Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Cytomegalovirus Glycoprotein B Genotype Distribution in Serum and Cerebrospinal Fluid Specimens Determined by a Novel Multiplex Nested PCR

ABSTRACT A novel and highly sensitive multiplex nested PCR assay has been developed for the simultaneous glycoprotein B (gB) typing of four gB genotypes of human cytomegalovirus (CMV) directly from clinical specimens. Specifically, a pair of primers to conserved regions of all gB genotypes within the gB gene (gB and gpUL55) was used for primary amplification. A mixture of nested primers to specific and conserved regions of each gB genotype was used for a secondary PCR amplification, yielding amplicons of different sizes for each gB genotype that could easily be differentiated by agarose gel electrophoresis. A total of 40 of 44 serum specimens and 26 of 26 cerebrospinal fluid (CSF) samples, which had previously tested positive for CMV in 66 of 70 AIDS patients with different CMV disease conditions, were gB genotyped by this novel assay. Significant differences in glycoprotein B genotype distribution between serum and CSF specimens were found (P = 0.001). gB genotype 3 (gB3) and gB2 were the most prevalent genotypes in sera (42.5%) and CSF (38.5%), respectively. A different distribution was also observed when only patients with CMV retinitis were studied (P = 0.005), suggesting a gB2 neuron tropism. Neither CMV disease nor any particular clinical manifestation of CMV disease was associated with gB genotypes (P > 0.05). A high incidence of mixed infection with the gB1 and gB3 genotypes (27.5%) was detected in serum specimens, indicating that reinfection and reactivation are common traits in advanced AIDS patients.
A Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification

Structure‐by‐structure analysis, in which the brain magnetic resonance imaging (MRI) is parcellated based on its anatomical units, is widely used to investigate chronological changes in morphology or signal intensity during normal development, as well as to identify the alterations seen in various diseases or conditions. The multi‐atlas label fusion (MALF) method is considered a highly accurate parcellation approach, and anticipated for clinical application to quantitatively evaluate early developmental processes. However, the current MALF methods, which are designed for neonatal brain segmentations, are not widely available. In this study, we developed a T1‐weighted, neonatal, multi‐atlas repository and integrated it into the MALF‐based brain segmentation tools in the cloud‐based platform, MRICloud. The cloud platform ensures users instant access to the advanced MALF tool for neonatal brains, with no software or installation requirements for the client. The Web platform by braingps.mricloud. org will eliminate the dependence on a particular operating system (eg, Windows, Macintosh, or Linux) and the requirement for high computational performance of the user's computers. The MALF‐based, fully automated, image parcellation could achieve excellent agreement with manual parcellation, and the whole and regional brain volumes quantified through this method demonstrated developmental trajectories comparable to those from a previous publication. This solution will make the latest MALF tools readily available to users, with minimum barriers, and will expedite and accelerate advancements in developmental neuroscience research, neonatology, and pediatric neuroradiology.
Effects of Emotional Contexts on Cerebello-Thalamo-Cortical Activity during Action Observation

Several studies investigated the neural and functional mechanisms underlying action observation in contexts with objects. However, actions seen in everyday life are often embedded in emotional contexts. The neural systems integrating emotion cues in action observation are still poorly understood. Previous findings suggest that the processing of both action and emotion information recruits motor control areas within the cerebello-thalamo-cortical pathways. It is therefore hard to determine whether social emotional contexts influence action processing via a direct modulation of motor representations coding for the observed action or via the affective state and implicit motor preparedness elicited in observers in response to emotional contexts. Here we designed a novel fMRI task to identify neural networks engaged by the affective appraisal of a grasping action seen in two different emotional contexts, while keeping the action kinematics constant. Results confirmed that observing the same acts of grasping but in different emotional contexts modulated activity in supplementary motor area, ventrolateral thalamus, anterior cerebellum. Moreover, changes in functional connectivity between left supplementary motor area and parahippocampus in different emotional contexts suggested a direct neural pathway through which emotional contexts may drive the neural motor system. Taken together, these findings shed new light on the malleability of motor system as a function of emotional contexts.
2 The Classical Search Model

This chapter discusses various methods that have been used to estimate structural models of search and survival models. Most of the focus is on using available data, usually on unemployment spell lengths and accepted wage o¤ers, to estimate the parameters of speci.c search models. In particular, we focus on estimating the parameters of the wage o¤er distribution, the reservation wage or reservation wage function, the cost of search, o¤er arrival rate, and discount rate. There is an added section on survival models because survival models have been used so extensively to look at unemployment spell data. Throughout we describe actual models, estimation procedures, and issues associated with identi.cation and estimation. There is not as much of an emphasis on results because we view the literature as still developing methodology. The frontier of the methodology for structural models involves estimating equilibrium search models and allowing for heterogeneity and interesting dynamics. We also think identi.cation issues should receive more attention. This chapter is divided up into sections. The next section presents the classical search model and how to estimate its parameters. We begin by presenting early ”semi-structural” attempts to estimate the model. Next, there is a discussion on estimating a basic structural search model. We build on the basic model by allowing for measurement error in wages, observed and unobserved heterogeneity, right censoring, continuous time, and observed rejected o¤ers. Next, there is a discussion of models with changing reservation wages. The third section deals with survival analysis. We construct the basic Cox proportional hazards model with unobserved heterogeneity and discuss how to estimate the e¤ects of observed covariates, the parameters of the baseline hazard function and the parameters of the unobserved heterogeneity density function. Then we discuss semiparametric approaches associated with estimating the baseline hazard and unobserved heterogeneity density function. The next section discusses empirical equilibrium search models. A few theoretical models are presented. Then we discuss how to estimate their structural parameters and to deal with special problems associated with such models. Given present data, identi.cation is an important issue. A conclusion ends the paper.
LQR and SMC Stabilization of a New Unmanned Aerial Vehicle

We present our ongoing work on the development of a new quadrotor aerial vehicle which has a tilt-wing mechanism. The vehicle is capable of take-off/landing in vertical flight mode (VTOL) and flying over long distances in horizontal flight mode. Full dynamic model of the vehicle is derived using Newton-Euler formulation. Linear and nonlinear controllers for the stabilization of attitude of the vehicle and control of its altitude have been designed and implemented via simulations. In particular, an LQR controller has been shown to be quite effective in the vertical flight mode for all possible yaw angles. A sliding mode controller (SMC) with recursive nature has also been proposed to stabilize the vehicle's attitude and altitude. Simulation results show that proposed controllers provide satisfactory performance in achieving desired maneuvers.
Mycobacterium tuberculosis Binding to Human Surfactant Proteins A and D, Fibronectin, and Small Airway Epithelial Cells under Shear Conditions

ABSTRACT A crucial step in infection is the initial attachment of a pathogen to host cells or tissue. Mycobacterium tuberculosis has evolved multiple strategies for establishing an infection within the host. The pulmonary microenvironment contains a complex milieu of pattern recognition molecules of the innate immune system that play a role in the primary response to inhaled pathogens. Encounters of M. tuberculosis with these recognition molecules likely influence the outcome of the bacillus-host interaction. Here we use a novel fluid shear assay to investigate the binding of M. tuberculosis to innate immune molecules that are produced by pulmonary epithelial cells and are thought to play a role in the lung innate immune response. Virulent and attenuated M. tuberculosis strains bound best to immobilized human fibronectin (FN) and surfactant protein A (SP-A) under this condition. Binding under fluid shear conditions was more consistent and significant compared to binding under static conditions. Soluble FN significantly increased the adherence of both virulent and attenuated M. tuberculosis strains to human primary small airway epithelial cells (SAEC) under fluid shear conditions. In contrast, SP-A and SP-D effects on bacterial adherence to SAEC differed between the two strains. The use of a fluid shear model to simulate physiological conditions within the lung and select for high-affinity binding interactions should prove useful for studies that investigate interactions between M. tuberculosis and host innate immune determinants.
Why the simplest notion of neocortex as an autoassociative memory would not work

We discuss the idea that long range cortico-cortical connections might be the substrate for an autoassociative memory mechanism, whereby features processed locally could be linked together over large portions of neocortex. The simplest version of this idea is shown to be implausibly inadequate in terms of storage capacity; although up to a fraction of a bit could be stored on each synapse, the number of global activity patterns that could be stored and individually retrieved would scale not with the size of the network but, effectively, only with the number of modifiable connections per cell.
Construction of a genetic linkage map in man using restriction fragment length polymorphisms.

We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci. " Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.
A Survey on Hair Modeling: Styling, Simulation, and Rendering

Realistic hair modeling is a fundamental part of creating virtual humans in computer graphics. This paper surveys the state of the art in the major topics of hair modeling: hairstyling, hair simulation, and hair rendering. Because of the difficult, often unsolved problems that arise in alt these areas, a broad diversity of approaches is used, each with strengths that make it appropriate for particular applications. We discuss each of these major topics in turn, presenting the unique challenges facing each area and describing solutions that have been presented over the years to handle these complex issues. Finally, we outline some of the remaining computational challenges in hair modeling
Na +,K+-ATPase Activity and Subunit Isoform Protein Abundance: Effects of Antenatal Glucocorticoids in the Frontal Cerebral Cortex and Renal Cortex of Ovine Fetuses

We examined the effects of single and multiple maternal glucocorticoid courses on cerebral cortical (CC) and renal cortical (RC) Na+,K+-ATPase activity and protein isoform abundance in fetal sheep. Ewes received four dexamethasone or placebo injections in the single course (SC) groups, and the same treatment once a week for five-weeks in the multiple course (MC) groups. CC Na +,K+-ATPase a2-abundance was higher (P<0.05) and β2-abundance lower in the SC dexamethasone than placebo group, but Na+,K+-ATPase activity did not change. CC Na+,K+-ATPase activity, a1-, β1 -, and β2-abundance were lower in the MC dexamethasone than placebo group, but a2- and a3-abundance did not change. Both dexamethasone courses did not affect CC cell number. RC Na +,K+-ATPase activity, a1- and β1 -abundance were higher in the MC dexamethasone than placebo group, but did not change in the SC dexamethasone group. We conclude MC, but not a SC of dexamethasone, affect fetal cerebral and renal Na+,K+-ATPase, and MC result in differential effects on Na+,K+-ATPase in these organs.
The effect of left hand conducting gesture on inappropriate vocal tension in individual singers

The purpose of this study was to examine the effect of six left hand conducting gestures on inappropriate vocal tension in singers. Singers (N=103), of varying levels of expertise, performed a musical selection while responding to a videotaped example of a conductor using a variety of left hand conducting gestures including: (1) left hand, no change; (2) left hand, fisted gesture; (3) left hand, palm up; (4) left hand, palm down; (5) left hand, stabbing gesture; and (6) left hand, sideways, phrase-shaping gesture. Results showed that there were significant differences in vocal tension ratings for all conducting conditions except the palm down condition. Of the remaining conducting conditions, the fisted gesture and stabbing gesture generated the highest mean difference scores. Comparisons were made between high schools singers, college singers, and conductors as well as between male and female singers.
Multi-Objective Evolutionary Algorithm -assisted automated parallel parking

The ease with which a human expert driver performs the complex tasks involved in parallel-parking a non-holonomic vehicle motivates the mimicry of an human driving behavior in automation of the task. This paper presents such an algorithm to achieve automated parallel parking in tight spaces. Unlike other approaches rooted in neural networks and/or fuzzy logic, the proposed algorithm performs maneuvers closely modeled after human driving instructions. Stevenspsila power law is employed in modeling perceived physical quantities on which the instructions operate while the uncertainty inherent in the natural language formulation is represented by Gaussian distribution. The algorithm consists of five stages: position alignment in preparation for the backward S-turn, the first half of the S-turn, position alignment for the second part of the S-turn, the second part of the S-turn and longitudinal adjustment. Negotiation of available parking space in the second part of the S-turn, arguably the most difficult part, is performed with the help of a rule base documenting the relation between steering angle, vehicle orientation and distance traversed. To achieve parking accuracy and avoid collision in the maneuver, the appropriate steering angle must be employed. This angle is approximated from the most suitable rule, which identification is essentially a multi-objective problem addressed here by a Multi-Objective Evolutionary Algorithm. Computer simulations demonstrate the success of the approach.
Secondary stroke prevention best practice recommendations: exploring barriers for rural family physicians.

INTRODUCTION Patients' risk of having a second stroke can be substantially reduced by implementing best practice recommendations for secondary stroke prevention. However, evidence indicates that rural practitioners may face barriers to implementing these recommendations into their practices. This research project developed a workshop to increase practitioner awareness of the recommendations, and to identify barriers to the application of recommendations for secondary prevention of stroke in rural practices. METHODS The workshop provided a venue for family physicians, specialists and health district representatives to discuss the recommendations. It was evaluated using a sequential explanatory mixed-methods approach using 3 methods of data collection: a questionnaire, documentation of comments made during discussion periods and post-workshop interviews. RESULTS Participants at the workshop increased their awareness of the recommendations, and they gained an increased appreciation of how they might collaborate with other practitioners and the health district to implement the recommendations. The workshop identified barriers to implementing recommendations, such as miscommunications with the local health district, role conflict among physicians regarding health promotion and difficulties coordinating care with specialists. CONCLUSION The workshop was an effective venue for improving communication between physicians and the health district and for reducing barriers to the implementation of recommendations.
Bayesian estimation of multiple clade competition from fossil data

Background: The diversification dynamics of clades is governed by speciation and extinction processes and is likely affected by multiple biotic, abiotic, and stochastic factors. Using quantitative methods to analyse fossil occurrence data, one may infer rates of speciation and extinction in a Bayesian framework. Moreover, Silvestro et al. (2015a) recently developed a Multiple Clade Diversity Dependence birth-death model (MCDD) to determine whether diversification dynamics can be explained by positive or negative effects of interactions within or between co-existing clades. However, the power and accuracy of this model and its general applicability have yet to be thoroughly investigated. Aims: Explore the properties of the existing MCDD implementation, which is based on Bayesian variable selection. Introduce an alternative parameterization based on the Horseshoe prior and show the properties of this approach for Bayesian shrinkage in complex models. Test the ability of the model to correctly identify within and between diversification interference under a suite of different diversification scenarios. Methods: Use simulations to assess and compare the power and accuracy of the two algorithms. Results: Diversity dependence within and between clades can be inferred with confidence in a wide range of scenarios using the MCDD model. The two implementations provide comparable results, but the new Horseshoe prior estimator appears to be more reliable, albeit slightly more conservative. The MCDD model is a powerful framework to analyse the putative effects of ecological interactions on macroevolutionary dynamics using fossil data and provides a sound statistical basis for future method developments.
Quantification of the TMS-EEG response in epilepsy

Purpose: The purpose of this thesis was to provide quantitative measures of the co-registration of transcranial magnetic stimulation (TMS) and electroencephalogram (EEG). The EEG is used to study changes in the neuronal activity evoked by the non-invasive technique TMS. These effects are determined mainly based on clinical judgment. Current uses in the diagnosis of epilepsy are based only on EEG, not taking into consideration the low sensitivity in the interictal period, in particular if routine recordings are used. Methods: Patient data was gathered, analyzed and compared to healthy controls. A total of ten patients and eighteen healthy subjects underwent sessions of 75 TMS pulses. The responses to the pulses were filtered and averaged. The use of topographical scalp plots of amplitude and power, and time-series analysis of power in search for late responses provide results which enable separation of epilepsy patients and healthy controls. By investigating the significance of the results it is also possible to determine, in a quantitative way how reliable the methods are for distinguishing between the two groups. Results: The definition of what is a response is critical in this project, and as such must consider: significant power change, be above a certain amplitude, and be localized. Still, this procedure results in a non distinguishable threshold to separate both groups. Conclusions: Analysis of the receiver operating characteristic (ROC) curves also led to the understanding the method established is not entirely reliable because it cannot in fact determine differences. Since all patients were under treatment with anti-epileptic drugs (AEDs), it becomes necessary to elaborate a pilot study with recently diagnosed subjects where hyperexcitability is still present.
THE RICH TRANSCRIPTION 2004 SPRING MEETING RECOGNITION EVALUATION

This paper presents the design and results of the Rich Transcription 2004 Spring Meeting Recognition Evaluation. The evaluation included both Speaker Segmentation (SPKR) and Speech-to-Text Transcription (STT) tasks. Three microphone type conditions were supported: Multiple Distant Microphones (the primary condition of interest), Single Distant Microphone (SDM), and Individual Head Microphones (IHM) (for the STT task only).
Nucleotides Flanking the Start Codon in hsp70 mRNAs with Very Short 5’-UTRs Greatly Affect Gene Expression in Haloarchaea

Leaderless translation is prevalent in haloarchaea, with many of these leaderless transcripts possessing short 5’-untranslated regions (UTRs) less than 10 nucleotides. Whereas, little is known about the function of this very short 5’-UTR. Our previous studies determined that just four nucleotides preceded the start codon of hsp70 mRNA in Natrinema sp. J7, with residues -3A and +4G, relative to the A of the ATG start codon, acting as the preferred bases around the start codon of all known haloarchaeal hsp70 genes. Here, we examined the effects of nucleotides flanking the start codon on gene expression. The results revealed that shortening and deletion of the short 5’-UTR enhanced transcript levels; however, it led to significant reductions in overall translational efficiency. AUG was efficiently used as start codons, in both the presence and absence of short 5’-UTRs. GUG also could initiate translation, even though it was so inefficient that it would not be detected without considerably elevated transcript. Nucleotide substitutions at position -4 to +6 were shown to affect gene expression by transcript and/or translational levels. Notably, -3A and A/U nucleotides at position +4~+6 were more optimal for gene expression. Nucleotide transversions of -3A to -3C and +4G to +4T with hsp70 promoter from either Haloferax volcanii DS70 or Halobacterium salinarum NRC-1 showed the same effects on gene expression as that of Natrinema sp. J7. Taken together, our results suggest that the nucleotides flanking the start codon in hsp70 mRNAs with very short 5’-UTRs play an important role in haloarchaeal gene expression.