Miracle-dz/UniFAR-FTUs huggingface dataset:
An evaluation of single nucleotide polymorphisms used to differentiate vaccine and wild type strains of varicella‐zoster virus

Rashes following immunization with the vaccine strain (vOka) of varicella‐zoster virus (VZV) may occur in up to 5% of children and 10% of adults. In 40% of cases, the causative virus is the vaccine strain and in 60% wild type virus is found. Several reports have identified three restriction site polymorphisms in ORF 62 and the loss of one in ORF 6, which differentiate vOka from wild type VZV, including the parental wild type strain from which vOka, is derived. Using polymerase chain reaction (PCR), restriction enzyme analysis, and sequencing, we analyzed the presence of these markers in the GlaxoSmithKline (GSK, UK) and Merck vaccine preparations as well as in 15 vaccine virus rashes and 15 wild type UK viruses. Our data suggest that a Sma1 positive and an Nae1 positive site in ORF 62 are present in the GSK and Merck vaccine preparations and all vaccine virus rashes. By contrast, a BssHII positive vaccine virus restriction site in ORF 62 and an Alu1 negative site in ORF 6 were mixed in the GSK and Merck vaccines and absent in some of the vaccine rashes. The BssHII site was also present in the European wild type C viruses in UK. The data suggest that unlike the Biken vaccine preparation, the Merck and GSK vaccine preparations are polymorphic for the BssHII and Alu1 restriction sites. These sites are also present variably in the vaccine viruses causing rashes following vaccination, and are therefore unreliable markers for differentiating vOka and wild type VZV strains. J. Med. Virol. 75:174–180, 2005. © 2005 Wiley‐Liss, Inc.
Sources of innovation, their combinations and strengths - benefits at the NPD project level

External sourcing is increasingly seen as important for obtaining new and valuable knowledge and resources for new product development. However, when it comes to the specifics of choosing between sources and types of relationships, little is known on the NPD project level. This paper strengthens and expands existing research by investigating how the mix of external partner types as well as the relationship strength is related to performance at the project level. The empirical background is a survey conducted among Danish SMEs in 2010. Ordinary least square regressions reveal that firms should not only consider the potential benefits of collaboration with external sources but also the downsides, including higher cost and lengthier projects. Firms should look for opportunities in the combination of sources if they are to gain advantages of collaboration, as our analyses show that a mix of market and science sources is related to decreased costs. Additionally, if firms are looking for increased market performance, they should aim at collaborating with suppliers that have a similar knowledge base, whereas if the aim is lower project costs, collaboration with a customer with a similar knowledge base is beneficial. However, the degree of novelty in the new product is lower when companies are very closely embedded with suppliers.
Fault model qualification by assertion mining

The process of measuring the quality of a fault model is a key ingredient for implementing effective verification/testing phases based on fault injection. Most of the existing approaches for the qualification of a fault model base their evaluation on the comparison of the achieved fault coverage against other code coverage metrics, or against the fault coverage achieved by different fault models, sometimes at the varying of the abstraction level. However, these approaches do not explicitly provide a measure of the accuracy of the fault injection with respect to the actual functional behaviours implemented in the design under verification/testing (DUV/T). Thus, the achievement of 100% fault coverage does not necessarily imply that all the design's behaviours have been accurately perturbed by the selected fault model. To provide a more accurate evaluation of fault models, this paper proposes a methodology based on assertion mining, i.e., automatic extraction of temporal assertions from the simulation of the DUV/T. Mined assertions are then used to highlight behaviours of the DUV/T that are not accurately perturbed by the selected fault model.
The topology of mental states . Combining data science and graph theory to reveal neural networks for cognitive functions

In this article we give a general introduction to the study of cognitive functions and dysfunctions from the perspective of data science and network science. We will use functional magnetic resonance imaging data since it is a privileged method to observe whole brain activity in a non-invasive way. The analysis of specific brain networks will provide a quantitative method to investigate the neural correlates of cognition and at the same time can be used to develop new diagnostic and therapeutic procedures for individual neuropsychiatric patients. The extraction of specific networks has to face the problem of a mixture of variability in brain activity. While extracting the network, for example, related to a given pathology, we want to assess the variability in this network between individual patients and filter out the variability due to repeated sampling. In order to face this problem we propose to simultaneously classify subjects and conditions (behavioral or pathologic). We base our classification pipeline on a network model of brain activity that enable us to extract the effective connectivity between brain regions. In contrast to recent attempts to classify individuals based on functional connectivity, our approach provides more stable and reliable estimation of connectivity to the purpose of the classification. Here we show that our method is able to classify a large number of subjects using few recording sessions and at the same time the behavioral condition of the sessions (resting or movie viewing). In addition we extract the networks that underlie the two classifications: The subject network is almost fully connected with several central nodes, located in frontal and cingulate regions; in comparison, the condition network is segregated into small isolated components. Finally we discuss some refinements of our pipeline that are needed for small sampling
Study of the Sparse Superposition Codes and the Generalized Approximate Message Passing Decoder for the Communication over Binary Symmetric and Z Channels

In this project, the behavior of Generalized Approximate Message-Passing Decoder for BSC and Z Channel is studied using i.i. d matrices for constructing the codewords. The performance of GAMP in AWGN Channel is already evaluated in the previous scientific work of Jean Barbier, therefore, this project mainly focuses on the performance of GAMP decoder for BSC and Z Channel. We evaluate the performance of the GAMP decoder for sparse superposition codes at various settings and compare the performance of decoder for different channels and parameters.
Psychometric properties of commonly used low back disability questionnaires: are they useful for older adults with low back pain?

OBJECTIVES To evaluate the psychometric properties of two commonly used low back pain (LBP) disability questionnaires in a sample solely comprising community-dwelling older adults. DESIGN Single-group repeated measures design. SETTING Four continuing care retirement communities in Maryland and in Virginia. Participants. Convenience sample of 107 community-dwelling men and women (71.9%) aged 62 years or older with current LBP. Outcome Measures. All participants completed modified Oswestry Disability (mOSW) and Quebec Back Pain Disability (QUE) questionnaires, as well as the Medical Outcomes Survey Short-Form 36 questionnaire at baseline. At follow-up, 56 participants completed the mOSW and the QUE for reliability assessment. RESULTS Test-retest reliability of the mOSW and QUE were excellent with intraclass correlation coefficients of 0.92 (95% confidence interval [CI]: 0.86, 0.95) and 0.94 (95% CI: 0.90, 0.97), respectively. Participants with high pain severity and high levels of functional limitation had higher scores on the mOSW (P < 0.0001) and QUE (P < 0.001) scales than other participants, which represents good construct validity for both scales. The threshold for minimum detectable change is 10.66 points for the mOSW and 11.04 points for the QUE. Both questionnaires had sufficient scale width to accurately measure changes in patient status. CONCLUSIONS It appears that both questionnaires have excellent test-retest reliability and good construct validity when used to evaluate LBP-related disability for older adults with varying degrees of LBP. Neither questionnaire appears to have superior psychometric properties; therefore, both the Oswestry and Quebec can be recommended for use among geriatric patients with LBP.
Biomechanical loads during common rehabilitation exercises in obese individuals.

BACKGROUND Squats and lunges are commonly prescribed rehabilitation exercises used to improve performance across a wide spectrum of patient populations. However, biomechanical studies have mainly examined young, normal weight populations performing these exercises at a difficulty level potentially too challenging for obese individuals. Understanding how obesity and different levels of difficulty affect lower extremity biomechanics could help to inform rehabilitation approaches used for obese individuals. PURPOSE The purpose of this study was to analyze and compare the lower extremity kinematics and kinetics in obese and normal weight females during performance of progressively more difficult squat and lunge exercises. STUDY DESIGN Cross-sectional study design. METHODS Ten obese females (mean age, 37.4 years; BMI 39.2 ± 3.7 kg/m(2)) and ten normal-weight, age-matched female controls (38.1 years, BMI < 23 kg/m(2)) volunteered for the study. Each group performed two exercises, each in three different iterations: squatting at three standardized knee angles (60°, 70°, and 80°) and lunging at three standardized distances (1.0, 1.1, and 1.2 times tibial length). Three dimensional motion analysis using infrared markers and force plates was used to calculate range of motion as well as hip, knee, ankle and support moments (normalized for body weight). A repeated measures ANOVA model was used to determine between and within group differences. RESULTS Support moments were higher in obese females for squat 70° (p=0.03) and 80° (p=0.01). Ankle extensor moments were higher in obese females for squat 80° (p=0.04). During lunge at all levels (1.0, 1.1, and 1.2), hip extensor moments were higher in obese subjects (p=0.004, 0.003, and 0.007 respectively). Within group, the support moments were significantly higher during squat 80° than squat 60° (p=0.01) in obese females. A non-linear relationship was found between hip moments and BMI during squat 60°, 70°, and 80°. CONCLUSION During two commonly prescribed rehabilitation exercises (squat and lunge), there were significantly greater support moments in obese individuals compared to normal controls. The non-linear associations between kinetic and anthropometric measures make the assessment of how best to approach exercise in obese individuals challenging. LEVEL OF EVIDENCE Level 3.
Specificity of mass spectrometry (MALDI-TOF) in the diagnosis of Babesia canis regarding to other canine vector-borne diseases.

UNLABELLED The canine vector-borne diseases (CVBD) is a term, which describes a range of infectious or/and parasitic diseases whose etiological agents are transmitted by vectors. CVBD are becoming more widely in the world in relation to global warming and the increasing number of infected vectors. The aim of this study was to assess rapid mass spectrometry (MS) - based proteomics analyses for diagnosis of Babesia canis, Anaplasma phagocytophilum and Borrelia burgdorferi infections in dogs. The study was conducted on four groups of dogs - healthy dogs (group 1, n=10) and dogs infected with B. canis (group 2, n=20), A. phagocytophilum (group 3, n=20) and B. burgdorferi (group 4, n=20) which demonstrated symptoms of the diseases. The MALDI-TOF (Matrix Assisted Laser Desorption Ionization with Time of Flight detector) MS technique revealed the presence of specific protein fraction of 51-52 kDa only in the blood serum of all the animals infected with the B. canis protozoa. The proteins are suspected to be disease markers, whereas the MALDI-TOF technique itself has high specificity and sensitivity and can be applied in the diagnosis of canine babesiosis. KEY WORDS Anaplasma phagocytophilum, Babesia canis, Borrelia burgdorferi, MALDI-TOF, proteomics.
Modeling Motivational States in Adaptive Robot Companions

Motivation impacts people’s lives in a powerful way and is at the heart of a plethora of day-to-day activities and achievement settings, from success at the workplace to learning and acquiring knowledge to trying to quit bad habits. The current work aims to develop an adaptive robot companion that models a user’s daily motivational state and chooses appropriate motivational strategies to keep the user on track for achieving a daily goal. The two main components we are focusing on in this context are creating an ontology-based user model of the person’s motivational states and using an appropriate strategy selection algorithm that chooses the best motivational strategies for the user each day based on the user model’s output. Speciﬁcally, we are focusing on the important application domain of physical activity and aim to help early adolescents achieve daily-recommended levels of physical activity. Our human-robot interaction system uses information acquired from the user to feed the user model and physical activity data from a wrist-band device to inform the strategy selection algorithm.
Serum Pro fi ling Identi fi es Novel Muscle miRNA and Cardiomyopathy-Related miRNA Biomarkers in Golden Retriever Muscular Dystrophy Dogs and Duchenne Muscular Dystrophy Patients

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 ajp.amjpathol. org 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 Serum Profiling Identifies Novel Muscle miRNA and Cardiomyopathy-Related miRNA Biomarkers in Golden Retriever Muscular Dystrophy Dogs and Duchenne Muscular Dystrophy Patients Laurence Jeanson-Leh,* Julie Lameth,* Soraya Krimi,* Julien Buisset,* Fatima Amor,* Caroline Le Guiner,*y Inès Barthélémy,z Laurent Servais,x Stéphane Blot,z Thomas Voit,{k and David Israeli* 85 86 87 88 From Genethon,* Evry, France; INSERM UMR 1089,y Atlantic Gene Therapies, Université de Nantes, CHU de Nantes, Nantes, France; the Université ParisEst,z Ecole Nationale Vétérinaire d’Alfort, UPR de Neurobiologie, Maisons-Alfort, France; the Department of Therapeutic Trials and Databases,x Université Pierre et Marie CurieParis 6,k UM 76, CNRS, UMR 7215, Institut de Myologie, Paris, France; and INSERM, UMRS_974,{ Paris, France 89 90 91 Accepted for publication
Implications of the Diabetes Control and Complications Trial

The Diabetes Control and Complications Trial has conclusively established that intensive control of insulin-dependent diabetes mellitus in persons aged 19 to 26 years (almost exclusively white, normotensive, nondyslipidemic, of normal weight, and insulin sensitive) reduces by ± 50% the likelihood of retinopathy, nephropathy, and neuropathy. In contrast, persons with non-insulin-dependent diabetes mellitus (NIDDM) are older, overweight, hypertensive, dyslipidemic, and insulin resistant. Glycemia is only one of their risk factors, and they die of macrovascular disease. Review of studies supporting glycemic control versus risk factor reduction as management of NIDDM suggests a clear need to address risk factors besides glycemic control for successful prevention of complications of NIDDM. A new schematic proposal for intervention based upon risk factor reduction is presented.
Small heterodimer partner deletion prevents hepatic steatosis and when combined with farnesoid X receptor loss protects against type 2 diabetes in mice

Nuclear receptors farnesoid X receptor (FXR) and small heterodimer partner (SHP) are important regulators of bile acid, lipid, and glucose homeostasis. Here, we show that global Fxr –/– Shp–/– double knockout (DKO) mice are refractory to weight gain, glucose intolerance, and hepatic steatosis when challenged with high‐fat diet. DKO mice display an inherently increased capacity to burn fat and suppress de novo hepatic lipid synthesis. Moreover, DKO mice were also very active and that correlated well with the observed increase in phosphoenolpyruvate carboxykinase expression, type IA fibers, and mitochondrial function in skeletal muscle. Mechanistically, we demonstrate that liver‐specific Shp deletion protects against fatty liver development by suppressing expression of peroxisome proliferator‐activated receptor gamma 2 and lipid‐droplet protein fat‐specific protein 27 beta. Conclusion: These data suggest that Fxr and Shp inactivation may be beneficial to combat diet‐induced obesity and uncover that hepatic SHP is necessary to promote fatty liver disease. (Hepatology 2017;66:1854–1865)
Intrinsic Images by Clustering

Decomposing an input image into its intrinsic shading and reflectance components is a long‐standing ill‐posed problem. We present a novel algorithm that requires no user strokes and works on a single image. Based on simple assumptions about its reflectance and luminance, we first find clusters of similar reflectance in the image, and build a linear system describing the connections and relations between them. Our assumptions are less restrictive than widely‐adopted Retinex‐based approaches, and can be further relaxed in conflicting situations. The resulting system is robust even in the presence of areas where our assumptions do not hold. We show a wide variety of results, including natural images, objects from the MIT dataset and texture images, along with several applications, proving the versatility of our method.
Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases

A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome–human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis.
Evaluation detector module of the miniPET-3 small animal PET scanner

We report on the development of an evaluation detector module built for our miniPET -3 small animal PET scanner. The module is based on an LySO scintillation matrix exactly matching that used in miniPET-II (so that the performance of the two PET scanners is easier to compare), followed by a Silicon Photomultiplier (SiPM) matrix array. The front-end electronics is designed to be modular, so that different readout concepts can be evaluated and prototype-tested. The readout electronics is based on a system-on-module with Spartan-6 FPGA and Gigabit Ethernet connectivity. Different SiPM readout concepts were tested using the module, and based on the evaluation results one was selected for implementation and testing.
Modeling napping, post-lunch dip, and other variations in human sleep propensity.

STUDY OBJECTIVES To model sleep propensity (SP) as a continuous variable across 24 hours and to model the post-noon nap zone, or post-lunch dip in performance, and the early evening trough in SP. METHODS The present model is a variant of the 2-process model with 2 major modifications. (1) The circadian threshold process was replaced by sleep drive R, derived from REM sleep propensity, which shows a strong circadian modulation. (2) The model is based on a multiplicative interaction between the 2 input variables S and R. The model parameters S and R were estimated from experimental data. Thus, SP is modeled by multiplicative interaction of 2 sleep drives, S and R, the former of homeostatic, the latter of circadian nature. In short: SP = S x R. RESULTS Under the condition of normal phase and duration of nighttime sleep, SP across 24 hours displays 4 characteristics, (a) a major peak at nighttime, (b) a secondary increase, which peaks post-noon, (c) a first local minimum at sleep offset in the morning, and (d) a second local minimum in the early evening hours. Model simulations with either delayed or advanced sleep times suggest that the magnitude of the post-noon nap zone depends on the phase of the major sleep period within 24 hours. While the nap zone is attenuated or disappears when night sleep is delayed, SP increases during daytime when night sleep is advanced. In all conditions, the evening local minimum of SP remained stable. CONCLUSIONS SP can be modeled as a continuous variable, based on the multiplicative interaction of 2 basic sleep drives. The model predictions are in agreement with known variations of SP across 24 hours.
Analysis of eddy-current loss for design of small active magnetic bearings with solid core and rotor

As the size of rotors levitated by active magnetic bearings (AMBs) gets smaller, it becomes increasingly difficult to make laminated cores and rotors that have low eddy-current loss, and solid cores and rotors have to be substituted. Thus, accurate modeling of eddy-current loss is important for small-size AMB systems with solid cores and rotor. In this paper, we propose a new eddy-current loss model for AMB systems, based on the eddy-current brake concept. We show that the eddy-current loss in AMBs strongly depends on the arrangement and size of poles. We compare test results for hetero- and homopolar AMBs having nonlaminated cores and rotor to analytical findings based on the eddy-current loss model. The experimental results confirm that the eddy-current loss in small homopolar AMBs with nonlaminated cores and rotor can be greatly reduced by optimizing the arrangement and size of poles.
Buffer Design to Minimize Current Collapse in GaN/AlGaN HFETs

The bulk trap-induced component of current collapse (CC) in GaN/AlGaN heterojunction field-effect transistors is studied in drift diffusion simulations, distinguishing between acceptor traps situated in the top and the bottom half of the bandgap, with Fe and C used as specific examples. It is shown that Fe doping results in an inherent but relatively minor contribution to dispersion under pulse conditions. This simulation is in reasonable quantitative agreement with double pulse experiments. Simulations using deep-level intrinsic growth defects produced a similar result. By contrast, carbon can induce a strong CC which is dependent on doping density. The difference is attributed to whether the trap levels, whether intrinsic or extrinsic dopants, result in a resistive n-type buffer or a p-type floating buffer with bias-dependent depletion regions. This insight provides a key design concept for compensation schemes needed to ensure semi-insulating buffer doping for either RF or power applications.