Miracle-dz/UniFAR-FTUs huggingface dataset:
GeneXpert MTB/RIF dans le dépistage de la tuberculose pulmonaire à l’Hôpital Provincial Général de Référence de Bukavu, à l’Est de la République Démocratique du Congo: quelles leçons tirées après 10 mois d’utilisation?

Introduction En Afrique subsaharienne, les méthodes de diagnostic de la tuberculose sont insuffisantes et reposent essentiellement sur la microscopie. Elles constituent un réel frein pour le contrôle de la tuberculose. La présente étude voudrait évaluer les performances du GeneXpert MTB/RIF vis à vis de la microscopie classique de Ziehl-Neelsen à l’Hôpital Provincial Général de Référence de Bukavu, à l’Est de la République Démocratique du Congo après 10 mois d’utilisation. Méthodes Les résultats de la coloration au Ziehl-Neelsen et de la biologie moléculaire sur GeneXpert MTB/RIF de 452 patients suspects de tuberculose ont été colligés. La validité d’un test par rapport à l’autre dans la détection de la tuberculose a été étudiée. Résultats Dans le groupe entier, la fréquence de la tuberculose pulmonaire était de 16.3%. La positivité était significativement plus élevée pour le GeneXpert MTB/RIF que pour le Ziehl-Neelsen dans le groupe entier (15.9% vs 9.3%, p= 0.03) et chez les séropositifs pour le VIH (52.0% vs 24.0%; p = 0.007). Cependant, la sensibilité de GeneXpert MTB/RIF comparé au Ziehl-Neelsen n’était pas maximale (95.2%). Enfin, GeneXpert MTB/RIF a détecté 20.8% de résistance à la rifampicine. Conclusion La présente étude confirme la supériorité de GeneXpert MTB/RIF sur la coloration de Ziehl-Neelsen dans la détection de la tuberculose et dans la prédiction de la multi résistance. Son utilisation systématique couplée au Ziehl-Neelsen permettrait de mieux contrôler la tuberculose en Afrique subSaharienne.
From Digital Interventions to Behavior Change Support Systems : Understanding Persuasive Systems ’ Development and Evaluation Process

This paper discusses early digital interventions and evolvement of persuasive technologies sometimes termed as behavior change technologies. In addition, it builds upon the conceptual behavior change support system (BCSSs) as an idyllic platform for developing effective persuasive technologies aimed to promote behavior change in a wide array of issues from everyday life. Background. The research field of persuasive technologies has gained significant momentum over recent years with encouraging results. Yet, a key weakness with prevalent persuasive technologies is their focus on singular problem domains and lack of enduring support for users resulting in high drop out rates. Objectives. This paper discourses the development of persuasive systems (PS); emergence of BCSSs and the scope of Persuasive Systems Design (PSD) model in developing successful behavior change support systems (BCSSs). Methods. To conduct literature review, key words such as Digital Interventions and Persuasive Systems were used via Google Scholar. In addition, a thorough review was performed from the proceedings of Persuasive 2007 to 2012. Finally; some open research questions are poised to instigate discussion with an aim to have a mutual understanding of BCSSs followed by concluding remarks. Conclusion. The paper has design implications for a broader research in persuasive systems design, digital health interventions and general IS.
Kernelizing the output of tree-based methods

We extend tree-based methods to the prediction of structured outputs using a kernelization of the algorithm that allows one to grow trees as soon as a kernel can be defined on the output space. The resulting algorithm, called output kernel trees (OK3), generalizes classification and regression trees as well as tree-based ensemble methods in a principled way. It inherits several features of these methods such as interpretability, robustness to irrelevant variables, and input scalability. When only the Gram matrix over the outputs of the learning sample is given, it learns the output kernel as a function of inputs. We show that the proposed algorithm works well on an image reconstruction task and on a biological network inference problem.
A discriminative classifier for in-air handwritten Chinese characters recognition

As the development of three-dimensional interaction, in-air writing arises as a novel interaction method, and brings traditional writing behavior to the 3D space. In this paper, we propose a discriminative three-level classifier for in-air handwritten Chinese character recognition. Since the existence of characters with similar shapes and structures results in one of the main difficulties of Chinese handwritten character recognition, this paper tackles the problem caused by similar characters using two discriminative analysis techniques. First, we exploit the learning vector quantization (LVQ) to obtain discriminative prototypes. Then, we use the adaptive discriminative locality alignment (ADLA) to distinguish candidate character class among similar character classes. In the experiments, we evaluate the proposed method on the IAHCC-UCAS2014 dataset constructed by ourselves using the writing-in-the-air system based on the Leap Motion Controller. The experimental results show that the proposed method obtain higher recognition accuracy with lower computational cost.
Shape matters in protein mobility within membranes

Significance Lateral Brownian diffusion of proteins in lipid membranes has been predicted by Saffman and Delbrück to depend only on protein size and on the viscosity of the membrane and of the surrounding medium. Using a single-molecule tracking technique on two transmembrane proteins that bend the membrane differently and are reconstituted in giant unilamellar vesicles, we show that the mobility of a membrane protein is crucially dependent on the local membrane deformation self-generated around the protein, which can be tuned by adjusting membrane tension. The feedback between membrane shaping and mobility is well explained by analytical and numerical models that include the friction of the deformed membrane patch with the surrounding medium and the friction internal to the bilayer. The lateral mobility of proteins within cell membranes is usually thought to be dependent on their size and modulated by local heterogeneities of the membrane. Experiments using single-particle tracking on reconstituted membranes demonstrate that protein diffusion is significantly influenced by the interplay of membrane curvature, membrane tension, and protein shape. We find that the curvature-coupled voltage-gated potassium channel (KvAP) undergoes a significant increase in protein mobility under tension, whereas the mobility of the curvature-neutral water channel aquaporin 0 (AQP0) is insensitive to it. Such observations are well explained in terms of an effective friction coefficient of the protein induced by the local membrane deformation.
Learning Track Representation and Trends for Conference Analytics

We propose a new system for facilitating the co-creation of conference tracks through data analytics and human knowledge. The system attempts to learn track representations based on a topic-track matching framework, infer historical track representations by topic evolution paths and investigate the evolution of track representations to figure out track trends. We thus aim to develop a data-driven approach for improving expert-designed track descriptions in future conference organization. One challenge in our work is how to learn track representations from limited publication papers of each year, and another challenge is to how to figure out track trends when track descriptions are not readily available in some years. We present two novel approaches on learning track representation by topic-track matching and analyzing track trends by constructing topic evolution paths, respectively. We also show interesting results on topical leaps and branches from year to year, obtained from papers of INTERSPEECH and ICASSP from 2010 to 2014. These findings should be reflected in the conference tracks to keep them up to date.
Bilinear processes with time dependent variance

If the noise »t in the state space representation of a superdiagonal bilinear model BL(p; q; p; q) is non-stationary, then the time series generated by this model will be non-stationary. In this paper, it is shown that the existence theorems and the invertibilty condition of the non stationary model is similar to the stationary case. Furthermore, it is shown that the e®ect of the non-stationary noise on the estimation of the parameters of the underlying BL(p; q; p; q) model is not signi ̄cant.
FTY720, a novel immunosuppressant, induces sequestration of circulating mature lymphocytes by acceleration of lymphocyte homing in rats. I. FTY720 selectively decreases the number of circulating mature lymphocytes by acceleration of lymphocyte homing.

FTY720, given i.v. or orally at 0.03 mg/kg or more, significantly prolonged skin allograft survival in a dose-dependent manner and showed more potent immunosuppressive activity than cyclosporin A (CsA) or tacrolimus (FK506) in MHC-incompatible rat strains of WKAH donors and F344 recipients. However, unlike CsA or FK506, FTY720 up to 1000 nM did not affect IL-2 production in allogeneic MLC. Within 3 to 24 h after a single oral administration of FTY720 at 0.1 to 1 mg/kg, the number of lymphocytes in the rats was markedly decreased in the peripheral blood and thoracic duct lymph and partially in spleen. By contrast, the number of lymphocytes in peripheral lymph nodes (PLN), mesenteric lymph nodes (MLN), and Peyer's patches (PP) was significantly increased at the same time. Intravenous transfusion of calcein-labeled rat lymphocytes into rats revealed that FTY720 significantly accelerated lymphocyte homing to PLN, MLN, and PP, dose dependently. Since FTY720-induced lymphocyte homing was completely blocked by simultaneous treatment of the calcein-labeled lymphocytes with mAbs against CD62L, CD49d, and CD11a before the transfusion, the acceleration of lymphocyte homing by FTY720 appears to be mediated by lymphocyte-homing receptors. These findings indicate that FTY720 sequesters circulating mature lymphocytes into PLN, MLN, and PP by acceleration of lymphocyte homing and thereby decreases the number of lymphocytes in peripheral blood, thoracic duct lymph, and spleen. Based on these observations, sequestration of circulating mature-lymphocytes is presumed to be a main mechanism of the immunosuppressive activity of FTY720.
Method development and validation study for quantitative determination of nifedipine and related substances by ultra-high-performance liquid chromatography.

A novel stability-indicating reversed phase ultra-high performance liquid chromatography (UPLC) coupled photodiode array gradient method was developed for determination of the nifedipine and related compounds. Furthermore, based on the chromatographic conditions and forced degradation studies performed through the development of the related substances method a UPLC isocratic method was validated for the determination of the assay of this active substance. An Acquity Shield RP18 (50 × 3.0 mm 1.7 µm) column was used for separation of nifedipine and its five potential impurities within 11 min, which is 5-fold less than the official method. A mobile phase consisting of 10 mm ammonium formate (pH 4.5) and methanol, delivered at a flow rate 0.5 mL/min, was employed to achieve a minimum resolution of 2.0 for all consecutive pairs of compounds. The precision value expressed as percentage relative standard deviation for method repeatability and reproducibility was <5.0%. The recoveries for all the related compounds were in the range of 99-105.0%. Linearity was found to be acceptable over the concentration range of 0.25-1.5 µg/mL for nifedipine and its impurities. The limit of quantification for nifedipine was 0.05 µg/mL, which is much less than the European Pharmacopoeia method.
Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils

Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.
Map Building and Monte Carlo Localization Using Global Appearance of Omnidirectional Images

In this paper we deal with the problem of map building and localization of a mobile robot in an environment using the information provided by an omnidirectional vision sensor that is mounted on the robot. Our main objective consists of studying the feasibility of the techniques based in the global appearance of a set of omnidirectional images captured by this vision sensor to solve this problem. First, we study how to describe globally the visual information so that it represents correctly locations and the geometrical relationships between these locations. Then, we integrate this information using an approach based on a spring-mass-damper model, to create a topological map of the environment. Once the map is built, we propose the use of a Monte Carlo localization approach to estimate the most probable pose of the vision system and its trajectory within the map. We perform a comparison in terms of computational cost and error in localization. The experimental results we present have been obtained with real indoor omnidirectional images.
Cocaine, Anemia, and Neurodevelopmental Outcomes in Children: A Longitudinal Study

This longitudinal study investigated the rates of iron-deficiency (ID) and iron-deficiency anemia (IDA) among prenatally cocaine-exposed and nonexposed two- and four-year-old children and assessed their relationships to neurodevelopmental outcomes. The sample consisted of 143 two-year-old (70 exposed and 73 nonexposed) and 274 four-year-old (139 exposed and 135 nonexposed) low socioeconomic status children recruited from an ongoing longitudinal study. Hematological assessments included hemoglobin, serum ferritin, mean corpuscular volume, transferrin saturation, and blood lead levels. The neurodevelopmental outcomes consisted of the Bayley Mental (MDI) and Motor (PDI) Development indices at two years, and the Wechsler Preschool and Primary Scales of Intelligence (WPPSI) and the Peabody Developmental Motor Scales (PDMS) at four years. The rate of IDA in four-year-old children was significantly greater among the cocaine-exposed compared to the nonexposed group (p = .026), while the rates at two years were not significant. Exposure to IDA at two years was associated with a significant decrease in concurrent motor scores (p = .011) after adjustment for relevant covariates. Peak exposure to IDA, defined as being anemic at 2 and/or 4 years of age, was associated with a significant (p < .05) decrease in Full Scale IQ after adjustment. Cocaine exposure was not a significant predictor of Full Scale IQ with the inclusion of peak IDA and lead in the model. These findings indicate the need for greater pediatric surveillance of IDA and lead in cocaine-exposed infants, in order to reduce long-term neuropsychological deficits.
Copula-dependent collateral default intensity and its application to CDS rate

In this paper, we consider a correlation between the default intensities to incorporate dependency between multivariate Cox process. Assuming that each obligor has its own default intensity process, we use multivariate shot noise intensity process where jumps (i.e. magnitude of contribution of primary events to default intensities) occur collaterally and their sizes are correlated. A homogeneous Poisson process is used to describe collateral event jumps in default intensities. The Farlie-Gumbel-Morgenstern (FGM) copulas with exponential margins are used to produce correlations between event jump sizes. Applying copula-dependent collateral default intensity to multivariate Cox process, we derive the joint Laplace transform that provides us with joint survival/default probability and other relevant joint probabilities. As an example of using joint survival/default probability, we calculate credit default swaps (CDS) rates assuming that a zerocoupon default-free bond price is deterministic. Standard martingale theory is used to derive the joint Laplace transforms.
Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

Microbial strains optimization for the overproduction of desired phenotype has been a popular topic in recent years. The strains can be optimized through several techniques in the field of genetic engineering. Gene knockout is a genetic engineering technique that can engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, the complexities of the metabolic networks have made the process to identify the effects of genetic modification on the desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to the combinatorial problem in obtaining optimal gene deletion strategy. Basically, the size of a genome-scale metabolic model is usually large. As the size of the problem increases, the computation time increases exponentially. In this paper, we propose Differential Bees Flux Balance Analysis (DBFBA) with OptKnock to identify optimal gene knockout strategies for maximizing the production yield of desired phenotypes while sustaining the growth rate. This proposed method functions by improving the performance of a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) by hybridizing Differential Evolution (DE) algorithm into neighborhood searching strategy of BAFBA. In addition, DBFBA is integrated with OptKnock to validate the results for improving the reliability the work. Through several experiments conducted on Escherichia coli, Bacillus subtilis, and Clostridium thermocellum as the model organisms, DBFBA has shown a better performance in terms of computational time, stability, growth rate, and production yield of desired phenotypes compared to the methods used in previous works.
Interactive Physics-Based Deformation for Virtual Worlds

When creating immersive interactive virtual worlds, it is important to not only provide plausible visuals, but also to allow the user to interact with the virtual scene in a natural way. While rigid-body physics simulations are widely used to provide basic interaction, realistic soft-body deformations of virtual objects are challenging and therefore typically not offered.We present a client-server architecture for interactive physics-based deformation, which makes it possible to add physically accurate response to interaction to any virtual environment. The architecture is highly flexible, can be used from any web enabled client, and facilitates synchronization of computed deformations across multiple users and devices.
Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel

The mechanosensitive channel of large conductance, which serves as a model system for mechanosensitive channels, has previously been crystallized in the closed form, but not in the open form. Ensemble measurements and electrophysiological sieving experiments show that the open-diameter of the channel pore is >25 Å, but the exact size and whether the conformational change follows a helix-tilt or barrel-stave model are unclear. Here we report measurements of the distance changes on liposome-reconstituted MscL transmembrane α-helices, using a ‘virtual sorting’ single-molecule fluorescence energy transfer. We observed directly that the channel opens via the helix-tilt model and the open pore reaches 2.8 nm in diameter. In addition, based on the measurements, we developed a molecular dynamics model of the channel structure in the open state which confirms our direct observations. DOI: http://dx.doi. org/10.7554/eLife.01834. 001
OPTIMA: An Ontology-Based PlaTform-specIfic software Migration Approach

Software migration is an inherently knowledge intensive activity, which requires a great amount of expertise and experience from different sources. Knowledge-based approach to software migration has a great potential for improving traditional approaches. In this paper, an Ontology-based PlaTform-specific software Migration Approach (OPTIMA) is proposed. Firstly, the background and the related work are introduced, and the ontology design for platform- specific software migration is discussed. Secondly, the architecture and workflow of OPTIMA are illustrated with a prototype tool. Thirdly, the case study is used for experiments with the approach and the prototype tool, and finally, the conclusion is drawn and further research directions are speculated.
Parents' Knowledge, Risk Perception and Willingness to Allow Young Males to Receive Human Papillomavirus (HPV) Vaccines in Uganda

The Ministry of Health in Uganda in collaboration with the Program for Appropriate Technology for Health (PATH) supported by Bill and Melinda Gates Foundation in 2008–2009 vaccinated approximately 10,000 girls with the bivalent humanpapilloma virus (HPV) vaccine. We assessed parent's knowledge, risk perception and willingness to allow son(s) to receive HPV vaccines in future through a cross-sectional survey of secondary school boys aged 10–23 years in 4 districts. 377 questionnaires were distributed per district and 870 were used in analysis. Parents that had ever heard about cervical cancer and HPV vaccines; those who would allow daughter(s) to be given the vaccine and those who thought that HPV infection was associated with genital warts were more willing to allow son(s) to receive the HPV vaccine. Unwilling parents considered HPV vaccination of boys unimportant (p = 0.003), believed that only females should receive the vaccine (p = 0.006), thought their son(s) couldn't contract HPV (p = 0.010), didn't know about HPV sexual transmissibility (p = 0.002), knew that males could not acquire HPV (p = 0.000) and never believed that the HPV vaccines could protect against HPV (p = 0.000). Acceptance of HPV vaccination of daughters and likelihood of recommending HPV vaccines to son(s) of friends and relatives predicted parental willingness to allow sons to receive HPV vaccines. Probable HPV vaccination of boys is a viable complement to that of girls. Successfulness of HPV vaccination relies on parental acceptability and sustained sensitization about usefulness of HPV vaccines even for boys is vital.
IRM enforcement of Java stack inspection

Two implementations are given for Java's stack inspection access-control policy. Each implementation is obtained by generating an inlined reference monitor (IRM) for a different formulation of the policy. Performance of the implementations is evaluated, and one is found to be competitive with Java's less flexible, JVM-resident implementation. The exercise illustrates the power of the IRM approach for enforcing security policies.