other hand. Our empirical study using panel data on a sample of twenty Muslim countries over the period (1990-2014), show that Islam does not promote economic growth. Its effect is lower and negative in the way that Muslim countries have high rates of illiteracy and unemployment.
Search‐based testing using constraint‐based mutation

Many modern automated test generators are based on either metaheuristic search techniques or use constraint solvers. Both approaches have their advantages, but they also have specific drawbacks: Search‐based methods may get stuck in local optima and degrade when the search landscape offers no guidance; constraint‐based approaches, on the other hand, can only handle certain domains efficiently. This paper describes a method that integrates both techniques and delivers the best of both worlds. On a high‐level view, the proposed method uses a genetic algorithm to generate tests, but the twist is that during evolution, a constraint solver is used to ensure that mutated offspring efficiently explores different control flow. Experiments on 20 case study programmes show that on average the combination improves branch coverage by 28% over search‐based techniques while reducing the number of tests by 55%, and improves coverage by 13% over constraint‐based techniques while reducing the number of tests by 73%. Copyright © 2013 John Wiley & Sons, Ltd.
The morbidity and mortality linked to melancholia: two cohorts compared, 1875–1924 and 1995–2005

For over a century, melancholia has been linked to increased rates of morbidity and mortality. Data from two epidemiologically complete cohorts of patients presenting to mental health services in North Wales (1874–1924 and 1995–2005) have been used to look at links between diagnoses of melancholia in the first period and severe hospitalized depressive disorders today and other illnesses, and to calculate mortality rates. This is a study of the hospitalized illness rather than the natural illness, and the relationship between illness and hospitalization remains poorly understood. These data confirm that melancholia is associated with a substantial increase in the standardized mortality rate both formerly and today, stemming from a higher rate of deaths from tuberculosis in the historical sample and from suicide in the contemporary sample. The data do not link melancholia to cancer or cardiac disease. The comparison between outcomes for melancholia historically and severe mood disorder today argue favourably for the effectiveness of asylum care.
Parent-reported executive function behaviors and clinician ratings of attention-deficit/hyperactivity disorder symptoms in children treated with lisdexamfetamine dimesylate.

OBJECTIVE The purpose of this article was to describe the relationships between parent-rated executive function (EF) and clinician-rated attention-deficit/hyperactivity disorder (ADHD) symptoms before and after lisdexamfetamine dimesylate (LDX) treatment in children with and without EF deficit. METHODS In post-hoc analyses of children with ADHD who participated in a 7 week open-label, dose-optimized (LDX 20-70 mg/day) trial, ADHD Rating Scale-IV (ADHD-RS-IV) change scores were compared (using two-sample t tests) between youth with and without clinically significant EF impairment at baseline. Clinically significant impairment was defined as parent-rated Behavior Rating Inventory of EF (BRIEF) Global Executive Composite (GEC) t scores ≥65. Relationships between baseline and endpoint BRIEF and ADHD-RS-IV scores were examined using Pearson correlations and generalized effect linear model. Safety assessment included treatment-emergent adverse events (TEAEs). RESULTS At baseline, 265/315 participants (84.1%) had a clinically significant BRIEF score. Their mean (SD) ADHD-RS-IV total score at baseline was 42.1 (6.64) for those with, and 36.5 (6.67) for those without, clinically significant BRIEF. At endpoint, ADHD-RS-IV total and subscale scores were significantly improved (p<0.0001) for both those with and those without clinically significant baseline BRIEF scores. Moderately strong, positive Pearson correlations were observed between BRIEF and ADHD-RS-IV total and subscale scores. In the generalized effect linear model, ADHD-RS-IV change scores were significantly correlated with endpoint BRIEF scores (r(2)=0.35, β=0.73, p<0.0001). In the subgroup without clinically significant BRIEF t scores at endpoint, parents and clinicians rated 90% and 95%, respectively, as improved. In the subgroup with clinically significant BRIEF t scores at endpoint, parents and clinicians rated 69% and 78%, respectively, as improved. TEAEs were experienced by 269/318 (84.9%) participants; most (82.7%) experienced events mild to moderate in intensity. A total of 12/318 (4.1%) participants discontinued because of TEAEs. CONCLUSION Clinically significant impairment of EF behaviors in children with ADHD was associated with more severe ADHD symptoms. LDX therapy improved ADHD symptom severity, and at endpoint, fewer participants displayed impairment of EF behaviors (versus baseline). The parent-rated BRIEF may describe clinically important EF behaviors not assessed by the 18-item ADHD-RS-IV.
A compact bandpass filter with transmission zero based on SIW triangular cavities

This paper proposes a compact bandpass cross - coupled substrate integrated waveguide (SIW) filter with transmission zero. By using five triangular cavities as basic elements, a pentagon bandpass filter is designed and fabricated on a single-layer substrate with the standard printed circuit boards (PCB) process. This structure shows the advantages of compact SIW triangular cavity. Furthermore, by moving out some via-holes between input and output cavity, the cross-coupling is implemented conveniently, and a transmission zero at the upper sideband is realized.
Discriminative codebook design using multiple vector quantization in HMM-based speech recognizers

Research on multiple vector quantization (MVQ) has shown the suitability of such a technique for speech recognition. Basically, MVQ proposes the use of one separate VQ codebook for each recognition unit. Thus, a MVQHMM model is composed of a VQ codebook and a discrete HMM model. This technique allows the incorporation in the recognition dynamics of the input sequence information wasted by discrete HMM models in the VQ process. The use of distinct codebooks also allows one to train them in a discriminative manner. We propose a new VQ codebook design method for MVQ-based systems, obtained from a modified maximum mutual information estimation. This method provides meaningful error reductions and is performed independently from the estimation of the discrete HMM part of the MVQ model. The results show that the proposed discriminative design turns the MVQHMM technique into a powerful acoustic modeling tool in comparison with other classical methods such as discrete or semicontinuous HMMs.
Co-classification sous contraintes par la somme des résidus quadratiques

Dans de nombreuses applications, une co-classification est plus facile a interpreter qu'une classification mono-dimensionnelle. Il s'agit de calculer une bi-partition ou collection de co-clusters : chaque co-cluster est un groupe d'objets associe a un groupe d'attributs et les interpretations peuvent s'appuyer naturellement sur ces associations. Pour exploiter la connaissance du domaine et ainsi ameliorer la pertinence des partitions, plusieurs methodes de classification sous contraintes ont ete proposees pour le cas mono-dimensionnel (e.g., exploitation de contraintes ``must-link'' et ``cannot-link''). Nous considerons ici la co-classification sous contraintes avec non seulement la gestion de contraintes ``must-link'' et ``cannot-link'' etendues aux dimensions des objets et des attributs, mais encore l'expression de contraintes de contiguite dans le cas de domaines ordonnes. Nous proposons un algorithme iteratif qui minimise la somme des residus quadratiques, une approche introduite en 2004 par Cho et al. pour la co-classification de donnees d'expression de genes. Nous presentons notre algorithme de co-classification qui permet l'exploitation active des contraintes. Nous montrons la valeur ajoutee de ce type d'extraction sur deux applications en analyse du transcriptome.
A fountain code-based fair scheme for multi-hop ad hoc networks

We propose an analytical cross-layer model to quantify tradeoffs between throughput and fairness. We study the effect of coding on the performance of the network while optimizing parameters that govern NETWORK, MAC and PHY layers. Indeed, the heart of our scheme is to code packets at MAC layer before transmitting them through the common lossy channel. To the best of our knowledge, we are the first to use Fountain codes at MAC layer. Indeed, coding packets is usually studied at APPLICATION [2], [6], [7] or TRANSPORT layers [5]. In standard IEEE 802.11, whenever a collision occurs the whole packet is lost and needs to be retransmitted. Our scheme uses an incremental combination of all previous copies of a backlogged packet to improve the decoding probability and therefore to correctly recover the original packet. Using Fountain coding increases the Jain's Fairness index over the network. It indeed improves the throughput on paths that suffer from high collision probability. However unfortunately, it may decrease the throughput on the other paths. This is due to the injected redundancy in coded packets and its negative effect on reducing the channel idle period seen by concurrent users.
Treatment of Murine Coccidioidomycosis with Polymyxin B

An agar dilution method was employed to test the susceptibility of 12 strains of Coccidioides immitis to polymyxin B (PB). After 3 days of incubation, eight strains were markedly inhibited by 5.0 μg of PB per ml and four strains did not grow. PB at 10 μg/ml inhibited the growth of all strains through 20 days of incubation. To determine whether PB has anticoccidioidal activity in vivo, mice in groups of 30 were infected intraperitoneally with a mean lethal dose (LD50) or 20 LD50 of arthrospores of C. immitis ATCC 28868 (Silveira). Treatment by intraperitoneal injection of PB (2.5 mg/kg) was begun 2 or 5 days after challenge. By 40 days after infection, 47 and 7% of the untreated mice challenged with an LD50, respectively, were alive. Of mice infected with an LD50 or 20 LD50 and treated with PB beginning 2 days after the challenge, 90% of each group were alive by day 40. Initiation of PB therapy 5 days after infection permitted survival of 84% of the mice infected with an LD50; however, only 27% of the mice infected with 20 LD50 survived by day 40. In this latter group there was evidence that PB prolonged life since 56% of the treated mice were alive by day 15 as compared with 30% of the controls. PB in vivo was fungistatic since the majority of treated mice had C. immitis in the liver, lungs, and spleen.
Differential effects of the HESR/HEY transcription factor family on dopamine transporter reporter gene expression via variable number of tandem repeats

The 3′‐untranslated region (UTR) of the human dopamine transporter (DAT1) gene contains a variable number of tandem repeats (VNTR) domain, which is thought to be associated with dopamine‐related psychiatric disorders, personality, and behavior. However, the molecular and neuronal functions of polymorphisms within the VNTR domain are unknown. We previously identified the transcription factor HESR1 (HEY1) as a VNTR‐binding protein. Hesr1 knockout mice exhibit DAT up‐regulation in the brain and low levels of spontaneous activity. Other members of the HESR (HEY) family, including HESR2 (HEY2) and 3 (HEYL), have similar DNA‐binding domains. In this study, we analyzed the effects of HESR1, ‐2, and ‐3 on DAT1 expression in human neuroblastoma SH‐SY5Y cells using luciferase reporter assays. We found that the VNTR domain played an inhibitory role in DAT1 reporter gene expression and that HESR1 and ‐2 inhibited expression via both the core promoter and the VNTR. The inhibitory effects of HESR family members on DAT reporter gene expression differed depending on the number of repeats in the VNTR domain. We also found that each Hesr was expressed in the dopaminergic neurons in the mouse midbrain. These results suggest that the HESR family is involved in DAT expression via the VNTR domain. © 2011 Wiley‐Liss, Inc.
Historical note on the origin of the LaSota strain of Newcastle disease virus.

It has been more than thirty years since live-virus Newcastle disease vaccines were introduced for use in poultry production. One aspect of the situation has never been reported: the complete history of the LaSota strain of vaccine virus, now used throughout the world. The writer is the last person alive who had intimate knowledge of the situation; the others were Dr. Fred R. Beaudette, Dr. Arthur D. Goldhaft, Dr. Nathan E. Wernicoff, and Charles B. Hudson.
Acidogenic value of feeds II. Effects of rumen acid load from feeds on dry matter intake, ruminal pH, fibre degradability and milk production in the lactating dairy cow

Rustomo, B. , AlZahal, O. , Cant, J. P., Fan, M. Z. , Duffield, T. F. , Odongo, N. E. and McBride, B. W. 2006. Acidogenic value of feeds. II. Effects of rumen acid load from feeds on dry matter intake, ruminal pH, fibre degradability and milk production in the lactating dairy cow. Can. J. Anim. Sci. 86: 119‐126. The previous study evaluated the acidogenic value (AV) of a series of feeds. The objective of the current study was to determine the effect of increasing feed AV on dry matter intake (DMI), ruminal pH, fibre degradability and milk production and composition in lactating dairy cows. Two isoenergetic and isonitrogenous concentrate diets with either a low AV (LAV) or high AV (HAV) were formulated and fed along with corn silage and alfalfa silage in a total mixed ration (TMR). The diets were fed for ad libitum intake with as-fed forage to concentrate ratio of 57:43. Four rumen fistulated dairy cows (230 ± 30 DIM) were randomly assigned to one of the two treatments in a crossover design. Increasing feed AV increased (P 0.05) on mean ruminal pH, DMI, and 4% fat corrected milk. These results emphasize the significance of ruminal pH variations and frequency distributions over time when evaluating the effect of feed AV on ruminal pH. The results suggest that feed AV could be used to predict ruminal pH in vivo.