Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Usability of Software Refactoring Tools

Post-deployment maintenance and evolution can account for up to 75% of the cost of developing a software system. Software refactoring can reduce the costs associated with evolution by improving system quality. Although refactoring can yield benefits, the process includes potentially complex, error-prone, tedious and time-consuming tasks. It is these tasks that automated refactoring tools seek to address. However, although the refactoring process is well-defined, current refactoring tools do not support the full process. To develop better automated refactoring support, we have completed a usability study of software refactoring tools. In the study, we analysed the task of software refactoring using the ISO 9241-11 usability standard and Fitts' List of task allocation. Expanding on this analysis, we reviewed 11 collections of usability guidelines and combined these into a single list of 38 guidelines. From this list, we developed 81 usability requirements for refactoring tools. Using these requirements, the software refactoring tools Eclipse 3.2, Condenser 1.05, RefactorIT 2.5. 1, and Eclipse 3.2 with the Simian UI 2.2. 12 plugin were studied. Based on the analysis, we have selected a subset of the requirements that can be incorporated into a prototype refactoring tool intended to address the full refactoring process.
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment

UNLABELLED Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants. This PheWAS implementation allows users to translate ICD-9 codes to PheWAS case and control groups, perform analyses using these and/or other phenotypes with covariate adjustments and plot the results. We demonstrate the methods by replicating a PheWAS on rs3135388 (near HLA-DRB, associated with multiple sclerosis) and performing a novel PheWAS using an individual's maximum white blood cell count (WBC) as a continuous measure. Our results for rs3135388 replicate known associations with more significant results than the original study on the same dataset. Our PheWAS of WBC found expected results, including associations with infections, myeloproliferative diseases and associated conditions, such as anemia. These results demonstrate the performance of the improved classification scheme and the flexibility of PheWAS encapsulated in this package. AVAILABILITY AND IMPLEMENTATION This R package is freely available under the Gnu Public License (GPL-3) from http://phewascatalog.org. It is implemented in native R and is platform independent.
The Neuroanatomical, Neurophysiological and Psychological Basis of Memory: Current Models and Their Origins

This review aims to classify and clarify, from a neuroanatomical, neurophysiological, and psychological perspective, different memory models that are currently widespread in the literature as well as to describe their origins. We believe it is important to consider previous developments without which one cannot adequately understand the kinds of models that are now current in the scientific literature. This article intends to provide a comprehensive and rigorous overview for understanding and ordering the latest scientific advances related to this subject. The main forms of memory presented include sensory memory, short-term memory, and long-term memory. Information from the world around us is first stored by sensory memory, thus enabling the storage and future use of such information. Short-term memory (or memory) refers to information processed in a short period of time. Long-term memory allows us to store information for long periods of time, including information that can be retrieved consciously (explicit memory) or unconsciously (implicit memory).
T-S Fuzzy Controller in Consideration of Input Constraint

This paper deals with stability analysis and control design for a class of nonlinear systems with input constraint when using T-S fuzzy model. After leading the control design to LMIs approach, the attention is paid to 1) how to easy the LMIs conditions so that the system is asymptotically stable in a so-called ellipsoid to be made as large as possible; and 2) how to relax the LMIs conditions so that the LMIs problem is more feasible.
Clearing Artifacts using a Constrained Stability Least Mean Square Algorithm from Cardiac Signals

In this paper, a novel least-mean-square (LMS) algorithm for filtering artifacts in the adaptive noise cancelation (ANC) is proposed. It is based on the minimization of the squared Euclidean norm of the difference weight vector under a stability constraint defined over a posteriori estimation error. The Lagrangian methodology has been used in order to propose a nonlinear adaptation rule defined in terms of the product of differential inputs and errors which means a generalization of the normalized LMS algorithm, the resultant algorithm is called as Constrained Stability Least Mean Square (CSLMS) algorithm. Different filter structures are presented to eliminate the diverse forms of noise like LMS, NLMS etc., Proposed algorithm is applied on real ECG signals obtained from the MIT-BIH (Massachusetts Institute of Technology-Beth Israel Hospital) data base and compared its performance with the conventional LMS algorithm. A simulation result demonstrates superior performance of this proposed algorithm.
RapidMRC: approximating L2 miss rate curves on commodity systems for online optimizations

Miss rate curves (MRCs) are useful in a number of contexts. In our research, online L2 cache MRCs enable us to dynamically identify optimal cache sizes when cache-partitioning a shared-cache multicore processor. Obtaining L2 MRCs has generally been assumed to be expensive when done in software and consequently, their usage for online optimizations has been limited. To address these problems and opportunities, we have developed a low-overhead software technique to obtain L2 MRCs online on current processors, exploiting features available in their performance monitoring units so that no changes to the application source code or binaries are required. Our technique, called RapidMRC, requires a single probing period of roughly 221 million processor cycles (147 ms), and subsequently 124 million cycles (83 ms) to process the data. We demonstrate its accuracy by comparing the obtained MRCs to the actual L2 MRCs of 30 applications taken from SPECcpu2006, SPECcpu2000, and SPECjbb2000. We show that RapidMRC can be applied to sizing cache partitions, helping to achieve performance improvements of up to 27%.
Evidence for synergistic control of glutamate biosynthesis by glutamate dehydrogenases and glutamate in Bacillus subtilis.

In the Gram-positive bacterium, Bacillus subtilis glutamate is synthesized by the glutamine synthetase and the glutamate synthase (GOGAT). During growth with carbon sources that exert carbon catabolite repression, the rocG glutamate dehydrogenase (GDH) gene is repressed and the transcription factor GltC activates the expression of the GOGAT encoding gltAB genes. In the presence of amino acids of the glutamate family, the GDH RocG is synthesized and the enzyme prevents GltC from binding to DNA. The dual control of glutamate biosynthesis allows the efficient utilization of the available nutrients. Here we provide genetic and biochemical evidence that, like RocG, also the paralogous GDH GudB can inhibit the transcription factor GltC, thereby controlling glutamate biosynthesis. Contradictory previous observations show that high level of GDH activity does not result in permanent inhibition of GltC. By controlling the intracellular levels of glutamate through feeding with exogenous arginine, we observed that the GDH-dependent control of GltC and thus expression of the gltAB genes inversely correlates with the glutamate pool. These results suggest that the B. subtilis GDHs RocG and GudB in fact act as glutamate sensors. In conclusion, the GDH-mediated control of glutamate biosynthesis seems to depend on the intracellular glutamate concentration.
Tiered Clustering to Improve Lexical Entailment

Many tasks in Natural Language Processing involve recognizing lexical entailment. Two different approaches to this problem have been proposed recently that are quite different from each other. The first is an asymmetric similarity measure designed to give high scores when the contexts of the narrower term in the entailment are a subset of those of the broader term. The second is a supervised approach where a classifier is learned to predict entailment given a concatenated latent vector representation of the word. Both of these approaches are vector space models that use a single context vector as a representation of the word. In this work, I study the effects of clustering words into senses and using these multiple context vectors to infer entailment using extensions of these two algorithms. I find that this approach offers some improvement to these entailment algorithms.
An In-House RD1-Based Enzyme-Linked Immunospot-Gamma Interferon Assay Instead of the Tuberculin Skin Test for Diagnosis of Latent Mycobacterium tuberculosis Infection

ABSTRACT Identification of individuals infected with Mycobacterium tuberculosis is essential for the control of tuberculosis (TB). The specificity of the currently used tuberculin skin test (TST) is poor because of the broad antigenic cross-reactivity of purified protein derivative (PPD) with BCG vaccine strains and environmental mycobacteria. Both ESAT-6 and CFP-10, two secretory proteins that are highly specific for M. tuberculosis complex, elicit strong T-cell responses in subjects with TB. Using an enzyme-linked immunospot (ELISPOT)-IFN-γ assay and a restricted pool of peptides derived from ESAT-6 and CFP-10, we have previously demonstrated a high degree of specificity and sensitivity of the test for the diagnosis of TB. Here, 119 contacts of individuals with contagious TB who underwent TST and the ELISPOT-IFN-γ assay were consecutively recruited. We compared the efficacy of the two tests in detecting latent TB infection and defined a more appropriate TST cutoff point. There was little agreement between the tests (k = 0.33, P < 0.0001): 53% of the contacts with a positive TST were ELISPOT negative, and 7% with a negative TST were ELISPOT positive. Furthermore, respectively 76 and 59% of the ELISPOT-negative contacts responded in vitro to BCG and PPD, suggesting that most of them were BCG vaccinated or infected with nontuberculous mycobacteria. The number of spot-forming cells significantly correlated with TST induration (P < 0.0001). Our in-house ELISPOT assay based on a restricted pool of highly selected peptides is more accurate than TST for identifying individuals with latent TB infection and could improve chemoprophylaxis for the control of TB.
Concurrent and prospective associations among biological maturation, and physical activity at 11 and 13 years of age

This study examined concurrent and prospective associations between objective measures of biological maturation, body composition and physical activity (PA) in adolescent males (n = 671) and females (n = 680). Participants born to women recruited to the Avon Longitudinal Study of Parents and Children birth cohort study were assessed at 11 and 13 years. Percentage of predicted adult stature was used as an estimate of biological maturation. PA and time sedentary was assessed over 7 consecutive days using Actigraph accelerometers. Body composition was assessed using whole‐body DXA scans. At 11 and 13 years, maturity in males was inversely associated with accelerometer counts‐per‐minute (CPM) and time engaged in light PA, and positively associated with time sedentary. In females, maturity was inversely associated with accelerometer (CPM) at 11 but not 13 years. Adjusting for accelerometer wear times and corresponding activity levels at 11 years, maturity and percentage fat mass at 11 years did not predict any indices of PA or sedentary behavior in males or females at 13 years. Whereas advanced maturation in males is associated with less PA and more sedentary behavior at 11 and 13 years, maturity at 11 does not predict PA or sedentary behavior at 13 years in either sex.
CAM02-1: Time-Driven Early Discard (TED) to Improve the Fairness of TCP Congestion Control

This paper proposes a novel adaptive AQM (advanced queue management) approach called Time-Driven Early Discard (TED). The basic underlying idea is to set a deadline on packet service time in routers, beyond which packets are discarded. TED is shown to improve fairness among TCP connections sharing congested links when the deadline is chosen proportional to their round trip time (RTT). TED is adaptive in limiting the throughput of only those connections that traverse congested links. In fact, as demonstrated by the presented results, TCP connections traversing parts of the network with enough available capacity can achieve the maximum throughput enabled by their transmission window as corresponding packets do not reach their deadline . Finally, the paper shows how TED can be instrumental in enabling TCP to deploy shorter retransmission timeouts, which results in prompter reactivity to loss, hence improved performance overall in terms of achieved goodput.
Review of MIMO-OFDM System for Time / Frequency Selective Fading Channel

Orthogonal frequency division multiplexing (OFDM) and Multiple-Input Multiple-Output (MIMO) are the popular technique for transmission of signals over wireless channels. They individually assisting multipath fading environment and improving link reliability without sacrificing bandwidth and also provide high data rate. The combination of OFDM and MIMO seems to be the key technology in next generation high data rate wireless mobile systems. In this paper firstly, MIMO and OFDM technology is introduce. Secondly, we provide an overview of spacetime (ST) coding, space-frequency (SF) coding and spacetime-frequency (STF) coding techniques for MIMO-OFDM systems which improve the reliability of system further. Finally performances comparison of the different coding techniques for OFDM-MIMO system is done.
Performance Debugging of Real-Time Systems Using Multicriteria Schedulability Analysis

Most of today's real-time embedded systems consist of a heterogeneous mix of fully-programmable processors, fixed-function components or hardware accelerators, and partially-programmable engines. Hence, system designers are faced with an array of implementation possibilities for an application at hand. Such possibilities typically come with different tradeoffs involving cost, power consumption and packaging constraints. As a result, a designer is no longer interested in one implementation that meets the specified real-time constraints (i.e. is schedulable), but would rather like to identify all schedulable implementations that expose the different possible performance tradeoffs. In this paper we formally define this multicriteria schedulability analysis problem and derive a polynomial-time approximation algorithm for solving it. This result is interesting because the problem of optimally computing even one schedulable solution in our setup (and in most common setups) is computationally intractable (NP-hard). Further, our algorithm is reasonably easy to implement, returns good quality (approximate) solutions, and offers significant speedups over optimally computing all schedulable tradeoffs
When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks

MOTIVATION Enormous and constantly increasing quantity of biological information is represented in metabolic and in protein interaction network databases. Most of these data are freely accessible through large public depositories. The robust analysis of these resources needs novel technologies, being developed today. RESULTS Here we demonstrate a technique, originating from the PageRank computation for the World Wide Web, for analyzing large interaction networks. The method is fast, scalable and robust, and its capabilities are demonstrated on metabolic network data of the tuberculosis bacterium and the proteomics analysis of the blood of melanoma patients. AVAILABILITY The Perl script for computing the personalized PageRank in protein networks is available for non-profit research applications (together with sample input files) at the address: http://uratim.com/pp.zip.
Optimal clock synchronization

We present a simple, efficient and unified solution to the problems of synchronizing clocks, initializing these clocks, and integrating new clocks, for both authenticated and nonauthenticated systems with arbitrary failures. This is the first known solution that achieves optimal accuracy, i.e., the accuracy of synchronized clocks (with respect to real time) is as good as that specified for the underlying hardware clocks. The algorithms presented are also optimal with respect to the number of faulty processes that can be tolerated to achieve this accuracy. 1. I n t r o d u c t i o n An important problem in distributed computing is that of synchronizing clocks in spite of faults. Given "hardware" clocks whose rate of drift from real time is within + Partial support for this work was provided by the National Science Foundation under grant MCS 83-03135. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the ACM copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Association for Computing Machinery. To copy otherwise, or to republish, requires a fee and /o r specific permission. ©1985 ACM 0-89791-167-9/1985/0800-0071 $00.75 known bounds, synchronization consists of maintaining logical clocks that are never too far apart. Processes maintain these logical clocks by computing periodic adju#tments to their hardware clocks. Although the underlying hardware clocks have a bounded rate of drift from real time, the drift of logical clocks can exceed this bound. In other words, synchronized logical clocks can have a lower accuracy (with respect to real time) than that specified for hardware clocks. This reduction in accuracy might appear to be an inherent consequence of synchronization. The rate of drift of faulty hardware clocks can be beyond the specified bounds, and correct logical clocks can be forced to drift with them. Furthermore, variation in message delivery times introduces uncertainty in evaluating values of clocks of other processes. All previous synchronization algorithms exhibit this reduction in accuracy [Lamp85, Halp84, Lund84, Dole84]. In this paper we show that accuracy need not be sacrificed in order to achieve synchronization. We present the first
PERL-a registerless architecture

Reducing processor memory speed gap is one of the major challenges computer architects face today. Efficient use of CPU registers reduces the number of memory accesses. However, registers do incur extra overhead of load/store, register allocation and saving of register context across procedure calls. Caches however do not have any such overheads and cache technology has matured to the extent that today the access time of on-chip cache is almost equal to that of registers. This motivates one to explore alternate ways to do away with the overheads of registers. We propose a registerless, memory to memory architecture of a processor. We call this architecture Performance Enhanced Registerless (PERL) processor. All instructions in this processor operate directly on memory operands thus eliminating the load/store and other overheads of registers. The performance of this machine is studied by simulations and results are reported in the paper.
Decentralized Power Management of a PV/Battery Hybrid Unit in a Droop-Controlled Islanded Microgrid

In this paper, a control strategy is proposed to achieve decentralized power management of a PV/battery hybrid unit in a droop-controlled islanded microgrid. In contrast to the common approach of controlling the PV unit as a current source, in the proposed strategy, the PV unit is controlled as a voltage source that follows a multi-segment adaptive power/frequency characteristic curve. The proposed power/frequency characteristics, of the hybrid unit and of the whole microgrid, adapt autonomously to the microgrid operating conditions so that the hybrid unit may supply the maximum PV power, match the load, and/or charge the battery, while maintaining the power balance in the microgrid and respecting the battery state-of-charge limits. These features are achieved without relying on a central management system and communications, as most of the existing algorithms do. The control strategy is implemented using multi-loop controllers, which provide smooth and autonomous transitions between the operating scenarios. Small-signal stability of the proposed control loops is investigated, and the system performance is experimentally validated on a 3.5 kVA microgrid.
An efficient homotopy method for finding DC operating points of nonlinear circuits

Finding the DC operating points of nonlinear circuits is an important problem in circuit simulation. The Newton-Raphson method employed in SPICE-like simulators often falls to converge to a solution. To overcome this convergence problem, homotopy methods have been studied from various viewpoints. There are several types of homotopy methods, one of which succeeded in solving bipolar analog circuits with more than 20,000 elements with the theoretical guarantee of global convergence. We propose an improved version of the homotopy method that can find DC operating points of practical nonlinear circuits smoothly and efficiently. Numerical examples show the effectiveness of the proposed method.
Sparse Multiple Relay Selection for Network Beamforming With Individual Power Constraints Using Semidefinite Relaxation

This paper deals with the multiple relay selection problem in two-hop wireless cooperative networks with individual power constraints at the relays. In particular, it addresses the problem of selecting the best subset of K cooperative nodes and their corresponding beamforming weights so that the signal-to-noise ratio (SNR) is maximized at the destination. This problem is computationally demanding and requires an exhaustive search over all the possible combinations. In order to reduce the complexity, a new suboptimal method is proposed. This technique exhibits a near-optimal performance with a computational burden that is far less than the one needed in the combinatorial search. The proposed method is based on the use of the l1-norm squared and the Charnes-Cooper transformation and naturally leads to a semidefinite programming relaxation with an affordable computational cost. Contrary to other approaches in the literature, the technique exposed herein is based on the knowledge of the second-order statistics of the channels and the relays are not limited to cooperate with full power.