Miracle-dz/UniFAR-FTUs huggingface dataset:
The new SIMD Implementation of the Smith-Waterman Algorithm on Cell Microprocessor

Algorithms for estimating similarity between two macromolecular sequences are of profound importance for molecular biology. The standard methods utilize so-called primary structure, that is a string of characters denoting the sequence of monomers in hetero-polymer. These methods find the substrings of maximal similarity, as defined by the so-called similarity matrix, for a pair of two molecules. The problem is solved either by the exact dynamic programming method, or by approximate heuristic methods. The approximate algorithms are almost two orders of magnitude faster in comparison with the standard version of the exact Smith-Waterman algorithm, when executed on the same hardware, hence the exact algorithm is relatively rarely used. Recently a very efficient implementation of Smith- Waterman algorithm utilizing SIMD extensions to the standard instruction set reduced the speed advantage of heuristic algorithms to factor of three. Here we present an improved implementation of the Smith-Waterman algorithm on the Cell processor. Implementation presented here achieves execution speed of approximately 9 GCUPS. The performance is independent on the scoring system. It is 4 to 10 times faster than best Smith-Waterman implementation running on a PC and 1.5 to 3 times faster than the same implementation running on Sony PlayStation 3. It is also 5 times faster than the recent implementation of the Smith- Waterman utilizing Nvidia GPU. Our implementation running on Sony PlayStation 3 has performance which is directly comparable with that of BLAST running on PC, being up to 4 times faster in the best case and no more than two times slower in the worst case. This performance level opens possibility for using the exact Smith-Waterman algorithm in applications, where currently approximate algorithms are used.
Appearance Frequency-Based Ranking Method for Improving Recommendation Diversity

Recommender systems are used to analyze users’ preferences through their past activities and to personalize recommendations for each user based on what they might be interested in. The performance of the recommender system is most commonly measured using only recommendation accuracy. However, recommending accurate items does not mean that the generated recommendation is the best for the user because it can be biased towards some items that have a higher chance of being liked by users, such as popular items. Recommendations become repetitive and obvious with biased item selection and are less likely to be personalized. To mitigate bias and repetitiveness, recommendation diversity has been studied. However, diversity has a trade-off relationship with accuracy. Modifying the recommendation algorithm to consider diversity while learning about user preferences would not only cause loss in accuracy, but also lead to less precise reading of user preferences. Instead, using ranking methods to re-rank the priority of items predicted, the recommendation algorithm would keep the preciseness of the algorithm. In this study, a ranking method using the appearance frequency of items to restrict the items from being frequently recommended will be proposed. The experimental results showed that the proposed method consistently improved diversity in multiple diversity metrics.
FUNCTORIALITY FOR THE EXTERIOR SQUARE OF GL4 AND THE SYMMETRIC FOURTH OF GL2

Let ∧ : GLn(C) −→ GLN (C), where N = n(n−1) 2 , be the map given by the exterior square. Then Langlands’ functoriality predicts that there is a map from cuspidal representations of GLn to automorphic representations of GLN , which satisfies certain canonical properties. To explain, let F be a number field, and let A be its ring of adeles. Let π = ⊗ v πv be a cuspidal (automorphic) representation of GLn(A). In what follows, a cuspidal representation always means a unitary one. Now by the local Langlands correspondence, ∧πv is well defined as an irreducible admissible representation of GLN (Fv) for all v (the work of Harris-Taylor [H-T] and Henniart [He2] on p-adic places and of Langlands [La4] on archimedean places). Let ∧π = ⊗ v ∧πv. It is an irreducible admissible representation of GLN (A). Then Langlands’ functoriality in this case is equivalent to the fact that ∧π is automorphic. Note that ∧(GL2(C)) ' GL1(C) and in fact for a cuspidal representation π of GL2(A), ∧π = ωπ, the central character of π. Furthermore, ∧(GL3(C)) ' GL3(C). In this case, given a cuspidal representation π of GL3(A), ∧π = π̃ ⊗ ωπ, where π̃ is the contragredient of π. In this paper, we look at the case n = 4. Let π = ⊗ v πv be a cuspidal representation of GL4(A). What we prove is weaker than the automorphy of ∧π. We prove (Theorem 5.3.1)
A behavior-based reconfigurable cache for the low-power embedded processor

In embedded processor designs, a cache becomes the main contributor of the power consumption as it greatly improves the performance. The conventional low-power techniques of a cache based on a fixed hardware configuration cannot be configured and it is independent on the program behavior. Thus, a configurable cache is proposed to save energy and improve performance by dynamically adjusting the cache parameters for the code that is executing. However, most existing configurable caches explore and adapt the optimal configuration based on successive time-intervals, which presents efficiency only if the program can keep its execution phase for a number of intervals. In this paper, we propose a behavior-based configurable cache, which can be dynamically adjusted based on the program behavior. The design adds very little hardware complexity and commits most workload to the software, so that it is very effective for the embedded microprocessors design. Simulation by using Spec 2000 shows that our proposed configurable cache can reduce the power consumption by up to 60.6% and 22.3% compared to a conventional set-associative cache and a temporal-based configurable cache, respectively. At the same time, performance degradation is about 0.75%.
Classical SMR Atomic Broadcast Application ( b ) Parallel SMR RequestResponse Client Service Execution Service Execution Parallelizer Atomic Broadcast Application Request Client Response Workers

Many services used in large scale web applications should be able to tolerate faults without impacting their performance. State machine replication is a well-known approach to implementing fault-tolerant services, providing high availability and strong consistency. To boost the performance of state machine replication, recent proposals have introduced parallel execution of commands. In parallel state machine replication, incoming commands may or may not depend on other commands that are waiting for execution. Although dependent commands must be processed in the same relative order at every replica to avoid inconsistencies, independent commands can be executed in parallel and benefit from multi-core architectures. Since many application workloads are mostly composed of independent commands, these parallel models promise high throughput without sacrificing strong consistency. The efficient execution of commands in such environments, however, requires effective scheduling strategies. Existing approaches rely on dependency tracking based on pairwise comparison between commands, which introduces scheduling contention. In this paper, we propose a new and highly efficient scheduler for parallel state machine replication. Our scheduler considers batches of commands, instead of commands individually. Moreover, each batch of commands is augmented with a compact data structure that encodes commands information needed to the dependency analysis. We show, by means of experimental evaluation, that our technique outperforms schedulers for parallel state machine replication by a fairly large margin. Keywords-parallel state machine replication; fault tolerance; high throughput; deterministic scheduling
Determination of Anodized Aluminum Material Characteristics by Means of Nano-Indentation Measurements

An aluminium AD-3 has been anodized under four different conditions, namely at low temperature (? 5℃), room temperature (25℃), with and without sealing the anodized coating in boiling distilled water. The solution used for formation of alumina layer in all cases was an electrolyte containing 180 g/l sulphuric acid at a constant forming voltage (voltastatic anodizing). In order to assess the mechanical properties of the obtained anodic alumina layers a series of nanoindentation tests was performed employing different indentation procedures. The two mechanical characteristics of the alumina films, the indentation hardness (HIT) and the indentation modulus (EIT), were determined by means of the instrumented indentation and the Oliver & Pharr approximation method. All measurements were done on Agilent G200 Nanoindenter fitted with a diamond Berkovich type tip. Time dependent effects were investigated by tests with different peak hold time and different loading rate. The change of the mechanical properties with indentation depth was also examined. The effect of the working temperature during the growth of the alumina layers and the influence of the pore sealing on the mechanical properties are evaluated via comparison of the average load-displacement curves. The role of the temperature of the electrolyte and the sealing process during the formation of the alumina films, with respect to possible changes of their chemical composition and structure, are discussed in order to explain the observed differences in the measured load-displacement curves and the determined HIT and EIT.
Genome Project Standards in a New Era of Sequencing

More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data. For over a decade, genome sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole-genome sequencing that requires reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker “draft”; however, these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and has contributed to many wasted hours. Exponential leaps in raw sequencing capability and greatly reduced prices have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The result is an ever-widening gap between drafted and finished genomes that only promises to continue (see the figure, page 236); hence, there is an urgent need to distinguish good from poor data sets.
HANKEN SCHOOL OF ECONOMICS Department of : Accounting and Commercial Law Type of work : Thesis

The Balanced Scorecard (BSC) came to the fore following drawbacks from using financial measures only to measure company performance. Managers are using BSC to communicate their strategy, for planning and controlling, for getting feedback and, for performance monitoring. This study examines the factors that influence managers to use the BSC. Identifying the factors will help to explain why some companies using BSC succeed while others fail. Also, it will help managers using BSC to know where to focus their attention in order that the goals of the organization can be met. With the help of Webropol, a survey questionnaire was created that was used to collect data for the study and the ordinary least square (OLS) regression method was used to analyse the data. The sample comprise of 34 managers using BSC in Finland out of the 300 questionnaires sent. Therefore, the response rate was 11.33%. Our goal was to examine the effects of the following independent variables: Other control systems (OCS) use in the organization, how managers evaluate their subordinates (ESM), how they perceive information from new sources (MRI) and the impact of technology (i.e. perceive usefulness (PU) and ease of use (PEOU) of BSC, on the dependent variable, i.e. use of the BSC by managers. The results show that the way managers perceive information from new sources (MRI) and the perceived ease of use (PEOU) of the BSC system by the managers‘ influences them to use BSC.
Research letters

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Modèles et outils pour la conception stratégique de réseaux de transport publics. (Methods and tools to help strategic network design in public transportation)

Nous proposons des methodes et des outils pour l'aide a la conception strategique de reseaux de transports publics en milieu urbain. Un etat de l'art des problemes de synthese de reseaux est suivi par la definition du probleme de synthese de reseaux de mobilite avec demande elastique (dependante de la qualite de service) . Nous declinons differentes modelisations et des extensions etudiees de maniere exacte sur de modestes instances. Les metaheuristiques GRASP et Tabou permettent d'obtenir de bonnes solutions sur des instances plus grandes. Nous utilisons pour cela la "geodesique", une description particuliere de circuit. La resolution est acceleree en introduisant une fonction objectif auxiliaire. Enfin, nous utilisons une methode inspiree du schema de Benders. En annexe, nous formalisons des schemas de conception de composants logiciels flexibles et performants avec la programmation generique. Nous presentons aussi le couplage par enrichissement, entre optimisation et simulation.
Use of rifabutin for the treatment of a latent tuberculosis infection in a patient after solid organ transplantation

Latent tuberculosis infection is an important problem for solid organ transplant recipients because of the frequency of its occurrence and its potential for reactivation. Because of the high mortality rate associated with active tuberculosis infections in transplant recipients, guidelines from the American Thoracic Society recommend treatment for latent tuberculosis in this population. However, the choice of treatments is often difficult because liver transplant recipients may be more sensitive to isoniazid hepatotoxicity, and rifampin has significant drug interactions with the calcineurin inhibitors used for immunosuppression. Two prior case reports described success with the use of rifabutin, a rifampin alternative, as part of a multidrug treatment regimen for active tuberculosis in posttransplant patients; however, there is no prior literature describing any experience with rifabutin for the treatment of latent tuberculosis in the posttransplant setting. We present a summary of tacrolimus drug levels and corresponding dose requirements for a single posttransplant patient during the administration of 3 different latent tuberculosis drug regimens: rifampin alone, rifampin plus ketoconazole, and rifabutin. In this patient's case, rifabutin allowed the maintenance of adequate tacrolimus levels, although an approximate 2.5‐fold increase in the dose was required. Rifampin alone was associated with inadequate immunosuppressant levels, and rifampin plus ketoconazole was associated with a problematically prolonged QT interval and concerns about inadequate tuberculosis treatment. Liver Transpl 19:457–461, 2013. © 2013 AASLD.
Comparative investigation of SGH performance prediction formulas, measurements and numerical modelling

Standard Gain Horns (SGH) often find use in modern antenna measurements. They are utilized frequently either as measurements antenna or as reference antenna in antenna gain measurements by comparison or substitution method [1]. They also find use as source antennas in anechoic test chambers and for many other purposes such as fixed site antennas. The most widespread SGH geometry has a rectangular cross-section and is pyramidal with optimized geometry to achieve maximum gain [2, 3, 4]. When used as a precision gain reference in antenna measurements the SGH is often calibrated by a reference facility or another third party. When external or internal calibration means are not available the SGH peak gain is often determined directly from the reference tables of the NRL report [2]. The quality of the original work is such that even today the associated uncertainty on these peak gain values are generally accepted to be within +/−0.3dB [1]. In this paper the accuracy of the NRL gain tables are investigated by comparison with a full wave numerical method based on FDTD [7] and measurements in different antenna test ranges. Performance variation of the SATIMO Standard Gain Horns due to the manufacturing and measurement accuracy has been also investigated with conducted and radiated experiments.
A Research Framework on Big Data awareness and Success Factors toward the Implication of Knowledge Management: Critical Review and Theoretical Extension

People have access to more data in single day than most people that have access to data in the previous decade. This data is created in many forms and it highlights the development of big data. Big data have transformed the way organizations across industries implement new approach to handle huge amount of data. It means change in skills, structures, technologies and architectures. Organizations rely to this data to achieve specific business priorities. The challenge is how to capture this data to be considered relevant for the specific organization activities because determining relevant data is a key to delivering value from massive amounts of data to support organizations knowledge. This paper proposes a framework to evaluate the level of big data awareness and success factors toward the implication of knowledge management in organizations. The framework incorporates big data and knowledge management. It will allow domain experts and entrepreneurs to evaluate the level of big data in their organizations by looking at the level of understanding, usefulness and effectiveness of big data. The contribution of this paper serve as a first step in understanding the relationship between big data and knowledge management.
Coronary heart disease risk factors: public impact of initial and later-announced risks.

The concept of risk factors is straightforward; however, the term has been frequently misinterpreted by the general public and media. The purpose of this communication is to help clarify some of the controversy and concerns that arise during discussions of risk factors with patients. The definition of the term risk factors is important. We define risk factors as specific pathophysiological mechanisms or clinical entities underlying diseases that promote increased morbidity and mortality. With respect to coronary heart disease (CHD), risk factors do not relate exclusively to occlusive coronary artery disease produced by atherosclerosis; CHD risk factors also concern hypertensive cardiovascular disease (HCVD). Moreover, even though CHD is frequently considered synonymous with atherosclerotic heart disease, its diagnosis and management are more complex. Pathophysiologically, HCVD is promoted by coronary arteriolar constriction, oxidative stress of these vessels, increased ventricular oxygen demand responsible for increased coronary blood flow and flow reserve, ventricular fibrosis, myocardial apoptosis, and ventricular remodeling.1-3 The term risk factors was first introduced by the team of investigators of the Framingham Heart Study (sidebar) who identified specific “factors of risk” that predispose otherwise healthy individuals to the increased risk of premature morbidity and mortality from CHD.4 In that 1961 publication, the first 3 risk factors identified to promote CHD were hypertension, hypercholesterolemia, and left ventricular hypertrophy (LVH). Throughout the following half-century, the Framingham investigators and other workers in the field identified a number of additional major risk factors that augment the risk demonstrated by the 3 initial CHD risk factors (Table). Table. Major Risk Factors Currently Known to Apply to Coronary Heart Disease This report aims to provide physicians, house staff members, and medical students with information intended to enhance communication in their doctor/patient relationships. It is necessary to comprehend why public confusion and controversy exist regarding the diagnostic and therapeutic management of the first 3 risk factors and the 3 more recently identified CHD risk factors (ie, smoking, obesity, and increased dietary sodium intake).