Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced reference guided assembly

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredible low cost if compared to Sanger sequencing. Despite this some old problems have become even more difficult, denovo assembly being on top of this list. In this paper we propose a novel method that aims at improving de-novo assembly in presence of a closely related reference. The idea is to combine de-novo assembly and reference guided assembly in order to obtain an enhanced assembly.
IGMP proxy for multicast services in wireless mobile networks

This paper presents a new IGMP multicast support system for wireless highspeed portable Internet (HPi) networks. The Internet group management protocol (IGMP) is common standard session-layer protocol for IP multicasting on the Internet. However, the network topology and the L2 protocol of the HPi make it difficult to adopt the IGMP on HPi networks. We propose the use of an IGMP proxy for multicast services because it provides the way of joining a multicast group over IEEE 802.16e and assists the fast multicast rejoining operations during handoff. Finally, using the multicast delay model, we present numerical results showing the effect of the fast multicast rejoining method.
Computationally Efficient Weighted Binary Decision Codes for Gas Identification With Array of Gas Sensors

Motivated by biological olfactory coding principles, rank-code-based classifiers have recently been proposed to facilitate integration of hardware-friendly gas identification platforms with an array of gas sensors. These classifiers operate on a simple principle of generating rank-codes by ranking the gas sensors' features instead of treating them as a multi-dimensional vector as in computation-intensive state-of-the-art gas classifiers. However, the performance of the rank-code-based classifiers is limited when distinguishing information about all the target gases is not found in the ranks of the gas sensors' features, but in their values. In this paper, we introduce a computationally efficient alternative solution to overcome this limitation. In this solution, an original multi-gas classification problem is decomposed into pairwise classifiers, and the gas is then predicted with the weighted binary decision codes in each of these classifiers, where each element of the code is generated by exploiting features individually. The weighted binary decision codes are formed by first using the nearest centroid approach, which exploits the mean value of each gas sensor's feature to generate binary decision codes, and then, a simple approach is used to assign a weight to each element of the code, depending upon its capability to discriminate the gases in each pairwise classifier. The added advantage of this classification approach is that two computationally efficient metrics are introduced to access the classifiers' applicability to the given data set and certainty about the prediction of any test sample. A classification performance of 97.87% is achieved with this approach on an extensive data set of ten gases experimentally obtained with Figaro series gas sensors, and this is increased to 100% by rejecting 3.37% of samples for which certainty about their predictions is below a 25% confidence level.
The complexity of losing voters

We consider the scenario of a parliament that is going to vote on a specific important issue. The voters are grouped in parties, and all voters of a party vote in the same way. The expected winner decision is known, because parties declare their intentions to vote, but before the actual vote takes place some voters may leave the leading party to join other parties. We investigate the computational complexity of the problem of determining how many voters need to leave the leading party before the winner changes. We consider both positional scoring rules (plurality, veto, k-approval, k-veto, Borda) and Condorcet-consistent methods (maximin, Copeland), and we study two versions of the problem: a pessimistic one, where we want to determine the maximal number of voters that can leave the leading party without changing the winner; and an optimistic one, where we want the minimal number of voters that must leave the leading party to be sure the winner will change. These two numbers provide a measure of the threat to the expected winner, and thus to the leading party, given by losing some voters. We show that for many positional scoring rules these problems are easy (except for the optimistic version with k-approval,for k at least 3, and Borda). Instead, for Condorcet-consistent rules, they are both computationally difficult, with both Maximin and Copeland.
The Effectiveness of Matrix Interventions in Improving Methadone Treatment

Background The treatment of opioid dependence disorder is one of the major problems in medical centers around the world. Although MMT has been the major treatment in last few years in Iran, the existence of relapse before and after detoxification is still high. Methadone treatment has had a very low percentage of complete success. Objectives To evaluate the effectiveness of matrix group interventions in improving methadone treatment in the addicted was the main goal of this research. Materials and Methods In a semi - experimental design, 24 male patients on the qualification cutoff score for the questionnaire survey (score less than 19 in depression test, and less than 21 in anxiety test) and the diagnosis of opioid dependence according to (DSM – IV) were substituted in two experimental and control groups randomly. At the beginning of the study, after the treatment period and in the follow-up phase (three months after the end of treatment), participants were evaluated by Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI) and the Anger Questionnaire (AQ), control group with no psychological treatment only took methadone. Data were analyzed using covariance analysis, chi square and Repeated Measures Analysis of Variance. Results Results showed that the effect of matrix group interventions on reducing relapse (P < 0.05), increasing the maintenance of treatment (P < 0.01), increasing the treatment compliance, reducing anger, anxiety and depression and methadone dose is more effective than methadone treatment (P < 0.05). Conclusions It seems matrix group interventions increase the effectiveness of methadone treatment by reducing the relapse prevention, the dose of methadone and remaining in treatment.
Book review: Danielle S McNamara, Arthur C Graesser, Philip M McCarthy and Zhiqiang Cai, Automated Evaluation of Text and Discourse with Coh-Metrix

speech circumstances, what features are identified, and what involves interpretation and explanation, two notoriously ambiguous concepts. For instance, the features under analysis consist of lexical-grammatical ones like lexical choices and syntactic patterns, and multimodal performance ones like appearance, manner and gesture. As well, userfriendly questions for CMA, which could be directly taken as guidelines for researchers’ work, are presented, for example: What counts as a metaphor? How are metaphors classified? Which political issues are metaphors used to describe? Charteris-Black stresses the importance of corpus methods in discourse analysis. He argues that a corpus, specifically the Corpus of Contemporary American English (COCA), provides a useful resource for testing the lexical cohesive device of the semantic relationship of collocation. The use of a corpus can also serve to identify whether the word is usually metaphorical and, if so, whether it is a novel, entrenched or conventional metaphor. If a metaphor occurs fewer than five times in a sample of 100 corpus entries, it is a candidate for being a novel metaphor. When more than half of the entries have a metaphoric sense, it is an entrenched metaphor. Conventional metaphors are likely to be those that occur somewhere between 5 and 50 times in a sample of 100 corpus entries. Charteris-Black always keeps in mind his main purpose for writing–to analyze political speeches–and illustrates theories by worked examples. In each chapter famous speeches on various occasions are deconstructed, ranging from a speech from Shakespeare’s play Henry V to Obama’s inaugural speech. The book makes a valuable methodological contribution to political discourse research and provides a replicable model for research on other types of public communication, such as business discourse and health discourse.
Delayed-release Multi Matrix System (MMX) mesalazine: in ulcerative colitis.

* Mesalazine appears to act locally on the mucosa of the colon and reduces the inflammation associated with ulcerative colitis. * Following oral administration, the majority (*78%) of a dose of delayed-release Multi Matrix System (MMX) mesalazine passes unabsorbed through the upper gastrointestinal tract to reach and traverse the entire length of the colon. * In a well designed phase III trial in patients with active, mild to moderate ulcerative colitis (n = 262), significantly (p < 0.01) more MMX mesalazine 2.4 (34%) or 4.8 g/day (29%) recipients than placebo recipients (13%) achieved clinical and endoscopic remission after 8 weeks of treatment. * In a second phase III trial (n = 341), clinical and endoscopic remission rates with MMX mesalazine 2.4 (40.5%) and 4.8 g/day (41.2%) were significantly (p < 0.01) greater than with placebo (22.1%) after 8 weeks, while the remission rate with non-MMX delayed-release mesalazine (Asacol) [32.6%] did not differ from placebo. * Overall, MMX mesalazine was generally well tolerated in controlled clinical trials, with a similar incidence of treatment-emergent adverse events in placebo (66%) and MMX mesalazine (56%) recipients in a pooled analysis; most adverse events were of mild or moderate severity. Two of 434 MMX mesalazine recipients experienced serious adverse events that were considered treatment related (pancreatitis caused by mesalazine sensitivity).
A New Text-Line Alignment Approach Based on Piece-Wise Painting Algorithm for Handwritten Documents

Because of writing styles of different individuals, some of the text-lines may be curved in shape. For recognition of such text-lines, their proper alignment is necessary. In this paper, we propose a text-line alignment technique based on painting algorithm. Here at first, Piece-wise Painting Algorithm (PPA) is used to get a number of black and white rectangular patches all along the text-line for text-line alignment. Identifying the degree of oscillation of the input text-line, some candidate pixels are also obtained based on horizontal projection and center points of the black patches. Using the degree of oscillation of the input text image and the candidate pixels a curve or straight line is fit to trace the baseline. Subsequently, all components of the text-line are deskewed based on analyzing the characteristic of the fit curve or line to align the components with respect to the horizontal imaginary baseline. The proposed algorithm was evaluated with 128 Persian handwritten text-lines containing 4317 sub words. Experimental analysis showed that 92.31% of the sub words were accurately aligned. Further, the proposed algorithm was tested with another Persian handwritten text-lines dataset [6] and remarkable results were achieved.
ADP-dependent Conformational Changes Distinguish Mycobacterium tuberculosis SecA2 from SecA1*

Background: Mycobacterium tuberculosis possesses a second SecA ATPase that is required for bacterial virulence. Results: ADP binding by SecA2 causes a conformational change observable by biochemical methods. Conclusion: ADP binding closes the clamp in SecA2. This is not observed in SecA1 or E. coli SecA. Significance: Nucleotide-dependent clamp closure suggests a mechanism by which mycobacterial SecA2 is distinguished from SecA1 by the translocation machinery. In bacteria, most secreted proteins are exported through the SecYEG translocon by the SecA ATPase motor via the general secretion or “Sec” pathway. The identification of an additional SecA protein, particularly in Gram-positive pathogens, has raised important questions about the role of SecA2 in both protein export and establishment of virulence. We previously showed in Mycobacterium tuberculosis, the causative agent of tuberculosis, the accessory SecA2 protein possesses ATPase activity that is required for bacterial survival in host macrophages, highlighting its importance in virulence. Here, we show that SecA2 binds ADP with much higher affinity than SecA1 and releases the nucleotide more slowly. Nucleotide binding also regulates movement of the precursor-binding domain in SecA2, unlike in SecA1 or conventional SecA proteins. This conformational change involving closure of the clamp in SecA2 may provide a mechanism for the cell to direct protein export through the conventional SecA1 pathway under normal growth conditions while preventing ordinary precursor proteins from interacting with the specialized SecA2 ATPase.
Joint phoneme segmentation inference and classification using CRFs

State-of-the-art phoneme sequence recognition systems are based on hybrid hidden Markov model/artificial neural networks (HMM/ANN) framework. In this framework, the local classifier, ANN, is typically trained using Viterbi expectation-maximization algorithm, which involves two separate steps: phoneme sequence segmentation and training of ANN. In this paper, we propose a CRF based phoneme sequence recognition approach that simultaneously infers the phoneme segmentation and classifies the phoneme sequence. More specifically, the phoneme sequence recognition system consists of a local classifier ANN followed by a conditional random field (CRF) whose parameters are trained jointly, using a cost function that discriminates the true phoneme sequence against all competing sequences. In order to efficiently train such a system we introduce a novel CRF based segmentation using acyclic graph. We study the viability of the proposed approach on TIMIT phoneme recognition task. Our studies show that the proposed approach is capable of achieving performance similar to standard hybrid HMM/ANN and ANN/CRF systems where the ANN is trained with manual segmentation.
Mutagenesis of the Catalytic and Cleavage Site Residues of the Hypovirus Papain-Like Proteases p29 and p48 Reveals Alternative Processing and Contributions to Optimal Viral RNA Accumulation

ABSTRACT The positive-stranded RNA genome of the prototypic virulence-attenuating hypovirus CHV-1/EP713 contains two open reading frames (ORF), each encoding an autocatalytic papain-like leader protease. Protease p29, derived from the N-terminal portion of ORF A, functions as a suppressor of RNA silencing, while protease p48, derived from the N-terminal portion of ORF B, is required for viral RNA replication. The catalytic and cleavage site residues required for autoproteolytic processing have been functionally mapped in vitro for both proteases but not confirmed in the infected fungal host. We report here the mutagenesis of the CHV-1/EP713 infectious cDNA clone to define the requirements for p29 and p48 cleavage and the role of autoproteolysis in the context of hypovirus replication. Mutation of the catalytic cysteine and histidine residues for either p29 or p48 was tolerated but reduced viral RNA accumulation to ca. 20 to 50% of the wild-type level. Mutation of the p29 catalytic residues caused an accumulation of unprocessed ORF A product p69. Surprisingly, the release of p48 from the ORF B-encoded polyprotein was not prevented by mutation of the p48 catalytic and cleavage site residues and was independent of p29. The results show that, while dispensable for hypovirus replication, the autocatalytic processing of the leader proteases p29 and p48 contributes to optimal virus RNA accumulation. The role of the predicted catalytic residues in autoproteolytic processing of p29 was confirmed in the infected host, while p48 was found to also undergo alternative processing independent of the encoded papain-like protease activities. IMPORTANCE Hypoviruses are positive-strand RNA mycoviruses that attenuate virulence of their pathogenic fungal hosts. The prototypic hypovirus CHV-1/EP713, which infects the chestnut bight fungus Cryphonetria parasitica, encodes two papain-like autocatalytic leader proteases, p29 and p48, that also have important functions in suppressing the RNA silencing antiviral defense response and in viral RNA replication, respectively. The mutational analyses of the CHV-1/EP713 infectious cDNA clone, reported here, define the requirements for p29 and p48 cleavage and the functional importance of autoproteolysis in the context of hypovirus replication and exposed an alternative p48 processing pathway independent of the encoded papain-like protease activities. These findings provide additional insights into hypovirus gene expression, replication, and evolution and inform ongoing efforts to engineer hypoviruses for interrogating and modulating fungal virulence.
Wide-angle localization of intraocular devices from focus

Future retinal therapies will be partially automated in order to increase the surgeons' ability to operate near the sensitive structure of the human eye retina. Untethered robotic devices that achieve the desired precision have been proposed, but require localization information for their control. Since the interior of the human eye is externally observable, vision can be used for localization. Previously, a focus-based paraxial localization algorithm using a Mechatronic Vitreoretinal Ophthalmoscope (MVO) was proposed and evaluated by the authors. In this paper, the first algorithm for wide-angle intraocular localization is presented. The effectiveness of this new localization approach is demonstrated by experiments using a model eye and a customized MVO, and there is clear improvement over previously reported results.
Virtual force display: direction guidance using asymmetric acceleration via periodic translational motion

This paper describes the development of a handheld haptic display based on a new force perception method. The method uses periodic translational motion to create asymmetric acceleration leading to a virtual force vector. The method is based on the sigmoidal relationship between perception and physical quantities (tactile and proprioceptive sensations); humans more strongly feel rapid acceleration than slow acceleration. A prototype of the haptic display that generates one-directional force using a relatively simple mechanism is fabricated and evaluated. Experiments verify the feasibility of the proposed method by examining the effect of the frequency of acceleration and amplitude of the force on the perception of the virtual force vector.
Framework for the participation of EV aggregators in the electricity market

The Electric Vehicle (EV) is one source of flexibility to the electric power system. When aggregated by a market agent, it can offer its flexibility in the balancing reserve market. In order to meet this goal, a framework of optimization and forecasting algorithms must designed to cover the different time horizons of the decision process. This paper describes a full framework for EV aggregators participating in different electricity market sessions. This framework is illustrated for the balancing reserve market and the impact of forecasts of different quality for the balancing reserve direction is evaluated. The test case consists in synthetic time series generated from real data for 3000 EV participating in the Iberian electricity market.
Posthumous personhood and the affordances of digital media

Abstract This article identifies and outlines some of the more prominent ways that digital media can extend one’s personhood following death. We consider three examples: when the digital persona of the deceased continues to interact with the living through a human surrogate; the emergence of autonomous and semi-autonomous software enabling the dead to use social media to intervene in current events; and finally the operation of algorithmic presence services like Eterni.me, where artificial intelligence creates a re-enlivened form of the deceased. Situating these examples in relation to sociological, anthropological and cultural literature foundational to ideas of distributed personhood and posthumous symbolic immortality, we suggest that digital codes and computational texts stand as key sites for contemporary forms of ‘distributed personhood’, including posthumous personhood. We then extend this body of literature by examining how the discursive politics of social media contributes to a social and commercial context, which supports ongoing interactions with the dead online. Through this process, we suggest that the persona of the dead, which remains after bodily death, can continue to maintain meaningful posthumous relationships with the living, presenting a new perspective on how we interact with the dead through digital media.
Randomly Generated 3D Environments for Serious Games

This paper describes a variety of methods that can be used to create realistic, random 3D environments for serious games requiring real-time performance. These include the generation of terrain, vegetation and building structures. An interactive flight simulator has been created as proof of concept. An initial evaluation with two small samples of users (remote and hallway) revealed some usability issues but also showed that overall the flight simulator is enjoyable and appears realistic and believable.
Priority based optimization of PID controller for automatic voltage regulator system using gravitational search algorithm

In this paper, an optimal design PID controller for automatic voltage regulator (AVR) using gravitational search algorithm (GSA) is presented. In the present work, a priority based error magnification technique is used. This technique emphasizes on the need of prioritizing certain characteristics of transient response of an AVR system. The proposed method consists of a fitness function that helps GSA to search optimum value of PID controller parameters quickly and efficiently. Results obtained using GSA is compared with that other optimization techniques such as genetic algorithm (GA) and particle swarm optimization (PSO). It is observed that the results obtained using GSA is the best in comparison to the results obtained using GA and PSO.
Build Fast and Accurate Lemmatization for Arabic

In this paper we describe the complexity of building a lemmatizer for Arabic which has a rich and complex derivational morphology, and we discuss the need for a fast and accurate lammatization to enhance Arabic Information Retrieval (IR) results. We also introduce a new data set that can be used to test lemmatization accuracy, and an efficient lemmatization algorithm that outperforms state-of-the-art Arabic lemmatization in terms of accuracy and speed. We share the data set and the code for public.
Networked Cultural Diffusion and Creation on YouTube: An Analysis of YouTube Memes

Web 2.0-based cultural diffusion occurs not only through viral word-of-mouth communication but also through Internet memes in which cultural consumers review, resemble, and recreate old cultural components, resulting in the creation of new cultural forms. YouTube features a platform for memetic creation with a host of user-generated parodies, reviews, and mashups derived from viral videos. This study examines the cultural ecosystem of YouTube memes inspired by Korean artist Psy’s viral production “Gangnam Style. ” The study focuses on the salience of various genres of YouTube memes and structural connections between memetic videos. According to the results, the viral video of “Gangnam Style” sparked a sizable amount of user creativity, including remixes, parodies, self-directed performances, and reviews, among others. A network analysis of connections between memetic videos shows that various memetic genres drew different levels of audience attention and actions across various stages of the 3-month-long diffusion process. In addition, the content of the traditional mass media played a key role in giving the viral video wider publicity and acknowledgement, but this role was later shared by user-generated content.