Miracle-dz/UniFAR-FTUs huggingface dataset:
Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential

A total of 133 Listeria monocytogenes isolates were characterized by ribotyping and allelic analysis of the virulence genes hly, actA, and inlA to uncover linkages between independent phylogenetic and specific virulence markers. PCR-restriction fragment length polymorphisms revealed 8 hly, 11 inl4, and 2 actA alleles. The combination of these virulence gene alleles and ribotype patterns separated L. monocytogenes into three distinct lineages. While distinct hly and inlA alleles were generally found to cluster into these three lineages, actA alleles segregated independently. These three phylogenetic lineages were confirmed when 22 partial actA DNA sequences were analyzed. The clinical history of the L. monocytogenes strains showed evidence for differences in pathogenic potential among the three lineages. Lineage I contains all strains isolated during epidemic outbreaks of listeriosis, while no human isolates were found in lineage III. Animal isolates were found in all three lineages. We found evidence that isolates from lineages I and III have a higher plaquing efficiency than lineage II strains in a cell culture assay. Strains from lineage III also seem to form larger plaques than strains from lineage II. A distinctive ribotype fragment and unique 16S rRNA gene sequences furthermore suggest that lineage III might represent a L. monocytogenes subspecies. None of the 20 human isolates available but 11% of our animal isolates were grouped in this lineage, indicating that strains in this lineage might have reduced virulence for humans.
Glaucoma Screening: Current Perspectives and Future Directions

ABSTRACT Introduction: Glaucoma is an optic neuropathy with characteristic progressive optic nerve degeneration. Early detection and treatment may prevent blindness; however, the value of glaucoma screening has been debated. Methods: Articles pertaining to glaucoma screening were reviewed. Results: In reviewing the glaucoma literature, there is a lack of a sensitive and specific screening test and concerns over cost-effectiveness. Methods of screening include population-based screening and opportunistic case finding, which both have advantages and disadvantages. Conclusions: Additional research is needed to better understand glaucoma progression as well as to identify improved screening tests. Consideration must be given not only to the feasibility of performing a glaucoma screening, but also to the follow-up and long-term care for glaucoma patients.
Olfactory memory capacity of the cricket Gryllus bimaculatus

Olfactory learning in insects is a useful model for studying neural mechanisms underlying learning and memory, but memory storage capacity for olfactory learning in insects has not been studied. We investigate whether crickets are capable of simultaneously memorizing seven odour pairs. Fourteen odours were grouped into seven A/B pairs, and crickets in one group were trained to associate A odours with water reward and B odours with saline punishment for all the seven pairs. Crickets in another group were trained with the opposite stimulus arrangement. Crickets in all the groups exhibited significantly greater preference for the odours associated with water reward for all the seven odour pairs. We conclude that crickets are capable of memorizing seven odour pairs at the same time.
Robust Multilevel Optimization of PMSM Using Design for Six Sigma

In this paper, a robust optimization method based on design for six sigma (DFSS) is combined to the optimization of a surface mounted permanent synchronous machine (PMSM) by using multilevel genetic algorithm (MLGA). First, MLGA and DFSS are introduced in the robust optimization. Second, by taking into account the tolerances of the motor products, important input parameters could be varied with six sigma distribution and Monte Carlo simulation (MCS) method is used to reduce the calculation cost. Third, to verify the new algorithm, the presented algorithm is applied to the optimization of a PMSM. The results compared with those of traditional GA and MLGA and the discussion of the robust optimization combined with MLGA are presented.
Lysophosphatidic acid signaling in ovarian cancer

Abstract Lysophosphatidic acid (LPA) is a bioactive phospholipid that is involved in signal transduction between cells. Plasma and ascites levels of LPA are increased in ovarian cancer patients even in the early stages and thus LPA is considered as a potential diagnostic marker for this disease. This review presents the current knowledge regarding LPA signaling in epithelial ovarian cancer. LPA stimulates proliferation, migration and invasion of ovarian cancer cells through regulation of vascular endothelial growth factor, matrix metalloproteinases, urokinase plasminogen activator, interleukin-6, interleukin-8, CXC motif chemokine ligand 12/CXC receptor 4, COX2, cyclin D1, Hippo-Yap and growth-regulated oncogene α concentrations. In this article, all of these targets and signal pathways involved in LPA influence are described.
Back to the Drawing Board: Revisiting the Design of Optimal Location Privacy-preserving Mechanisms

In the last years we have witnessed the appearance of a variety of strategies to design optimal location privacy-preserving mechanisms, in terms of maximizing the adversary's expected error with respect to the users' whereabouts. In this work, we take a closer look at the defenses created by these strategies and show that, even though they are indeed optimal in terms of adversary's correctness, not all of them offer the same protection when looking at other dimensions of privacy. To avoid "bad" choices, we argue that the search for optimal mechanisms must be guided by complementary criteria. We provide two example auxiliary metrics that help in this regard: the conditional entropy, that captures an information-theoretic aspect of the problem; and the worst-case quality loss, that ensures that the output of the mechanism always provides a minimum utility to the users. We describe a new mechanism that maximizes the conditional entropy and is optimal in terms of average adversary error, and compare its performance with previously proposed optimal mechanisms using two real datasets. Our empirical results confirm that no mechanism fares well on every privacy criteria simultaneously, making apparent the need for considering multiple privacy dimensions to have a good understanding of the privacy protection a mechanism provides.
In Vitro Phenotypic Characterization of Hepatitis C Virus NS3 Protease Variants Observed in Clinical Studies of Telaprevir

ABSTRACT Telaprevir is a linear, peptidomimetic small molecule that inhibits hepatitis C virus (HCV) replication by specifically inhibiting the NS3·4A protease. In phase 3 clinical studies, telaprevir in combination with peginterferon and ribavirin (PR) significantly improved sustained virologic response (SVR) rates in genotype 1 chronic HCV-infected patients compared with PR alone. In patients who do not achieve SVR after treatment with telaprevir-based regimens, variants with mutations in the NS3·4A protease region have been observed. Such variants can contribute to drug resistance and limit the efficacy of treatment. To gain a better understanding of the viral resistance profile, we conducted phenotypic characterization of the variants using HCV replicons carrying site-directed mutations. The most frequently observed (significantly enriched) telaprevir-resistant variants, V36A/M, T54A/S, R155K/T, and A156S, conferred lower-level resistance (3- to 25-fold), whereas A156T and V36M+R155K conferred higher-level resistance (>25-fold) to telaprevir. Rarely observed (not significantly enriched) variants included V36I/L and I132V, which did not confer resistance to telaprevir; V36C/G, R155G/I/M/S, V36A+T54A, V36L+R155K, T54S+R155K, and R155T+D168N, which conferred lower-level resistance to telaprevir; and A156F/N/V, V36A+R155K/T, V36M+R155T, V36A/M+A156T, T54A+A156S, T54S+A156S/T, and V36M+T54S+R155K, which conferred higher-level resistance to telaprevir. All telaprevir-resistant variants remained fully sensitive to alpha interferon, ribavirin, and HCV NS5B nucleoside and nonnucleoside polymerase inhibitors. In general, the replication capacity of telaprevir-resistant variants was lower than that of the wild-type replicon.
Des textes communautaires à la recommandation

La these concerne la transformation de donnees textuelles non structurees en donnees structurees et exploitables par des systemes de recommandation. Deux grandes categories d'informations sont utilisees dans le domaine des moteurs de recommandation : les donnees descriptives de contenus comme les meta-donnees ou les tags (filtrage thematique), et les donnees d'usages qui peuvent etre des notes ou encore des pages Web visitees par exemple (filtrage collaboratif). D'autres donnees sont presentes sur le Web et ne sont pas encore reellement exploitees. Avec l'emergence du Web 2.0, les internautes sont de plus en plus amenes a partager leurs sentiments, opinions, experiences sur des produits, personnalites, films, musiques, etc. Les donnees textuelles produites par les utilisateurs representent potentiellement des sources riches d'informations qui peuvent etre complementaires des donnees exploitees actuellement par les moteurs de recommandation et peuvent donc ouvrir de nouvelles voies d'etudes dans ce domaine en plein essor. Notre objectif dans le cadre de la these est de produire, a partir de commentaires issus de sites communautaires (blogs ou forums), des matrices d'entrees pertinentes pour les systemes de recommandation. L'idee sous-jacente est de pouvoir enrichir un systeme pour un service debutant, qui possede encore peu d'utilisateurs propres, et donc peu de donnees d'usages, par des donnees issues d'autres utilisateurs. Nous faisons tout d'abord un etat de l'art de la recommandation automatique. Nous presentons ensuite le moteur ainsi que les donnees utilisees pour les experimentations. Le chapitre suivant decrit les premieres experimentations en mode thematique. Nous faisons ensuite un nouvel etat de l'art sur la classification d'opinion. Pour finir, nous decrivons les experimentations menees pour l'approche collaborative a l'aide de la classification d'opinion.
An Update on Sec61 Channel Functions, Mechanisms, and Related Diseases

The membrane of the endoplasmic reticulum (ER) of nucleated human cells harbors the protein translocon, which facilitates membrane integration or translocation of almost every newly synthesized polypeptide targeted to organelles of the endo- and exocytotic pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins and complexes that are permanently or transiently associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, modification of precursor polypeptides in transit through the Sec61 complex, and Sec61 channel gating, i.e., dynamic regulation of the pore forming subunit to mediate precursor transport and calcium efflux. Recently, cryoelectron tomography of translocons in native ER membrane vesicles, derived from human cell lines or patient fibroblasts, and even intact cells has given unprecedented insights into the architecture and dynamics of the native translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion, and translocation of newly synthesized polypeptides as well as the putative physiological roles of the Sec61 channel as a passive ER calcium leak channel. Furthermore, the structural insights into the Sec61 channel are incorporated into an overview and update on Sec61 channel-related diseases—the Sec61 channelopathies—and novel therapeutic concepts for their treatment.
α‐Actinin‐2 deficiency results in sarcomeric defects in zebrafish that cannot be rescued by α‐actinin‐3 revealing functional differences between sarcomeric isoforms

α‐Actinins are actin‐binding proteins that can be broadly divided into Ca2+‐sensitive cytoskeletal and Ca2+‐insensitive sarcomeric isoforms. To date, little is known about functional differences between the isoforms due to their indistinguishable activities in most in vitro assays. To identify functional differences in vivo between sarcomeric isoforms, we employed computational and molecular approaches to characterize the zebrafish (Danio rerio) genome, which contains orthologoues of each human α‐actinin gene, including duplicated copies of actn3. Each isoform exhibits a distinct and unique pattern of gene expression as assessed by mRNA in situ hybridization, largely sharing similar expression profiles as seen in humans. The spatial conservation of expression of these genes from lower invertebrates to humans suggests that regulation and subsequent functions of these genes are conserved during evolution. Morpholino‐based knockdown of the sarcomeric isoform, actn2, leads to skeletal muscle, cardiac, and ocular defects evident over the first week of development. Remarkably, despite the high degree of sequence conservation between actn2 and actn3, the phenotypes of α‐actinin‐2 deficient zebrafish can be rescued by overexpression of α‐actinin‐2 but not by α‐actinin‐3 mRNAs from zebrafish or human. These data provide functional evidence that the primary sequences of α‐actinin‐2 and α‐actinin‐3 evolved differences to optimize their functions. —Gupta, V. , Discenza, M. , Guyon, J. R. , Kunkel, L. M. , Beggs, A. H. α‐Actinin‐2 deficiency results in sarcomeric defects in zebrafish that cannot be rescued by α‐actinin‐3 revealing functional differences between sarcomeric isoforms. FASEB J. 26, 1892‐1908 (2012). www.fasebj. org
Study on Stress Models of Chinese Disyllable

This paper investigates the stress distributions of Chinese disyllables in 1+1, 2+2 and 4+4. The result shows that: 1) most of Chinese disyllables do not have fixed stress models, moreover, two syllables have equal opportunities of being stressed; 2) disyllables in 2+2 and 4+4 have obviously initial-stressed inclination due to “neutralization” in final syllable; 3) not only pitch and duration, but also break level and the position in the prosodic phrase influence the distributions of word stress.
Evaluation of urinary resveratrol as a biomarker of dietary resveratrol intake in the European Prospective Investigation into Cancer and Nutrition (EPIC) study

Abstract In vitro studies have shown several beneficial properties of resveratrol. Epidemiological evidence is still scarce, probably because of the difficulty in estimating resveratrol exposure accurately. The current study aimed to assess the relationships between acute and habitual dietary resveratrol and wine intake and urinary resveratrol excretion in a European population. A stratified random subsample of 475 men and women from four countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) cross-sectional study, who had provided 24-h urine samples and completed a 24-h dietary recall (24-HDR) on the same day, were included. Acute and habitual dietary data were collected using standardised 24-HDR software and a validated country-specific dietary questionnaire, respectively. Phenol-Explorer was used to estimate the intake of resveratrol and other stilbenes. Urinary resveratrol was analysed using tandem MS. Spearman’s correlation coefficients between estimated dietary intakes of resveratrol and other stilbenes and consumption of wine, their main food source, were very high (r>0·9) when measured using dietary questionnaires and were slightly lower with 24-HDR (r>0·8). Partial Spearman’s correlations between urinary resveratrol excretion and intake of resveratrol, total stilbenes or wine were found to be higher when using the 24-HDR (R 2 partial approximately 0·6) than when using the dietary questionnaires (R 2 partial approximately 0·5). Moderate to high correlations between dietary resveratrol, total stilbenes and wine, and urinary resveratrol concentrations were observed. These support the earlier findings that 24-h urinary resveratrol is an effective biomarker of both resveratrol and wine intakes. These correlations also support the validity of the estimation of resveratrol intake using the dietary questionnaire and Phenol-Explorer.
Selection of a fungal isolate for the control of the pink hibiscus mealybug Maconellicoccus hirsutus.

BACKGROUND Maconellicoccus hirsutus Green is a widely distributed pest of numerous crops. Although synthetic pesticides are used to control this pest, entomopathogenic fungi may provide an alternative control mechanism. Three experiments were carried out to select a fungal isolate with the potential to be used as a microbial control agent. The in vitro growth of five isolates of Beauveria bassiana sensu lato (Bals.) Vuill and Metarhizium anisopliae sensu lato (Metschn.) Sorokín, along with three isolates of Lecanicillium lecanii (Zimm.) Zare & W. Gams and Isaria fumosoroseus (Wize), was assessed at four temperatures. The in vivo sporulation of eight selected isolates was then evaluated, followed by the susceptibility of third-instar M. hirsutus to a single dose (1 × 10(8) conidia mL(-1) ) of each of these isolates. RESULTS Growth was greatest by isolates of I. fumosoroseus and L. lecanii at 15 and 20 °C and by isolates of M. anisopliae at 25 and 30 °C. In vivo conidium production was greatest when infected with B. bassiana isolate GHA and M. anisopliae isolate Ma65. Mortality was greatest when inoculated with M. anisopliae isolates Ma65 and Ma129. CONCLUSION Isolate Ma65 shows the best potential to be developed as a microbial control agent for M. hirsutus.
Projected Cost Comparison of Trabectome, iStent, and Endoscopic Cyclophotocoagulation Versus Glaucoma Medication in the Ontario Health Insurance Plan

Purpose:To compare the direct cost of treating glaucoma patients with Trabectome, iStent, and endoscopic cyclophotocoagulation (ECP) versus topical medications in Ontario, Canada. Costs are projected over a 6-year period, and presented on a per-patient level from the perspective of the Ontario Health Insurance Plan (OHIP). Methods:The per-bottle cost of each medication was obtained from the 2011 Ontario Drug Benefit (ODB) formulary. A wastage adjustment fee was added to the cost, as was a pharmacy markup, and an ODB dispensing fee. Previously published medication prescription rates were used to determine the frequency with which each medication is prescribed. We estimated the overall cost by taking a weighted average of the cost of each class of glaucoma medications.The cost of each glaucoma device was determined by contacting local distributors. We then added the cost of disposables used during surgery (viscoelastic and keratome) to the cost of each procedure. Start-up costs for each device and surgeons’ fees were excluded from the overall cost. Results:At 6 years, treatment with the Trabectome offered a cumulative cost savings of $279.23, $1572.55, and $2424.71 per patient versus monodrug, bidrug, and tridrug therapy, respectively. A cumulative cost difference of −$20.77, $1272.55, and $2124.71 per patient were found when comparing iStent versus monodrug, bidrug, and tridrug therapy, respectively. Treatment with ECP yielded a cost savings of $779.23, $2072.55, and $2924.71 per patient versus monodrug, bidrug, and tridrug therapy, respectively. Conclusions:Over a projected period of 6 years, the Trabectome, iStent, and ECP may all offer a modest cost savings to OHIP versus the cost of glaucoma medication. Further analysis of direct and indirect costs to patients as well as quality of life assessments will help further delineate the role of these treatments in the glaucoma treatment paradigm.
Dynamic Range Enhancement in Digital Camera Acquisition of Prostheses Hip Xrays

The typical radiographic film exhibits a dynamic range of some 75dB. The digital capture of such radiography with a consumer-grade digital still camera significantly decreases the dynamic range to some 48dB. We propose a method that boosts the dynamic range, by the combining a set of digital images of the same Xray, acquired under different exposure values. The fusion of the acquired images is performed according to a weighting scheme derived from the confidence information extracted from an experimentally derived digital still camera response function. The resulting image can be obtained at various high dynamic range values and shows improved feature visibility.
Understanding dynamics of trending topics in Twitter

In the era of online social networks and microblogging services, we encounter trending topics in each of such platform. Understanding such trends is not a trivial task. It requires a technical analysis of such scenario in order to infer a particular conclusion. Such analysis helps us in characterizing user or community behavior in any online social platform. In this paper, we study twitter, which is a microblogging service that provides users 140 characters to share their feelings, known as Tweets. Our study focuses on dynamics of trending topics on twitter. Understanding dynamics of trending topics helps us in finding and classifying the positive and negative campaigns done on the twitter platform.
Collaborative-Learning-Automata-Based Channel Assignment With Topology Preservation for Wireless Mesh Networks Under QoS Constraints

Wireless mesh networks have emerged as a new technology for providing cost-effective broadband Internet access to users living in different communities across the globe. However, due to changes in a network topology across different paths, it is a challenging task to handle heavy data traffic in a multichannel environment. To address this issue, we propose a new collaborative-learning-automata-based channel assignment with topology preservation in this paper. In the proposed scheme, learning automata (LA) are deployed at the nearest mesh routers to collaborate with each other for information sharing and data transmission while learning from an environment. For each performed action, the LA get a reward or a penalty from the environment. Based on the inputs from the environment, the LA update their action probability vector and then decide the next action. The performance of the proposed scheme is evaluated with respect to various metrics such as throughput, data delivery ratio, switching and buffering delays, effective transmission, and effective channel utilization.
Résumé de données en extraction de connaissances à partir des données (ECD) : application aux données relationnelles et textuelles

Les travaux presentes dans cette these ont ete realises dans le cadre d'un contrat CNET JMINER, dont le but est l'etude de pre-traitement et post-traitements en extraction de connaissances a partir des donnees, appliques aux lettres de reclamation de France Telecom. Les caracteristiques particulieres des donnees de cette application ont oriente nos travaux de recherche. Nous nous sommes tout d'abord interesses aux problemes lies a l'extraction de connaissances a partir de tres importants volumes de donnees. Nous proposons, pour resoudre ces problemes, de remplacer les donnees a traiter par un resume de ces donnees possedant les memes caracteristiques. Cette proposition s'est concretisee par le developpement du logiciel CFSUMM, un systeme de creation de resumes de donnees utilisant des mesures de similarites et d'indiscernabilites entre instances. Nous montrons pourquoi et comment les caracteristiques de ce logiciel le destine particulierementa la reduction d'importants volumes de donnees, qu'ils soient issus de bases de donnees relationnelles ou d'indexation de documents non structures (texte, html, etc).