Miracle-dz/UniFAR-FTUs huggingface dataset:
A comprehensive and scalable method for analyzing fine-grained source code change patterns

This paper presents a comprehensive method for identifying fine-grained change patterns in the source code of large-scale software projects. Source code changes are computed by differencing abstract syntax trees of adjacent versions and transferred to a set of logical statements called a factbase. A factbase contains information for tracking and relating source code entities across versions and can be used to integrate analysis results of other tools such as call graphs and control flows. Users can obtain a list of change pattern instances by querying the factbase. Experiments conducted on the Linux-2.6 kernel, which involve more than 4 billions of facts, are reported to demonstrate capability of the method.
Industrial Monitoring by Evolving Fuzzy Systems

Industrial monitoring of complex processes with hundreds or thousands of variables is a hard task faced in this work through evolving fuzzy systems. The Visbreaker process of the Sines Oil Refinery is the case studied. Firstly dimension reduction is performed by multidimensional scaling, obtaining the process evolution in a three dimensional space. Then an evolving fuzzy system (eFS) is developed to detect eventual malfunction of sensors. This eFS takes the data in the three reduced dimensions as antecedents and classifies the process state into normal and abnormal states. A software platform- the eFSLab (Evolving Fuzzy Systems Laboratory) - , with which this work has been developed, is presented and discussed. Several strategies for rule creation and evolution of rules, for Takagi-Sugeno (and for Mamdani system obtained from these) , are implemented in eFSLab. The obtained eFS shows a promising performance in the case studied, classifying in some simulations the state of the process into abnormal-normal condition in about 95% of the cases, with a number of rules between 5 and 8.
Predictive Factors of Early Mortality in Children With Developmental Disabilities: A Case-Comparison Analysis

The aim of this study was to identify the risk factors for early mortality in children with neurodevelopmental disabilities. Of 1000 children who were sequentially referred to the same child developmental center over the period 1975—1985, 81 children died between the ages of 6 months and 22 years (mean, 8.04 years; 6.1 SD). A group of 81 age-matched children and another group of 81 developmentally and age-matched children also referred to the center served as comparison groups. Following multivariate analysis, low developmental quotient, restricted mobility, assisted feeding, and genetic etiology were risk factors for early mortality when compared to the age-matched group (P < .01). In comparison to the developmentally matched group, restricted mobility, genetic etiology, and hearing deficit were identified as significant risk factors (P < .01). Comprehensive treatment at the child development center was demonstrated to be a significant protective factor (P = .004). Socioeconomic variables were not significant in predicting an increased mortality risk in disabled individuals. In conclusion, in addition to mobility and feeding skills, a genetic etiology and hearing deficit are risk factors for early mortality, whereas socioeconomic variables are not. A comprehensive treatment program was found to be a protective factor.
Effective spatially fractionated GRID radiation treatment planning for a passive grid block.

OBJECTIVE To commission a grid block for spatially fractionated grid radiation therapy (SFGRT) treatments and describe its clinical implementation and verification through the record and verify (R&V) system. METHODS SFGRT was developed as a treatment modality for bulky tumours that cannot be easily controlled with conventionally fractionated radiation. Treatment is delivered in the form of open-closed areas. Currently, SFGRT is performed by either using a commercially available grid block or a multileaf collimator (MLC) of a linear accelerator. In this work, 6-MV photon beam was used to study dosimetric characteristics of the grid block. We inserted the grid block into a commercially available treatment planning system (TPS), and the feasibility of delivering such treatment plans on a linear accelerator using a R&V system was verified. Dose measurements were performed using a miniature PinPoint(TM) ion chamber (PTW, Freiburg, Germany) in a water phantom and radiochromic film within solid water slabs. PinPoint ion chamber was used to measure the output factors, percentage depth dose (PDD) curves and beam profiles at two depths, depth of maximum dose (zmax) and 10 cm. Film sheets were used to measure dose profiles at zmax and 10-cm depth. RESULTS The largest observed percentage difference between output factors for the grid block technique calculated by the TPS and measured with the PinPoint ion chamber was 3.6% for the 5 × 5-cm(2) field size. Relatively significant discrepancies between measured and calculated PDD values appear only in the build-up region, which was found to amount to <4%, while a good agreement (differences <2%) at depths beyond zmax was observed. Dose verification comparisons performed between calculated and measured dose distributions were in clinically acceptable agreements. When comparing the MLC-based with the grid block technique, the advantage of treating large tumours with a single field reduces treatment time by at least 3-5 times, having significant impact on patient throughput. CONCLUSION The proposed method supports and helps to standardize the clinical implementation of the grid block in a safer and more accurate way. ADVANCES IN KNOWLEDGE This work describes the method to implement treatment planning for the grid block technique in radiotherapy departments.
Embedding guidelines into direct physician order entry: simple methods, powerful results

Kaiser Permanente in the Northwest Region has implemented a comprehensive outpatient computer-based patient record (CPR). Using this system, clinicians electronically order laboratory tests, radiology tests, and prescriptions. Clinicians also use this comprehensive CPR to document encounters, code diagnoses and procedures, maintain problem lists, and to send patient-specific messages and referrals to other medical providers. Healthcare for our entire membership of 440,000 covered lives is now provided through this system [1]. Implementation of a comprehensive CPR with direct physician order-entry provides the opportunity to embed guidelines into the ordering process. This article describes the underlying theme and various simple but effective methods we use to embed guidelines into the ordering process. Our experience demonstrates the powerful effect of these simple methods to reduce unnecessary variation and to reduce cost while maintaining or improving the quality of care delivery.
The ONE simulator for DTN protocol evaluation

Delay-tolerant Networking (DTN) enables communication in sparse mobile ad-hoc networks and other challenged environments where traditional networking fails and new routing and application protocols are required. Past experience with DTN routing and application protocols has shown that their performance is highly dependent on the underlying mobility and node characteristics. Evaluating DTN protocols across many scenarios requires suitable simulation tools. This paper presents the Opportunistic Networking Environment (ONE) simulator specifically designed for evaluating DTN routing and application protocols. It allows users to create scenarios based upon different synthetic movement models and real-world traces and offers a framework for implementing routing and application protocols (already including six well-known routing protocols). Interactive visualization and post-processing tools support evaluating experiments and an emulation mode allows the ONE simulator to become part of a real-world DTN testbed. We show sample simulations to demonstrate the simulator's flexible support for DTN protocol evaluation.
Imaging of upper urinary tract cancer: using conventional MRI and diffusion-weighted MRI with different b values

Background Diffusion-weighted magnetic resonance imaging (DW-MRI) has been considered to be useful in diagnosing upper urinary tract (UUT) disease; however, the value of DW-MRI with different b values has not been reported. Purpose To evaluate the performance of using conventional MRI alone and in combination with DWI with different b values in diagnosing UUT cancer. Material and Methods Seventy patients with suspected UUT cancer underwent conventional MRI (T1-weighted and T2-weighted) and DW-MRI (b = 500 and 1500 s/mm2) on a 3 T-MRI scanner. The ureteroscopic and histopathologic findings were compared with the imaging findings. The utility of detecting UUT cancer using conventional MRI (set A), combined DW-MRI (b = 500 s/mm2) and conventional MRI (set B), and combined DW-MRI (b = 1500 s/mm2) and conventional MRI (set C) were independently evaluated by two readers. Results A total of 32 patients had verified cancer; 23 patients had benign UUT diseases, and 15 had no abnormality. Sets B and C had significantly improved diagnostic accuracy for UUT cancer compared with set A; the specificity in diagnosing UUT cancer was significantly improved when using set C compared with sets A and B. In patients without UUT obstructions, improved sensitivity and accuracy in diagnosis was achieved when using sets B and C compared with set A. Conclusion Using DW-MRI in combination with conventional MRI provides increased diagnostic accuracy and sensitivity in patients without UUT obstruction. The combination of conventional MRI and DW-MRI with a higher b value (1500 s/mm2) improved the specificity in diagnosing UUT cancer compared to conventional sequences and DW-MRI with a lower b value (500 s/mm2).
Non-Hookean Elastic Behavior and Crystallite Orientation in Carbon Fibers

Four different PAN-based carbon fibers (high strength, high modulus, and two enhanced strain fibers) were investigated in the standard single filament tensile tests. Nonlinear response was observed in all tested carbon fibers, but the nonlinearity in these fibers was not of the same extent. The tangential fiber modulus values for successive strain intervals (from zero up to failure strain) were fitted by linear as well as the second-order polynomial regression method. The coefficients of linear and square regression as well as the mean square deviation of experimental points from the points on a fitted curve were equal in all tested groups of fibers. The fitted square regression curve has a theoretical foundation, but the empirical expression is obtained by linear regression of modulus—strain data in carbon fibers. However, since the obtained linear relations include the coefficient γ, which can be a measure of elastic nonlinearity, deduced γ coefficient values were correlated to the parameters of carbon fiber crystallite structure as well as crystallites orientation.
Perception of spontaneous narrative structure

The present paper reports the results of a perceptual experiment that was conducted in order to find out to what extent naïve, untrained labelers can benefit from prosodic information present in spontaneous narratives so as to derive an underlying structure associated with them. Results from inter-rater agreements suggest that even when the lexical, syntactic, and semantic information of a narrative is blocked, labelers can still identify its underlying structure, which clearly indicates that listeners make substantial use of prosodic information in the task of identifying the structure of spontaneous narratives.
Soluble Extract from Moringa oleifera Leaves with a New Anticancer Activity

Moringa oleifera has been regarded as a food substance since ancient times and has also been used as a treatment for many diseases. Recently, various therapeutic effects of M. oleifera such as antimicrobial, anticancer, anti-inflammatory, antidiabetic, and antioxidant effects have been investigated; however, most of these studies described only simple biological phenomena and their chemical compositions. Due to the increasing attention on natural products, such as those from plants, and the advantages of oral administration of anticancer drugs, soluble extracts from M. oleifera leaves (MOL) have been prepared and their potential as new anticancer drug candidates has been assessed in this study. Here, the soluble cold Distilled Water extract (4°C; concentration, 300 µg/mL) from MOL greatly induced apoptosis, inhibited tumor cell growth, and lowered the level of internal reactive oxygen species (ROS) in human lung cancer cells as well as other several types of cancer cells, suggesting that the treatment of cancer cells with MOL significantly reduced cancer cell proliferation and invasion. Moreover, over 90% of the genes tested were unexpectedly downregulated more than 2-fold, while just below 1% of the genes were upregulated more than 2-fold in MOL extract-treated cells, when compared with nontreated cells. Since severe dose-dependent rRNA degradation was observed, the abnormal downregulation of numerous genes was considered to be attributable to abnormal RNA formation caused by treatment with MOL extracts. Additionally, the MOL extract showed greater cytotoxicity for tumor cells than for normal cells, strongly suggesting that it could potentially be an ideal anticancer therapeutic candidate specific to cancer cells. These results suggest the potential therapeutic implications of the soluble extract from MOL in the treatment of various types of cancers.
Attentional Control in the Aging Brain: Insights from an fMRI Study of the Stroop Task

Several recent studies of aging and cognition have attributed decreases in the efficiency of working memory processes to possible declines in attentional control, the mechanism(s) by which the brain attempts to limit its processing to that of task-relevant information. Here we used fMRI measures of neural activity during performance of the color-word Stroop task to compare the neural substrates of attentional control in younger (ages: 21-27 years old) and older participants (ages: 60-75 years old) during conditions of both increased competition (incongruent and congruent neutral) and increased conflict (incongruent and congruent neutral). We found evidence of age-related decreases in the responsiveness of structures thought to support attentional control (e.g., dorsolateral prefrontal and parietal cortices), suggesting possible impairments in the implementation of attentional control in older participants. Consistent with this notion, older participants exhibited more extensive activation of ventral visual processing regions (i.e., temporal cortex) and anterior inferior prefrontal cortices, reflecting a decreased ability to inhibit the processing of task-irrelevant information. Also, the anterior cingulate cortex, a region involved in evaluatory processes at the level of response (e.g., detecting potential for error), showed age-related increases in its sensitivity to the presence of competing color information. These findings are discussed in terms of newly emerging models of attentional control in the human brain.
Contrast Effects in Flavour Preference Learning

In four experiments the role of contrast effects in producing learned flavour preferences was examined. The experiments showed that contrast effects are pervasive in flavour preference learning, producing results that are often paradoxical from a traditional reinforcement point of view. In Experiment 1, rats preferred a reinforced flavour over a nonreinforced flavour more if the reinforcer was 1% sucrose than if the reinforcer was 8% sucrose. Because the cue flavour was dissolved in 8% sucrose, this represents an anticipatory positive contrast effect. In Experiment 2, the relationship between cue and consequence was shown to be important in flavour preference learning, as expected if contrast effects are involved. In Experiment 3, rats preferred a flavour that was reinforced 4 times, and they preferred this flavour more than one reinforced 8 times, presumably because the greater the expectancy of the consequence, the greater the anticipatory negative contrast. In Experiment 4, rats consumed less of 0.15% saccharin if they received 32% sucrose randomly 90 min either before or after the 0.15% saccharin than if they received only 0.15% saccharin, a simultaneous negative contrast effect.
Unifying measures of gene function and evolution

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein–protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein–protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's ‘importance’, or the ‘status’ of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein–protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's ‘adaptability’ whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC ‘reactivity’. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.
Relationship between Musical Characteristics and Temporal Breathing Pattern in Piano Performance

Although there is growing evidence that breathing is modulated by various motor and cognitive activities, the nature of breathing in musical performance has been little explored. The present study examined the temporal breath pattern in piano performance, aiming to elucidate how breath timing is related to musical organization/events and performance. In the experiments, the respiration of 15 professional and amateur pianists, playing 10 music excerpts in total (from four-octave C major scale, Hanon's exercise, J. S. Bach's Invention, Mozart's Sonatas, and Debussy's Clair de lune), was monitored by capnography. The relationship between breathing and musical characteristics was analyzed. Five major results were obtained. (1) Mean breath interval was shortened for excerpts in faster tempi. (2) Fluctuation of breath intervals was reduced for the pieces for finger exercise and those in faster tempi. Pianists showing large within-trial fluctuation also exhibited large inter-excerpt difference. (3) Inter-trial consistency of the breath patterns depended on the excerpts. Consistency was generally reduced for the excerpts that could be performed mechanically (i.e., pieces for finger exercise), but interestingly, one third of the participant showed consistent patterns for the simple scale, correlated with the ascending/descending sequences. (4) Pianists tended to exhale just after the music onsets, inhale at the rests, and inhibit inhale during the slur parts. There was correlation between breathing pattern and two-voice polyphonic structure for several participants. (5) Respiratory patterns were notably different among the pianists. Every pianist showed his or her own characteristic features commonly for various musical works. These findings suggest that breathing in piano performance depends not only on musical parameters and organization written in the score but also some pianist-dependent factors which might be ingrained to individual pianists.
A Geometrical-Based Vertical Gain Correction for Signal Strength Prediction of Downtilted Base Station Antennas in Urban Areas

Base station antenna downtilt is one of the most important parameters for optimizing a cellular network with tight frequency reuse. By downtilting, inter-site interference is reduced, which leads to an improved performance of the network. In this study we show that a simple geometrical-based extension to standard empirical path loss prediction models can give quite reasonable accuracy in predicting the signal strength from tilted base station antennas in small urban macro-cells. Our evaluation is based on measurements on several sectors in a 2.6 GHz Long Term Evolution (LTE) cellular network, with electrical antenna downtilt in the range from 0 to 10 degrees, as well as predictions based on ray-tracing and 3D building databases covering the measurement area. Although the calibrated ray-tracing predictions are highly accurate compared with the measured data, the combined LOS/NLOS COST-WI model with downtilt correction performs similarly for distances above a few hundred meters. Generally, predicting the effect of base station antenna tilt close to the base station is difficult due to multiple vertical sidelobes.
Medical biometrics in mobile health monitoring

This work investigates the feasibility of ECG-based identity management in mobile health monitoring applications. A body area network that operates in conjunction with ECG biometric recognition is explored for mobile monitoring of patients, rescuers, pilots, soldiers, or field agents in general. Among the major challenges of this technology is the stability of the signals over the monitoring duration. Time dependency is responsible for ECG destabilization, which becomes a significant issue for reliable monitoring. We propose a novel framework that addresses this inadequacy, by updating a gallery template when feature matching is compromised. In addition, strategies for tackling privacy issues in medical data management are proposed. A protocol level solution is discussed, to deal with the ethical issues of this technology. An automatic way of aggregating and managing personal information is presented, designated to operate on the basis of anonymity. The experimental performance measured over long-ECG recordings demonstrates promising results. Copyright © 2010 John Wiley & Sons, Ltd.