Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia

H5N1 highly pathogenic avian influenza (HPAI) viruses have seriously affected the Asian poultry industry since their recurrence in 2003. The viruses pose a threat of emergence of a global pandemic influenza through point mutation or reassortment leading to a strain that can effectively transmit among humans. In this study, we present phylogenetic evidences for the interlineage reassortment among H5N1 HPAI viruses isolated from humans, cats, and birds in Indonesia, and identify the potential genetic parents of the reassorted genome segments. Parsimony analyses of viral phylogeography suggest that the reassortant viruses may have originated from greater Jakarta and surroundings, and subsequently spread to other regions in the West Java province. In addition, Bayesian methods were used to elucidate the genetic diversity dynamics of the reassortant strain and one of its genetic parents, which revealed a more rapid initial growth of genetic diversity in the reassortant viruses relative to their genetic parent. These results demonstrate that interlineage exchange of genetic information may play a pivotal role in determining viral genetic diversity in a focal population. Moreover, our study also revealed significantly stronger diversifying selection on the M1 and PB2 genes in the lineages preceding and subsequent to the emergence of the reassortant viruses, respectively. We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses.
The global ‘order’, socioeconomic status and the economics of African identity

Chronic elitism within Africa has created a two‐tier milieu in which those Africans who are in a position to take advantage of the global economic system often do so at the expense of other Africans. The effects of social class and indicators of individual economic mobility on African identity were thus examined. 213 Kenyans participated in this questionnaire‐based study for structural equation analysis. The main finding was that socioeconomic status (SES) positively predicts individual economic mobility, which then negatively influences African identity concepts, and that the significance of economic concepts for African identity depends on social class. For example, in the high SES group, materialism and cynicism about Africa's future economic global prospects were found to have a negative effect on commitment to the national economy and African identity. The general implication is that anti‐group economic behaviour in Africa (e.g. corruption, worker exploitation) is attributable to individual mobility, as well as to intra‐national and global economic structures.
Effect of atomic scale plasticity on hydrogen diffusion in iron: Quantum mechanically informed and on-the-fly kinetic Monte Carlo simulations

We present an off-lattice, on-the-fly kinetic Monte Carlo (KMC) model for simulating stress-assisted diffusion and trapping of hydrogen by crystalline defects in iron. Given an embedded atom (EAM) potential as input, energy barriers for diffusion are ascertained on the fly from the local environments of H atoms. To reduce computational cost, on-the-fly calculations are supplemented with precomputed strain-dependent energy barriers in defect-free parts of the crystal. These precomputed barriers, obtained with high-accuracy density functional theory calculations, are used to ascertain the veracity of the EAM barriers and correct them when necessary. Examples of bulk diffusion in crystals containing a screw dipole and vacancies are presented. Effective diffusivities obtained from KMC simulations are found to be in good agreement with theory. Our model provides an avenue for simulating the interaction of hydrogen with cracks, dislocations, grain boundaries, and other lattice defects, over extended time scales, albeit at atomistic length scales.
Multimodality in the GARCH Regression Model

Several aspects of GARCH(p,q) models that are relevant for empirical applications are investigated. In particular, it is noted that the inclusion of dummy variables as regressors can lead to multimodality in the GARCH likelihood. This invalidates standard inference on the estimated coefficients. Next, the implementation of different restrictions on the GARCH parameter space is considered. A refinement to the Nelson and Cao (1992) conditions for a GARCH(2,q) model is presented, and it is shown how these can then be implemented by parameter transformations. It is argued that these conditions may also be too restrictive, and a simpler alternative is introduced which is formulated in terms of the unconditional variance. Finally, examples show that multimodality is a real concern for models of the £/$ exchange rate, especially when p>2.
Intradomain Overlays: Architecture and Applications

We introduce an architecture for “Intradomain Overlays”, where a subset of routers within a domain is augmented with a dedicated host. These strategically placed hosts form an overlay network, and we describe a number of applications for such overlays. These applications include efficient network monitoring, policyand load-based packet re-routing, and network resource accounting. In this paper, we elaborate on the network monitoring application and describe a distributed protocol for monitoring routers within an AS which has been augmented with a few overlay nodes. The routers and other infrastructure are unaware of the overlay nodes, and the monitoring of individual elements is conducted using plain SNMP. We describe techniques for efficiently synthesizing and transporting the monitored SNMP data, and present results using trace data collected from an AS with 400+ routers. Our results show that the overlay-based monitoring reduces overheads by 2–4 orders of magnitude, and thus enables much finer grained monitoring and traffic engineering than is otherwise possible.
SMOS soil moisture downscaling based on back propagation neural network with MODIS LST and EVI

Soil Moisture and Ocean Salinity (SMOS) is the first L-band passive microwave mission dedicated to soil moisture (SM) monitoring but has coarse resolution. SMOS SM was downscaled by Back propagation neural network (BPNN) and MODIS LST and EVI, and was evaluated by intensive 56 stations in-situ obtained from the mesoscale Tibetan Plateau Soil Moisture/Temperature Monitoring Network (SMTMN) during 2010-2012 over Naqu. It showed that downscaled rmse and bias were close for BPNN and regression, downscaled r was significantly improved by BPNN. In terms of r, it was improved greatly by downscaling comparing with original SMOS evaluations. Besides, descending of SMOS (D_SMOS) got better downscaled SM than ascending of SMOS and evaluation of downscaled D_SMOS (r=0.849, rmse=0.056m3/m3 and bias=0.016 m3/m3) was nice in SMTMN scale. The fine SM BPNN downscaled by SMOS can be used for regional or local studies.
Toward Practical Deployment of Fingerprint-Based Indoor Localization

This article addresses several challenges for practical deployment of Wi-Fi fingerprinting localization. First, the signals of virtual access points (VAPs) from the same physical access point have high correlation, and hence should be filtered for computational efficiency. Second, because heterogeneous devices might report the same signal differently, their readings must be calibrated appropriately. Finally, to provide a better user experience, it's necessary to properly estimate the localization error. To overcome these challenges, the authors present three plug-ins for existing localization systems. They merge VAPs using a clique-finding algorithm, propose a crowdsourced approach to accommodate new devices, and derive the region where the target might be located. Extensive experimental trials in indoor sites support the practicality and effectiveness of the solutions.
Probucoi Increases the Selective Uptake of HDL Cholesterol Esters by Hep G 2 Human Hepatoma Cells

A previous study in rats showed that even though probucoi substantially lowers high density lipoprotein (HDL) levels, near-normal mass transport of HDL cholesterol esters (CE) to the liver is maintained by the induction of "selective" (direct) uptake of HDL CE. The present study describes a parallel result in cultured Hep G2 human hepatoma cells. Cells were preincubated in the presence or absence of probucoi before measuring the uptake of doubly labeled HDL, in the absence of probucoi. Preincubation with probucoi decreased the uptake of HDL, particles (iodine-125-labeled JV-methyltyramlne cellobioseapolipoprotein [I-NMTC-apo] A-I uptake) but increased the uptake of [H]cholesteryl oleyl ether in excess of I-NMTC-apo A-I (i.e., selective uptake) in a dose-dependent fashion. The reversibly cell-associated pool of CE tracer, a precursor for selective uptake, enlarged on probucoi treatment, but the increase was not in proportion to the increase in selective uptake. HDL, particle uptake decreased on probucoi treatment The decrease was evident after <20 minutes of probucoi exposure and was maximal after 6 hours; in contrast, HDL, CE selective uptake increased only after > 13 hours and had not reached a plateau after 20 hours. Thus, effects on particle uptake and selective uptake were dissociated in time. (Arteriosclerosis and Thrombosis 1992;12:870-878)
Global‐view coefficients: a data management solution for parallel quantum Monte Carlo applications

Quantum Monte Carlo (QMC) applications perform simulation with respect to an initial state of the quantum mechanical system, which is often captured by using a cubic B‐spline basis. This representation is stored as a read‐only table of coefficients and accesses to the table are generated at random as part of the Monte Carlo simulation. Current QMC applications, such as QWalk and QMCPACK, replicate this table at every process or node, which limits scalability because increasing the number of processors does not enable larger systems to be run. We present a partitioned global address space approach to transparently managing this data using Global Arrays in a manner that allows the memory of multiple nodes to be aggregated. We develop an automated data management system that significantly reduces communication overheads, enabling new capabilities for QMC codes. Experimental results with QWalk and QMCPACK demonstrate the effectiveness of the data management system. Copyright © 2016 John Wiley & Sons, Ltd.
Naloxone and shock-elicited freezing in the rat.

The freezing behavior of the rat that occurs following painful electric shock was found to increase when the animal was pretreated with the opiate antagonist naloxone. Freezing was a positive linear function of drug dose and shock intensity (Experiment 2). Naloxone pretreatment enhanced freezing only when the animal was given two or three shocks but did not affect freezing when the animal was given only one shock or not shocked at all (Experiments 3, 4, and 5). Naloxone must be present during shock, not just during the observation period, in order to increase freezing (Experiment 6). These results suggest that when an animal is shocked, it releases endogenous analgesics (endorphins) that make a subsequent shock less aversive. Naloxone, by blocking the endorphin system, makes the shock more aversive than it would normally be. Peptides with properties similar to the narcotic analgesics have recently been isolated (Hughes, 1975). These substances, designated endorphins, are blocked by the narcotic antagonist naloxone (Belluzzi, Grant, Garsky, Sarantakis, Wise, & Stein, 1976; Loh, Tseng, Wei, & Li, 1976; Malick & Goldstein, 1977; Walker, Berntson, Sandman, Coy, Schally, & Kastin, 1977). One physiological role of these endogenous analgesics may be to reduce the aversiveness of painful stimuli. Such a mechanism would allow an animal to engage in defensive be
Extended message sequence charts with time-interval semantics

The paper describes the main ideas of an extension of Message Sequence Charts (MSCs) in a time-interval structure to improve the temporal knowledge of the environment where a software system will be built. The extended MSC could be used at the requirements analysis phase and its interpretation is not limited to the analysis of real-time software systems (where MSCs are mostly used), but rather is aimed for helping the quantitative temporal analysis of the application domain, whatever the software solution for the system. The paper briefly overviews MSCs, describes the goals of the proposed interpretation for basic MSCs, and defines their syntax and semantics.
Obtaining Party Positions on Immigration from Party Manifestos

Expert surveys are often considered the gold standa rd when it comes to positioning political parties. Alternative methods are necessary when exp ert surveys are not available, such as in regional contexts, or if a study is interested in p ast positions. Most commonly, researchers are concerned with relatively comprehensive issues, suc h as left-right positions, or social issues. This paper provides an agnostic assessment of diffe rent methods, with a focus on party positions on immigration as a specific dimension. T he paper compares: a pooled expert survey with manual coding of manifestos using a conventional codebook, manual coding using checklists, automatic coding using Wordscores , and automatic coding using a dictionary of keywords. The results suggest that there are hig h correlations between expert data on the one hand, and manual coding using a codebook or checklist on the other hand. There are high correlations with Wordscores, but the associations are not consistent, whereas automatic dictionary coding seems to lead to poor results.
Learning based Obstacle Detection for Textural Path

Obstacle Detection is a quite important problem in the field of image processing. Various algorithms have been introduced to solve this problem with different environment. This paper proposes procedure to detect any obstacle in the textural path on the basis of some learning techniques. These learning techniques makes easy to detect any obstacle in Textural path. In this paper we have divided an image into some part, describing as left, right and ground or front part. These separate part matches with the environment by using learning. LEP (Local Edge Pattern) and Colour histogram will be used for efficient matching and front part will be segmented to find the obstacle, if exists. Learning is used to take any decision about the obstacle appearance.
Activation of Islet Autoreactive Naïve T Cells in Infants Is Influenced by Homeostatic Mechanisms and Antigen-Presenting Capacity

Islet autoimmunity precedes type 1 diabetes onset. We previously found that islet autoimmunity rarely starts before 6 months of age but reaches its highest incidence already at ∼1 year of age. We now examine whether homeostatic expansion and immune competence changes seen in a maturating immune system may account for this marked variation in islet autoimmunity risk in the first year of life. We found naïve proinsulin- and GAD65-responsive T cells in cord blood (CB) of healthy newborns, with highest responses observed in children with type 1 diabetes-susceptible HLA-DRB1/DQB1 genotypes. Homeostatic expansion characteristics with increased IL-7 concentrations and enhanced T-cell responsiveness to IL-7 were observed throughout the first year of life. However, the ability of antigen-presenting cells to activate naïve T cells was compromised at birth, and CB monocytes had low surface expression of CD40 and HLA class II. In contrast, antigen presentation and expression of these molecules had reached competent adult levels by the high incidence age of 8 months. We propose that temporal changes in islet autoimmunity seroconversion in infants are a consequence of the changing balance between homeostatic drive and antigen presentation competence. These findings are relevant for early prevention of type 1 diabetes.
Portfolios for assessment and learning: Guide Supplement 45.1 – Viewpoint

Med 85:148–154. Carlson M. 2004. Performance: A critical introduction. New York: Routledge. Cleland J, Abe K, Rethans J. 2009. The use of simulated patients in medical education: AMEE Guide No 42. Med Teach 31:477–486. Hodges B. 2010. The objective structured clinical examination. Koln: LAP Lambert Academic Publishing. Jha V, Quinton N, Bekker H, Roberts T. 2009. Strategies and interventions for the invovlement of real patients in medical education: A systematic review. Med Educ 43:10–20. Kneebone R, Bello F, Nestel D, Mooney N, Codling A, Yadollahi F, Tierney T, Wilcockson D, Darzi A. 2008. Learner-centred feedback using remote assessment of clinical procedures. Med Teach 30:795–801. Kneebone R, Nestel D. 2010. Learning and teaching clinical procedures. In: Dornan SE, editor. Medical education: Theory and practice. London: Elsevier. Kneebone R, Nestel D, Wetzel C, Black S, Jacklin R, Aggarwal R, Yadollahi F, Wolfe J, Vincent C, Darzi A. 2006a. The human face of simulation: Patient-focused simulation training. Acad Med 81:919–924. Kneebone R, Nestel D, Yadollahi F, Brown R, Nolan C, Durack J, Brenton H, Moulton C, Archer J, Darzi A. 2006b. Assessing procedural skills in context: Exploring the feasibility of an Integrated Procedural Performance Instrument (IPPI). Med Educ 40:1105–1114. Meyer-Dinkgrafe D. 2001. Approaches to acting: Past and Present. London: Continuum. Milling J, Ley G. 2001. Modern theories of performance: From Stanislavski to Boal. Basingstoke, Hampshire and New York: Palgrave Macmillan. Nestel D, Barry K. 2006. Association of standardized patient educators. Med Teach 28:746–747. Nestel D, Bello F, Kneebone RKA, Darzi A. 2008a. Remote assessment and learner-centred feedback using the Imperial College Feedback and Assessment System (ICFAS). Clin Teach 5:88–92. Nestel D, Cecchini M, Calandrini M, Chang L, Dutta R, Tierney T, Brown R, Kneebone R. 2008b. Real patient involvement in role development evaluating patient focused resources for clinical procedural skills. Med Teach 30:795–801. Nestel D, Kneebone R. 2010. Authentic patient perspectives in simulations for procedural and surgical skills. Acad Med 85:889–893. Rethans J, Gorter S, Bokken L, Morrison L. 2007. Unannounced standardised patients in real practice: A systematic literature review. Med Educ 41:537–549. Schechner R. 2006. Performance studies: An introduction. New York: Routledge. Schreiber T. 2005. Acting: Advanced techniques for the actor, director, and teacher. New York: Allworth Press. Stanislavski C. 1936. An actor prepares. New York: Routledge. Stewart M, Belle-brown JB, Weston WW, McWhinney IR, Mcwilliam CL, Freeman TR. 2003. Patient-centered medicine: Transfoming the clinical method. Oxford: Radcliffe Medical Press. Turner V. 1986. The anthroplogy of performance. New York: PAJ Publications. Wallace P. 2006. Coaching standardized patients for use in assessment of clinical competence. New York: Springer. Wenger E. 1998. Communities of practice: Learning, meaning and identity. Cambridge: Cambridge University Press.
Strategy Representation and Reasoning for Incomplete Information Concurrent Games in the Situation Calculus

Strategy representation and reasoning for incomplete information concurrent games has recently received much attention in multi-agent system and AI communities. However, most of the logical frameworks are based on concrete game models, lack the abilities to reason about strategies explicitly or specify strategies procedurally, and ignore the issue of coordination within a coalition. In this paper, by a simple extension of a variant of multiagent epistemic situation calculus with a strategy sort, we develop a general framework for strategy representation and reasoning for incomplete information concurrent games. Based on Golog, we propose a strategy programming language which can be conveniently used to specify collective strategies of coalitions at different granularities. We present a formalization of joint abilities of coalitions under commitments to strategy programs. Different kinds of individual strategic abilities can be distinguished in our framework. Both strategic abilities in ATL and joint abilities of Ghaderi et al. can be considered as joint abilities under special programs in our framework.We illustrate our work with a variant of Levesque's Squirrels World.
Using Phoneme Segmentation in Conjunction with Missing Feature Approaches for Noise Robust Speech Recognition

Cluster-based reconstruction is a feature based method that shown promising results in improvement of speech recognition accuracy but in low SNR values and multiple clusters, classification of noisy vectors is badly degrade the recognition accuracy. Main idea of this paper is to take advantage of phonetic properties and phonetic clustering to overcome disadvantage of classification step. We proposed three different clustering strategies in order to solve clustering misclassification problem and improve speech recognition accuracy in presence of additive noise through Phoneme Segmentation in conjunction with Missing Feature approaches. Third method results show an average improvement of 14.4% in 0 dB and 8.35% in -10 dB in comparison with conventional cluster-based reconstruction.
Low loss micromachined lead zirconate titanate, contour mode resonator with 50Ω termination

This paper reports lead zirconate titatanate (PZT)-on-silicon electromechanical resonators with excellent, 50 Ω terminated, performances for RF applications. A low 2.14 dB insertion loss is demonstrated for a length extensional, PZT-on-2-μm-silicon 15 MHz resonator. A 22 dB return loss and maximum unloaded quality factor, QUL, max, of ~540 in air resulted for this resonator. Similar performances with a QUL, max of 2850 are also demonstrated with a PZT fabricated on 10-μm-silicon device. The competing effects of decreased motional resistance and increased transducer capacitances with increased transduction area are addressed through analytical models and experimental results. Additionally, a third order length extensional mode piezoelectric resonator with asymmetric input and output electrodes were also designed to assess its potential performance as a piezoelectric resonant transformer; a 2.1× voltage boost is demonstrated for a 14.7 MHz extensional mode resonator.
Two mutations of BRCA2 gene at exon and splicing site in a woman who underwent oncogenetic counseling.

BACKGROUND Although most BRCA sequence variants are clearly deleterious and unequivocally pathogenetic, several are still classified as variants of unknown significance. PATIENTS AND METHODS We followed families undergoing oncogenetic counseling from risk identification to risk definition by genetic testing and risk management. RESULTS We identified two germline mutations in the BRCA2 gene in a woman with breast and ovarian cancer. One sequence alteration was 859/G>A in exon 7 (V211I). The other second sequence alteration (IVS13-2A>T) affected the splicing site in intron 13. The latter alteration is not yet listed in the Breast Cancer Information Core database. RT-PCR resulted in transcription of a sequence lacking exon 7 and a subsequent anomalous stop codon in exon 9 thereby confirming altered messenger RNA (mRNA) maturation. Amplification of the mutation in intron 13 resulted in transcription of a sequence lacking exon 14 and an anomalous stop codon in exon 15 thereby confirming altered mRNA maturation. Both mutations led to a truncated BRCA2 protein in its carboxy-terminal region. CONCLUSION The two BRCA2 mutations identified affect mRNA splicing fidelity and play a pathogenetic role in breast and ovarian cancer.