Miracle-dz/UniFAR-FTUs huggingface dataset:
The Construction of Support Vector Machine Classifier Using the Firefly Algorithm

The setting of parameters in the support vector machines (SVMs) is very important with regard to its accuracy and efficiency. In this paper, we employ the firefly algorithm to train all parameters of the SVM simultaneously, including the penalty parameter, smoothness parameter, and Lagrangian multiplier. The proposed method is called the firefly-based SVM (firefly-SVM). This tool is not considered the feature selection, because the SVM, together with feature selection, is not suitable for the application in a multiclass classification, especially for the one-against-all multiclass SVM. In experiments, binary and multiclass classifications are explored. In the experiments on binary classification, ten of the benchmark data sets of the University of California, Irvine (UCI), machine learning repository are used; additionally the firefly-SVM is applied to the multiclass diagnosis of ultrasonic supraspinatus images. The classification performance of firefly-SVM is also compared to the original LIBSVM method associated with the grid search method and the particle swarm optimization based SVM (PSO-SVM). The experimental results advocate the use of firefly-SVM to classify pattern classifications for maximum accuracy.
A Shared Parallel Built-In Self-Repair Scheme for Random Access Memories in SOCs

Embedded memories currently constitute a significant portion of the chip area for typical system-on-chip (SOC) designs. Built-in self-repair (BISR) techniques have been widely used for enhancing the yield of embedded memories. This paper proposes a shared parallel BISR scheme for random access memories (RAMs) in SOCs. The shared parallel BISR can test and repair multiple RAMs simultaneously. A global time-multiplexed built-in redundancy analyzer (TM-BIRA) is used to allocate redundancies of the RAMs under test and repair. We also design a 1500-compatible wrapper for chip-level control of the shared parallel BISR circuits. In comparison with the dedicated parallel BISR scheme (each memory has a self-contained BISR circuit), the proposed parallel BISR scheme can achieve 20% reduction of area cost by paying additional 0.005% test and repair time for serving 5 RAMs with spare rows and spare columns.
Prediction of protein coding regions in DNA sequences using Fourier spectral characteristics

Existing discrete Fourier transform (DFT)-based algorithms for identifying protein coding regions in DNA sequences (S. Tiwari et al., 1997, D. Anastassiou, 2001, D. Kotlar et al., 2003) exploit the empirical observation that the spectrum of protein coding regions of length N nucleotides has a peak at frequency k=N/3. In this paper, we prove the aforementioned and several other empirical observations attributed to DNA sequences. Our analytical results lead to faster and more accurate DFT-based algorithms for predicting coding regions.
Probabilistic Correspondence Matching using Random Walk with Restart

This paper presents a probabilistic method for correspondence matching with a framework of the random walk with restart (RWR). The matching cost is reformulated as a corresponding probability, which enables the RWR to be utilized for matching the correspondences. There are mainly two advantages in our method. First, the proposed method guarantees the non-trivial steady-state solution of a given initial matching probability due to the restarting term in the RWR. It means the number of iteration, a crucial parameter which influences the performance of algorithm, is not needed in contrast to the conventional methods. This gives the consistent results regardless of the evolution time. Second, only an adjacent neighborhood is considered when the matching probabilities are inferred, which lowers the computational complexity while not sacrificing performance. Experimental results show that the performance of the proposed method is competitive to that of state-of-the-art methods both qualitatively and quantitatively.
On the Second Spectral Peak of Front Vowels: a Perceptual Study of the Role of the Second and Third Formants

A set of vowel stimuli with different values of mean and separation of the second and third formant frequencies were synthesized by means of series-connected resonant circuits, and formal listening tests were conducted where Swedish subjects identified each stimulus as one of three syllables consisting of a long close front vowel, /i : /, /y : /, or /u :/. The commonly accepted notion of representing the vowel quality in a two-dimensional space is criticized in view of the experimental result. Some supplemental tests of the ABX-comparison type have been conducted, and results concerning the perceptual acuity in regard to slight shifts of the formant conditions are also reported.
Power-performance trade-offs for energy-efficient architectures: A quantitative study

The drastic increase in power consumption by modern processors emphasizes the need for power-performance trade-offs in architecture design space exploration and compiler optimizations. This paper reports a quantitative study on the power-performance trade-offs in software pipelined schedules for an Itanium-like EPIC architecture with dual-speed pipelines, in which functional units are partitioned into fast ones and slow ones. We have developed an integer linear programming formulation to capture the power-performance tradeoffs for software pipelined loops. The proposed integer linear programming formulation and its solution method have been implemented and tested on a set of SPEC2000 benchmarks. The results are compared with an Itanium-like architecture (baseline) in which there are four functional units (FUs) and all of them are fast units. Our quantitative study reveals that by introducing a few slow FUs in place of fast FUs in the baseline architecture, the total energy consumed by FUs can be considerably reduced. When 2 out of 4 FUs are set as slow, the total energy consumed by FUs is reduced by up to 31.1% (with an average reduction of 25.2%) compared with the baseline configuration, while the performance degradation caused by using slow FUs is small. If performance demand is less critical, then energy reduction of up to 40.3% compared with the baseline configuration can be achieved.
Uniform random sampling of planar graphs in linear time

This article introduces new algorithms for the uniform random generation of labelled planar graphs. Its principles rely on Boltzmann samplers, as recently developed by Duchon, Flajolet, Louchard, and Schaeffer. It combines the Boltzmann framework, a suitable use of rejection, a new combinatorial bijection found by Fusy, Poulalhon, and Schaeffer, as well as a precise analytic description of the generating functions counting planar graphs, which was recently obtained by Giménez and Noy. This gives rise to an extremely efficient algorithm for the random generation of planar graphs. There is a preprocessing step of some fixed small cost; and the expected time complexity of generation is quadratic for exact‐size uniform sampling and linear for uniform approximate‐size sampling. This greatly improves on the best previously known time complexity for exact‐size uniform sampling of planar graphs with n vertices, which was a little over O(n7). © 2009 Wiley Periodicals, Inc. Random Struct. Alg. , 2009
Use of the fluorescent probe 1-N-phenylnaphthylamine to study the interactions of aminoglycoside antibiotics with the outer membrane of Pseudomonas aeruginosa

The mode of interaction of the polycationic aminoglycoside antibiotics with the surface of Pseudomonas aeruginosa cells was studied with the hydrophobic fluorescent probe 1-N-phenylnaphthylamine (NPN). The addition of the aminoglycoside gentamicin to intact cells in the presence of NPN led to a shift in the fluorescence emission maximum from 460 to 420 nm. At the same time the NPN fluorescence intensity increased fourfold. Gentamicin caused no such effects when added to outer membrane vesicles, suggesting that the increased fluorescence resulted from the interaction of gentamicin with intact cells. Gentamicin-promoted NPN uptake was inhibited by the divalent cations Mg2+ and Ca2+, but occurred in the absence of gentamicin transport across the inner membrane. Low concentrations of gentamicin (2 micrograms/ml) caused NPN fluorescence to increase over a period of 4 min in a sigmoidal fashion. At higher concentrations (50 micrograms/ml) the increase occurred within a few seconds. The final fluorescence intensity was almost independent of the gentamicin concentration. A centrifugation technique was used to demonstrate that gentamicin caused actual uptake of NPN from the supernatant. The initial rate of NPN uptake varied according to the gentamicin concentration in a sigmoidal fashion. Similar data were obtained for seven other aminoglycoside antibiotics. The data, when reanalyzed as a Hill plot, gave a series of lines with a mean slope (the Hill number) of 2.26 +/- 0.26, suggesting that the interaction of aminoglycosides with the cell surface to permeabilize it to NPN involved at least three sites and demonstrated positive cooperativity. There was a statistically significant relationship between the pseudoassociation constant K, from the Hill plots and the minimal inhibitory concentrations for the eight antibiotics. These results are consistent with the concept that aminoglycosides interact as a divalent cation binding site on the P. aeruginosa outer membrane and permeabilize it to the hydrophobic prove NPN.
Kinematics Control for a 7-DOF Cable-Driven Anthropomorphic Arm

Based on the current research results of anthropomorphic-arm bionics and parallel manipulators, a motion control approach for a 7-DOF cable-driven manipulator is proposed. This paper introduces mechanical structure design of this anthropomorphic-arm first. For the inverse kinematics of the 7-DOF manipulator, a hybrid algorithm, based on gradient projection method and Paden-Kahan sub problems, is proposed to make the trajectory tracing of the manipulator in task space with high accuracy; a joint rate redistribution approach is also employed to optimize kinematic performance criterion and improve the fault-tolerance of the manipulator. The coupling cable lengths among the different joint modules, i.e., shoulder, elbow, and wrist joints, are analyzed in detail. Finally, to demonstrate the proposed algorithm, by utilizing ADAMS software, a straight-line trajectory motion simulation for the 7-DOF cable-driven manipulator is realized
Subtlex-UK: A New and Improved Word Frequency Database for British English

We present word frequencies based on subtitles of British television programmes. We show that the SUBTLEX-UK word frequencies explain more of the variance in the lexical decision times of the British Lexicon Project than the word frequencies based on the British National Corpus and the SUBTLEX-US frequencies. In addition to the word form frequencies, we also present measures of contextual diversity part-of-speech specific word frequencies, word frequencies in children programmes, and word bigram frequencies, giving researchers of British English access to the full range of norms recently made available for other languages. Finally, we introduce a new measure of word frequency, the Zipf scale, which we hope will stop the current misunderstandings of the word frequency effect.
Performance Comparison of IP and CCN as a Communication Infrastructure for Smart Grid

The infrastructure for smart grid is classified into three categories: infrastructure for electric power generation, delivery, and consumption, infrastructure for information measurement, surveillance, and management, and infrastructure for information communication. In this paper, we derive the total amount of traffic in the network, average end-to-end communication delay, and availability when using IP and CCN (Content-Centric Networking) as the communication infrastructure for a smart grid, respectively. Through several numerical examples, we clarify under what conditions either IP or CCN is suitable for the communication infrastructure of a smart grid. We found that, in terms of the total amount of traffic and the average end-to-end communication delay, CCN is effective compared with IP except when cache hit rates in RGCC (Remote Grid Control Center) and LGCC (Local Grid Control Center) are very low. We also found that, in terms of availability, the performance advantage of CCN over IP is marginal.
Summary of the NTCIR-10 INTENT-2 task: subtopic mining and search result diversification

The NTCIR INTENT task comprises two subtasks: {\em Subtopic Mining}, where systems are required to return a ranked list of {\em subtopic strings} for each given query; and {\em Document Ranking}, where systems are required to return a diversified web search result for each given query. This paper summarises the novel features of the Second INTENT task at NTCIR-10 and its main findings, and poses some questions for future diversified search evaluation.
microRNA-31 modulates skeletal patterning in the sea urchin embryo

MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. microRNA-31 (miR-31) is known to play a role in cancer, bone formation and lymphatic development. However, studies to understand the function of miR-31 in embryogenesis have been limited. We examined the regulatory role of miR-31 in early development using the sea urchin as a model. miR-31 is expressed at all stages of development and its knockdown (KD) disrupts the patterning and function of primary mesenchyme cells (PMCs), which form the embryonic skeleton spicules. We identified that miR-31 directly represses Pmar1, Alx1, Snail and VegfR7 within the PMC gene regulatory network using reporter constructs. Further, blocking the miR-31-mediated repression of Alx1 and/or VegfR7 in the developing embryo resulted in defects in PMC patterning and skeletogenesis. The majority of the mislocalized PMCs in miR-31 KD embryos did not express VegfR10, indicating that miR-31 regulates VegfR gene expression within PMCs. In addition, miR-31 indirectly suppresses Vegf3 expression in the ectoderm. These results indicate that miR-31 coordinately suppresses genes within the PMCs and in the ectoderm to impact PMC patterning and skeletogenesis. This study identifies the novel function and molecular mechanism of miR-31-mediated regulation in the developing embryo. Summary: In sea urchin, miRNA-31 acts in primary mesenchyme cells to inhibit components of the gene regulatory network that promotes skeletogenesis.
Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport

Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM, focusing on some of the fundamental issues and general aspects. Using the language of stochastic Markov processes, we emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violates detailed balance, since such systems serve to model a wide variety of phenomena in nature. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process. It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena. Successes and limitations of these simple models are also highlighted.
Privacy for DisCSP-based Modeling in Multi-Agent Planning

Constraint Satisfaction and SAT can model planning problems (Kautz & Selman 1996) and this approach is quite successful. There is an increasing interest in distributed and asynchronous search algorithms for solving distributed constraint satisfaction problems (DisCSP). An important motivation for distributed problem solving is the agents’ ability to keep their constraints private. Cryptographic techniques (Goldwasser & Bellare 1996) offer a certain protection from several types of attacks. However, when an attack succeeds, no agent can know how much privacy he has lost. We assume that agents enforce their privacy by dropping out of the search process whenever the estimated value of the information that they need to reveal in the future exceeds that attached to a successful solution of the DisCSP. We compare several distributed search algorithms as to how likely they are to terminate prematurely for privacy reasons, and arrange the algorithms in a hierarchy that reflects this relation.
Drug Discovery via Human-Derived Stem Cell Organoids

Patient-derived cell lines and animal models have proven invaluable for the understanding of human intestinal diseases and for drug development although both inherently comprise disadvantages and caveats. Many genetically determined intestinal diseases occur in specific tissue microenvironments that are not adequately modeled by monolayer cell culture. Likewise, animal models incompletely recapitulate the complex pathologies of intestinal diseases of humans and fall short in predicting the effects of candidate drugs. Patient-derived stem cell organoids are new and effective models for the development of novel targeted therapies. With the use of intestinal organoids from patients with inherited diseases, the potency and toxicity of drug candidates can be evaluated better. Moreover, owing to the novel clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 genome-editing technologies, researchers can use organoids to precisely modulate human genetic status and identify pathogenesis-related genes of intestinal diseases. Therefore, here we discuss how patient-derived organoids should be grown and how advanced genome-editing tools may be applied to research on modeling of cancer and infectious diseases. We also highlight practical applications of organoids ranging from basic studies to drug screening and precision medicine.
Genetic markers for the efficacy of tumour necrosis factor blocking therapy in rheumatoid arthritis

Background: Rheumatoid arthritis (RA) is a genetically complex disease where the response to different treatments varies greatly between different patients. This is the case with the tumour necrosis factor (TNF) blocking agents, where 20–40% of patients have been described as non-responders. No predictive markers exist as yet for the prognosis of response. Objective: To analyse whether polymorphisms of several cytokine genes are associated with the responsiveness to TNF blockade with etanercept. Methods: 123 patients with active RA were treated with etanercept and response rates were determined after three months using American College of Rheumatology (ACR)20 and disease activity score (DAS)28 response criteria. Genotyping was done for TNF (−308 TNFA), interleukin (IL)10 (−1087 IL10), transforming growth factor (TGF)β1 (codon 25 TGFB1), and IL1 receptor antagonist (intron 2 IL1RN). Results: 24 patients (20%) were defined as non-responders owing to their failure to fulfil any of the ACR20 or DAS28 response criteria. None of the recorded alleles was alone significantly associated with responsiveness to treatment. However, a certain combination of alleles (−308 TNF1/TNF1 and −1087 G/G) was associated with good responsiveness to etanercept (p<0.05). In addition, a combination of alleles influencing interleukin 1 receptor antagonist (IL1Ra) and TGFβ1 production (A2 allele for IL1RN and rare C allele in codon 25 of TGFB1 gene) was associated with non-responsiveness (p<0.05). Conclusion: Genetic polymorphisms, which may influence the balance of pro- and anti-inflammatory cytokines of relevance for the course of RA, are associated with clinical responsiveness to etanercept treatment.
A pattern language for efficient, predictable, scalable, and flexible dispatching mechanisms for distributed object computing middleware

In many application domains, the distributed object computing (DOC) middleware is responsible for dispatching upcalls to one or more application objects when events or requests arrive from clients. Implementing efficient, predictable, and scalable middleware dispatching mechanisms is hard and implementing them for multi-threaded systems is even harder. In particular dispatching mechanisms must be prepared to dispatch upcalls to multiple objects, to handle recursive requests originated from application-provided upcalls, and must often collaborate with the application to control object life-cycle. In our DOC middleware research we have implemented many dispatching mechanisms that repeatedly apply common solutions to solve the challenges outlined above. Moreover, we have discovered that the forces constraining dispatching mechanisms often differ slightly thereby requiring alternative solutions. This paper presents two contributions to the design and implementation of efficient, predictable, scalable and flexible DOC middleware and applications. First, it shows how patterns can be applied to the object-oriented systems to capture key design and performance characteristics of proven dispatching mechanisms. Second it presents a pattern language that describes successful solutions that are appropriate for key dispatching challenges that arise in various real-time DOC middleware and applications.
A compact Representation of prosodically relevant Knowledge in a Speech Dialogue System

The acceptance of speech dialogue systems by the user is critically dependent on the degree of "naturalness" realized. The speech generation and synthesis modules have to be able to run in real time and to produce high-quality speech output. To produce naturally sounding speech, the synthesizer has to have not only the knowledge of the words to utter and the order in which they appear but also information about their structural relationship. The latter is expressed acoustically in the form of prosody, i.e. how the voice raises and falls during an utterance, the rhythm, where pauses are set, etc. Prosody is also influenced by the properties associated with given words in the context of an utterance, e.g. the focus of a sentence or certain emphatic elements. This article describes a compact representation for conveying this type of information from the generator to the synthesizer in a modular system and describes how (parts of) this information is (are) derived in the EFFENDI system, the generation module for a speech dialogue system for train inquiries.
Beyond processor sharing

While the (Egalitarian) Processor-Sharing (PS) discipline offers crucial insights in the performance of fair resource allocation mechanisms, it is inherently limited in analyzing and designing differentiated scheduling algorithms such as Weighted Fair Queueing and Weighted Round-Robin. The Discriminatory Processor-Sharing (DPS) and Generalized Processor-Sharing (GPS) disciplines have emerged as natural generalizations for modeling the performance of such service differentiation mechanisms. A further extension of the ordinary PS policy is the Multilevel Processor-Sharing (MLPS) discipline, which has captured a pivotal role in the analysis, design and implementation of size-based scheduling strategies. We review various key results for DPS, GPS and MLPS models, highlighting to what extent these disciplines inherit desirable properties from ordinary PS or are capable of delivering service differentiation.