Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeography of Human T-lymphotropic Virus Type 1 (HTLV-1) Lineages Endemic to Japan

We conducted phylogenetic analyses and an estimation of coalescence times for East Asian strains of HTLV-1. Phylogenetic analyses showed that the following three lineages exist in Japan: “JPN”, primarily comprising Japanese isolates; “EAS”, comprising Japanese and two Chinese isolates, of which one originated from Chengdu and the other from Fujian; and “GLB1”, comprising isolates from various locations worldwide, including a few Japanese isolates. It was estimated that the JPN and EAS lineages originated as independent lineages approximately 3,900 and 6,000 years ago, respectively. Based on archaeological findings, the “Out of Sunda” hypothesis was recently proposed to clarify the source of the Jomon (early neolithic) cultures of Japan. According to this hypothesis, it is suggested that the arrival of neolithic people in Japan began approximately 10,000 years ago, with a second wave of immigrants arriving between 6,000 and 4,000 years ago, peaking at around 4,000 years ago. Estimated coalescence times of the EAS and JPN lineages place the origins of these lineages within this 6,000–4,000 year period, suggesting that HTLV-1 was introduced to Japan by neolithic immigrants, not Paleo-Mongoloids. Moreover, our data suggest that the other minor lineage, GLB1, may have been introduced to Japan by Africans accompanying European traders several centuries ago, during or after “The Age of Discovery. ” Thus, the results of this study greatly increase our understanding of the origins and current distribution of HTLV-1 lineages in Japan and provide further insights into the ethno-epidemiology of HTLV-1.
Organ-Specific Role of MyD88 for Gene Regulation during Polymicrobial Peritonitis

ABSTRACT Sepsis leads to the rapid induction of proinflammatory signaling cascades by activation of the innate immune system through Toll-like receptors (TLR). To characterize the role of TLR signaling through MyD88 for sepsis-induced transcriptional activation, we investigated gene expression during polymicrobial septic peritonitis by microarray analysis. Comparison of gene expression profiles for spleens and livers from septic wild-type and MyD88-deficient mice revealed striking organ-specific differences. Whereas MyD88 deficiency strongly reduced sepsis-induced gene expression in the liver, gene expression in the spleen was largely independent of MyD88, indicating organ-specific transcriptional regulation during polymicrobial sepsis. In addition to genes regulated by MyD88 in an organ-dependent manner, we also identified genes that exhibited an organ-independent influence of MyD88 and mostly encoded cytokines and chemokines. Notably, the expression of interferon (IFN)-regulated genes was markedly increased in septic MyD88-deficient mice compared to that in septic wild-type controls. Expression of IFN-regulated genes was dependent on the adapter protein TRIF. These results suggest that the influence of MyD88 on gene expression during sepsis strongly depends on the organ compartment affected by inflammation and that the lack of MyD88 may lead to disbalance of the expression of IFN-regulated genes.
Myosin Ib modulates the morphology and the protein transport within multi-vesicular sorting endosomes

Members of at least four classes of myosin (I, II, V and VI) have been implicated in the dynamics of a large variety of organelles. Despite their common motor domain structure, some of these myosins, however, are non processive and cannot move organelles along the actin tracks. Here, we demonstrate in the human pigmented MNT-1 cell line that, (1) the overexpression of one of these myosins, myosin 1b, or the addition of cytochalasin D affects the morphology of the sorting multivesicular endosomes; (2) the overexpression of myosin 1b delays the processing of Pmel17 (the product of murine silver locus also named GP100), which occurs in these multivesicular endosomes; (3) myosin 1b associated with endosomes coimmunoprecipitates with Pmel17. All together, these observations suggest that myosin 1b controls the traffic of protein cargo in multivesicular endosomes most probably through its ability to modulate with actin the morphology of these sorting endosomes.
Pulmonary nodules at chest CT: effect of computer-aided diagnosis on radiologists' detection performance.

PURPOSE To evaluate the effect of computer-aided diagnosis (CAD) on radiologists' detection of pulmonary nodules. MATERIALS AND METHODS Fifty chest computed tomographic (CT) examination cases were used. The mean nodule size was 0.81 cm +/- 0.60 (SD) (range, 0.3-2.9 cm). Alternative free-response receiver operating characteristic (ROC) analysis with a continuous rating scale was used to compare the observers' performance in detecting nodules with and without use of CAD. Five board-certified radiologists and five radiology residents participated in an observer performance study. First they were asked to rate the probability of nodule presence without using CAD; then they were asked to rate the probability of nodule presence by using CAD. RESULTS For all radiologists, the mean areas under the best-fit alternative free-response ROC curves (Az) without and with CAD were 0.64 +/- 0.08 and 0.67 +/- 0.09, respectively, indicating a significant difference (P <.01). For the five board-certified radiologists, the mean Az values without and with CAD were 0.63 +/- 0.08 and 0.66 +/- 0.09, respectively, indicating a significant difference (P <.01). For the five resident radiologists, the mean Az values without and with CAD were 0.66 +/- 0.04 and 0.68 +/- 0.04, respectively, indicating a significant difference (P =.02). At observer performance analyses, there were no significant differences in Az values obtained either without (P =.61) or with (P =.88) CAD between the board-certified radiologists and the residents. For all radiologists, in the detection of pulmonary nodules 1.0 cm in diameter or smaller, the mean Az values without and with CAD were 0.60 +/- 0.11 and 0.64 +/- 0.11, respectively, indicating a significant difference (P <.01). CONCLUSION Use of the CAD system improved the board-certified radiologists' and residents' detection of pulmonary nodules at chest CT.
An empirical Bayes approach to inferring large-scale gene association networks

MOTIVATION Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standard algorithms for graphical models inapplicable, and inferring genetic networks an 'ill-posed' inverse problem. METHODS We introduce a novel framework for small-sample inference of graphical models from gene expression data. Specifically, we focus on the so-called graphical Gaussian models (GGMs) that are now frequently used to describe gene association networks and to detect conditionally dependent genes. Our new approach is based on (1) improved (regularized) small-sample point estimates of partial correlation, (2) an exact test of edge inclusion with adaptive estimation of the degree of freedom and (3) a heuristic network search based on false discovery rate multiple testing. Steps (2) and (3) correspond to an empirical Bayes estimate of the network topology. RESULTS Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.
Teacher Experiences In Performance Management System (Pms) In Zimbabwe: Focus On Assessment Reviews And Teachers’ Response

This study investigated teacher experiences of, and response to the manner they were assessed or appraised in implementation of Performance Management System (PMS) in Zimbabwe amid concerns over difficulties in the determination of the link between an individual’s job performance and organizational performance, subjectivity in the conduct of performance appraisals and the interplay of personal biases in performance assessment and ratings. Using mixed methods approach, research designs included the survey, case study and phenomenology. From two randomly selected districts of the Midlands Province, 5.2% of primary school teachers and 3.5% of secondary school teachers were randomly sampled from randomly picked schools in the two districts. School heads of sampled schools and district education officers were purposively selected. Data generation tools included questionnaire, semi-structured interviews, document analysis and non-participant observation. Analysis employed descriptive statistics (numbers and corresponding percentages) for quantitative data, and thematic analysis for qualitative data respectively. The major finding was that training on PMS was inadequate for supervisors and teachers. Consequently, teachers and supervisors did not understand what they were expected to do in PMS. Furthermore, school heads’ concern lay with summative supervision and enforcement of PMS through coercive, dictatorial approaches akin to policing for compliance. Without adhering to procedure, crisis management combined reviews and appraisal ratings in a single meeting in some cases. Teachers perceived supervisors’ role negatively, resulting in teachers cheating or resisting, thus defeating professional development benefits of PMS. Findings point to the need for training and resourcing, or modification of the system to suit context.
Worldsheet boundary conditions in Poisson-Lie T-duality

We apply canonical Poisson-Lie T-duality transformations to bosonic open string worldsheet boundary conditions, showing that the form of these conditions is invariant at the classical level, and therefore they are compatible with Poisson-Lie T-duality. In particular the conditions for conformal invariance are automatically preserved, rendering also the dual model conformal. The boundary conditions are defined in terms of a gluing matrix which encodes the properties of D-branes, and we derive the duality map for this matrix. We demonstrate explicitly the implications of this map for D-branes in two non-Abelian Drinfel'd doubles.
Mitochondrial Manganese Superoxide Dismutase Prevents Neural Apoptosis and Reduces Ischemic Brain Injury: Suppression of Peroxynitrite Production, Lipid Peroxidation, and Mitochondrial Dysfunction

Oxidative stress is implicated in neuronal apoptosis that occurs in physiological settings and in neurodegenerative disorders. Superoxide anion radical, produced during mitochondrial respiration, is involved in the generation of several potentially damaging reactive oxygen species including peroxynitrite. To examine directly the role of superoxide and peroxynitrite in neuronal apoptosis, we generated neural cell lines and transgenic mice that overexpress human mitochondrial manganese superoxide dismutase (MnSOD). In cultured pheochromocytoma PC6 cells, overexpression of mitochondria-localized MnSOD prevented apoptosis induced by Fe2+, amyloid β-peptide (Aβ), and nitric oxide-generating agents. Accumulations of peroxynitrite, nitrated proteins, and the membrane lipid peroxidation product 4-hydroxynonenal (HNE) after exposure to the apoptotic insults were markedly attenuated in cells expressing MnSOD. Glutathione peroxidase activity levels were increased in cells overexpressing MnSOD, suggesting a compensatory response to increased H2O2 levels. The peroxynitrite scavenger uric acid and the antioxidants propyl gallate and glutathione prevented apoptosis induced by each apoptotic insult, suggesting central roles for peroxynitrite and membrane lipid peroxidation in oxidative stress-induced apoptosis. Apoptotic insults decreased mitochondrial transmembrane potential and energy charge in control cells but not in cells overexpressing MnSOD, and cyclosporin A and caspase inhibitors protected cells against apoptosis, demonstrating roles for mitochondrial alterations and caspase activation in the apoptotic process. Membrane lipid peroxidation, protein nitration, and neuronal death after focal cerebral ischemia were significantly reduced in transgenic mice overexpressing human MnSOD. The data suggest that mitochondrial superoxide accumulation and consequent peroxynitrite production and mitochondrial dysfunction play pivotal roles in neuronal apoptosis induced by diverse insults in cell culture and in vivo.
Dynamic allocation of attention in aging and Alzheimer disease: uncoupling of the eye and mind.

CONTEXT Visual attention can be distributed focally, in the direction of gaze, or globally, throughout the extrapersonal space. Aging, and especially Alzheimer disease (AD), may influence global attention, resulting in shifts of gaze to attend to the global workspace. OBJECTIVE To determine if subjects who have AD and cognitively intact older subjects shift their gaze more often than young subjects while viewing a dynamic stimulus that emphasizes global attention. DESIGN Experimental study of eye fixation patterns in response to a simulated driving scene with stationary and moving distractors. SETTING Urban, medical school, National Institute on Aging-funded Alzheimer's Disease Center. PARTICIPANTS Thirteen subjects with mild probable AD, 13 age-comparable cognitively intact older control subjects, and 11 young control subjects. MAIN OUTCOME MEASURE Proportion of eye fixations within and outside of a central region of interest encompassing the "road" surface. RESULTS Young controls made significantly more eye fixations (mean number of eye fixations, 47.5) than either of the other 2 groups (older controls mean, 33.2; patients with AD mean, 32.2). However, 76% of their fixations remained within the central region of interest. Older controls and subjects with AD made proportionately fewer fixations within this region (48% and 49%, respectively) than young controls and moved their eyes more often to the periphery but did not differ from one another. CONCLUSIONS Young controls maintain central eye position regardless of peripheral distraction. Older controls move their eyes to the periphery, presumably to widen the window of attention. Subjects with mild AD did not experience an additional disadvantage beyond that associated with aging.
A Multi-Agent System for Dynamic Ontologies

In the article, we present Dynamo (an acronym of DYNAMic Ontologies), a tool based on an adaptive multi-agent system to construct and maintain an ontology from a domain-specific set of texts. The originality of our proposal is that the adaptative multi-agent system is used both to represent the ontology itself and to produce the ontology. This enables us to propose a system building and maintaining dynamically an ontology according to interactions with the user (also called the ontologist). We present our system and the mechanisms used to build and maintain the ontology from the texts and for the interactions with the ontologist. We also give results of the evaluation of our system.
Noether theorem for μ-symmetries

We give a version of Noether theorem adapted to the framework of μ-symmetries; this extends to such case recent work by Muriel, Romero and Olver in the framework of λ-symmetries, and connects μ-symmetries of a Lagrangian to a suitably modified conservation law. In some cases this ‘μ-conservation law’ actually reduces to a standard one; we also note a relation between μ-symmetries and conditional invariants. We also consider the case where the variational principle is itself formulated as requiring vanishing variation under μ-prolonged variation fields, leading to modified Euler–Lagrange equations. In this setting, μ-symmetries of the Lagrangian correspond to standard conservation laws as in the standard Noether theorem. We finally propose some applications and examples.
A Failsafe Distributed Routing Protocol

An algorithm for constructing and adaptively maintaining routing tables in communication networks is presented. The algorithm can be employed in message as well as circuit switching networks, uses distributed computation, provides routing tables that are loop-free for each destination at all times, adapts to changes in network flows, and is completely failsafe. The latter means that after arbitrary failures and additions, the network recovers in finite time in the sense of providing routing paths between all physically connected nodes. For each destination, the routes are independently updated by an update cycle triggered by the destination.
Smart Parking System (SPS) Architecture Using Ultrasonic Detector

With the increase in vehicle production and world population, more and more parking spaces and facilities are required. In this paper a new parking system called Smart Parking System (SPS) is proposed to assist drivers to find vacant spaces in a car park in a shorter time. The new system uses ultrasonic (ultrasound) sensors to detect either car park occupancy or improper parking actions. Different detection technologies are reviewed and compared to determine the best technology for developing SPS. Features of SPS include vacant parking space detection, detection of improper parking, display of available parking spaces, and directional indicators toward vacant parking spaces, payment facilities and different types of parking spaces (vacant, occupied, reserved and handicapped) through the use of specific LEDs. This paper also describes the use of an SPS system from the entrance into a parking lot until the finding of a vacant parking space. The system is designed for a four-level parking lot with 100 parking spaces and five aisles on each floor. The system architecture defines the essential design features such as location of sensors, required number of sensors and LEDs for each level, and indoor and outdoor display boards.
Superposition Coding for Wireless Mesh Networks Paper ID : 1569031665

A major barrier for the adoption of wireless mesh networks is severe limits on throughput. In this paper, we design a new wireless mesh network architecture based on superposition coding to substantially improve network capacity in large, dense wireless mesh networks. Superposition coding is a physical layer technique that allows a transmitter to simultaneously send independent packets to multiple receivers. While superposition coding has been studied extensively by the physical layer community, we present the first design of practical and effective MAC and routing protocols to take advantage of superposition coding in wireless mesh networks. Extensive evaluations show that superposition coding can be a practical method to increase the throughput of large, dense wireless mesh networks. Specifically, in a mesh network with 2 to 64 active receivers and one gateway, we show that our system can increase throughput up to 283%, with average gain ranging from 15% to 51%. When there are multiple gateways, our system gains up to 190%, with average gain ranging from 31% to 71%. These results clearly demonstrate the potential benefits of our system. We also present a prototype implementation using GNU Radio.
Simplified Multicast Forwarding

This document describes a Simplified Multicast Forwarding (SMF) mechanism that provides basic Internet Protocol (IP) multicast forwarding suitable for limited wireless mesh and mobile ad hoc network (MANET) use. It is mainly applicable in situations where efficient flooding represents an acceptable engineering design trade- off. It defines techniques for multicast duplicate packet detection (DPD), to be applied in the forwarding process, for both IPv4 and IPv6 protocol use. This document also specifies optional mechanisms for using reduced relay sets to achieve more efficient multicast data distribution within a mesh topology as compared to Classic Flooding. Interactions with other protocols, such as use of information provided by concurrently running unicast routing protocols or interaction with other multicast protocols, as well as multiple deployment approaches are also described. Distributed algorithms for selecting reduced relay sets and related discussion are provided in the appendices. Basic issues relating to the operation of multicast MANET border routers are discussed, but ongoing work remains in this area and is beyond the scope of this document. This document defines an Experimental Protocol for the Internet community.
Turn rate estimation based on curve fitting in maneuvering target tracking

Tracking of highly maneuvering targets with unknown behavior is a difficult problem in state estimation. This paper presents an interacting multiple model algorithm (IMM) utilizing adaptive turn rate models to track a maneuvering target. The turn rate is calculated at each step form the estimator of velocity and the radius of curvature of the trajectory of the target by using Least Square (LS) and curve fitting theory. Simulation in different scenario proves that the turn-rate estimation techniques in this adaptive framework can significantly solve the problem of tracking maneuvering targets.
Hot-Spot-Driven Framework Development

Most excellent object-oriented frameworks are still the product of a more or less chaotic development process, typically carried out in the realm of research-like settings. Overall, flexibility has to be injected into a framework in appropriate doses 1. Framework adaptation takes place at points of predefined refinement that we call hot spots. As the quality of a framework depends directly on the appropriateness of hot spots, hot spot identification has to become an explicit activity in the framework development process. Means for documenting and communicating hot spots between domain experts and software engineers become crucial. This contribution first discusses the few essential framework construction principles, that is, how to keep object-oriented architectures flexible for adaptations. We introduce hot spot cards as means to capture flexibility requirements, and illustrate how to apply them in combination with the essential framework construction principles. The presented heuristics form a hot-spot-driven framework design process which leads to a more systematic framework construction with fewer (re)design iterations.
Research of Food Safety Event Detection Based on Multiple Data Sources

Online event detection techniques are usually used in single data source. This paper analyzes event detection in the perspective of multiple data sources, combining news reports and microblogs. Detect events from news, combining microblogs to do event monitoring and early warning. Also improve feature selection methods for multiple data sources event detection. Finally, the methods are applied to the detection of food safety events and the results of the research show that event detection with multiple data sources is meaningful and valuable.
A Surrogate-based Generic Classifier for Chinese Movie Reviews

With the emerging of various online video platforms like Youtube, Youku and LeTV, online movie reviews become more and more important both for movie viewers and producers. As a result, automatically classifying reviews according to different requirements evolves as a popular research topic and is very essential in our daily life. In this paper, we focused on reviews of hot TV series in China and successfully trained generic classifiers based on 8 predefined categories. The experimental results showed promising performance and effectiveness of its generalization to different TV series.