Miracle-dz/UniFAR-FTUs huggingface dataset:
Full Genome Characterisation of Bluetongue Virus Serotype 6 from the Netherlands 2008 and Comparison to Other Field and Vaccine Strains

In mid September 2008, clinical signs of bluetongue (particularly coronitis) were observed in cows on three different farms in eastern Netherlands (Luttenberg, Heeten, and Barchem), two of which had been vaccinated with an inactivated BTV-8 vaccine (during May-June 2008). Bluetongue virus (BTV) infection was also detected on a fourth farm (Oldenzaal) in the same area while testing for export. BTV RNA was subsequently identified by real time RT-PCR targeting genome-segment (Seg-) 10, in blood samples from each farm. The virus was isolated from the Heeten sample (IAH “dsRNA virus reference collection” [dsRNA-VRC] isolate number NET2008/05) and typed as BTV-6 by RT-PCR targeting Seg-2. Sequencing confirmed the virus type, showing an identical Seg-2 sequence to that of the South African BTV-6 live-vaccine-strain. Although most of the other genome segments also showed very high levels of identity to the BTV-6 vaccine (99.7 to 100%), Seg-10 showed greatest identity (98.4%) to the BTV-2 vaccine (RSAvvv2/02), indicating that NET2008/05 had acquired a different Seg-10 by reassortment. Although Seg-7 from NET2008/05 was also most closely related to the BTV-6 vaccine (99.7/100% nt/aa identity), the Seg-7 sequence derived from the blood sample of the same animal (NET2008/06) was identical to that of the Netherlands BTV-8 (NET2006/04 and NET2007/01). This indicates that the blood contained two different Seg-7 sequences, one of which (from the BTV-6 vaccine) was selected during virus isolation in cell-culture. The predominance of the BTV-8 Seg-7 in the blood sample suggests that the virus was in the process of reassorting with the northern field strain of BTV-8. Two genome segments of the virus showed significant differences from the BTV-6 vaccine, indicating that they had been acquired by reassortment event with BTV-8, and another unknown parental-strain. However, the route by which BTV-6 and BTV-8 entered northern Europe was not established.
Finance and Economics Discussion Series Optimal Portfolio Allocation in a World without Treasury Securities Optimal Portfolio Allocation in a World without Treasury Securities

NOTE: Staff working papers in the Finance and Economics Discussion Series (FEDS) are preliminary materials circulated to stimulate discussion and critical comment. The analysis and conclusions set forth are those of the authors and do not indicate concurrence by other members of the research staff or the Board of Governors. References in publications to the Finance and Economics Discussion Series (other than acknowledgement) should be cleared with the author(s) to protect the tentative character of these papers. Abstract If current projections of future budget surpluses materialize, investing in Treasury securities–an asset class with which investors have long been familiar–could eventually become a thing of the past. In this paper, I examine the extent to which investors' portfolio allocation decisions are likely to be affected by the retirement of all federal government debt. The analysis suggests only small effects for most investors, especially, as is effectively the case for many institutional investors, when a no short sale constraint is in place. Under such circumstances, highly conservative investors–whose portfolios have risk-return characteristics akin to money market instruments–and very aggressive investors–who hold mostly equities–stand to be the least affected by the removal of Treasuries from the pool of investable assets. The analysis abstracts from indirect beneficial effects on investors from a Treasury debt payoff, such as the potential for greater productivity growth (and faster wealth accumulation) as more resources are freed up for investment in the private sector. Sack for helpful comments. Joseph Rosenberg provided excellent research assistance. The opinions expressed in this paper are not necessarily shared by anyone else in the Federal Reserve System. Reinhart and Sack (2000) discuss the main factors behind these budgetary developments.
Mycobacterium abscessus and Children with Cystic Fibrosis

We prospectively studied 298 patients with cystic fibrosis (mean age 11.3 years; range 2 months to 32 years; sex ratio, 0.47) for nontuberculous mycobacteria in respiratory samples from January 1, 1996, to December 31, 1999. Mycobacterium abscessus was by far the most prevalent nontuberculous mycobacterium: 15 patients (6 male, 9 female; mean age 11.9 years; range 2.5–22 years) had at least one positive sample for this microorganism (versus 6 patients positive for M. avium complex), including 10 with >3 positive samples (versus 3 patients for M. avium complex). The M. abscessus isolates from 14 patients were typed by pulsed-field gel electrophoresis: each of the 14 patients harbored a unique strain, ruling out a common environmental reservoir or person-to-person transmission. Water samples collected in the cystic fibrosis center were negative for M. abscessus. This major mycobacterial pathogen in children and teenagers with cystic fibrosis does not appear to be acquired nosocomially.
Intimate partner violence during pregnancy and its association with preterm birth and low birth weight in Tanzania: A prospective cohort study

Introduction Intimate partner violence (IPV) is a public health problem that affects millions of women worldwide. The role of violence as an underlying factor in poor birth outcomes remains an area where strong evidence is lacking. The aim of this study was to determine the association between intimate partner violence (IPV) and preterm delivery (PTB) and low birth weight (LBW). Materials and methods A prospective cohort study was conducted among 1112 pregnant women attending antenatal care in Moshi–Tanzania. The women were enrolled before 24 weeks gestation, followed-up at week 34 to determine exposure to violence during pregnancy, and after delivery to estimate gestation age at delivery and birth weight. Logistic regression analysis was performed to assess the association between exposure to IPV during pregnancy and PTB and LBW while adjusting for possible confounders. In addition, stratified analysis based on previous history of adverse pregnancy outcome was performed. Results One-third of the women experienced IPV during pregnancy, 22.3% reported emotional, 15.4% sexual and 6.3% physical violence. Women exposed to physical IPV were three times more likely to experience PTB (AOR = 2.9; CI 95%: 1.3–6.5) and LBW (AOR = 3.2; CI 95%: 1.3–7.7). Women with previous adverse pregnancy outcomes and exposure to physical IPV had a further increased risk of PTB (AOR = 4.5; CI 95%: 1.5–13.7) and LBW (AOR = 4.8; CI 95%: 1.6–14.8) compared to those without previous history of adverse outcome. Conclusion Women who are exposed to IPV during pregnancy are at increased risk of PTB and LBW. The risk is even stronger if the women additionally have suffered a previous adverse pregnancy outcome. Interventions addressing IPV are urgently needed to prevent occurrence and reoccurrence of PTB and LBW.
Predictors of leadership style, organizational commitment and turnover of information systems professionals

This research describes a multivariate model predicting leadership style, organizational commitment and turnover of information systems professionals. The proposed model integrates established antecedents of organizational commitment such as job involvement and job satisfaction with two systems related variables, user satisfaction and user involvement and adds two group level factors, team-member exchange quality and leadership style tc a causal network of relationships. The proposed model is currently being tested in a large federal agency which employs approximately 2500 information systems professionals. The data will be analyzed using linear structural equation modeling techniques (EQS). The results are predicted to reveal recursive relationships among some of the antecedents and shed some light on the nature of the relationships among a complex set of constructs drawn from the @1992ACM089791-501-l/92/ooo4/0171 $1.50 organizational behavior and management information literature.
Building power analysis resistant implementations of Keccak

In this paper we report on Keccak implementations that offer a high level of resistance against power analysis by using the technique of masking (secret sharing). In software, we show that two shares are required and if implemented carefully, sufficient. In dedicated hardware, three shares are required. We show that Multi-Gbit/s. throughput can be obtained with cores of area around 100 KGates. We demonstrate that there is a trade-off between area and performance by detailing two different architectures. Finally, we give arguments why the technique of secret sharing offers a very high level of protection against power analysis.
Audio-visual tracking for natural interactivity

The goal in user interfaces is natural interactivity unencumbered by sensor and display technology. In this paper, we propose that a multi-modal approach using inverse modeling techniques from computer vision, speech recognition, and acoustics can result in such interfaces. In particular, we demonstrate a system for audio-visual tracking, showing that such a system is more robust, more accurate, more compact, and yields more information than using a single modality for tracking. We also demonstrate how such a system can be used to find the talker among a group of individuals, and render 3D scenes to the user.
Macromolecular NMR spectroscopy for the non‐spectroscopist

NMR spectroscopy is a powerful tool for studying the structure, function and dynamics of biological macromolecules. However, non‐spectroscopists often find NMR theory daunting and data interpretation nontrivial. As the first of two back‐to‐back reviews on NMR spectroscopy aimed at non‐spectroscopists, the present review first provides an introduction to the basics of macromolecular NMR spectroscopy, including a discussion of typical sample requirements and what information can be obtained from simple NMR experiments. We then review the use of NMR spectroscopy for determining the 3D structures of macromolecules and examine how to judge the quality of NMR‐derived structures.
Leveraging Pattern Semantics for Extracting Entities in Enterprises

Entity Extraction is a process of identifying meaningful entities from text documents. In enterprises, extracting entities improves enterprise efficiency by facilitating numerous applications, including search, recommendation, etc. However, the problem is particularly challenging on enterprise domains due to several reasons. First, the lack of redundancy of enterprise entities makes previous web-based systems like NELL and OpenIE not effective, since using only high-precision/low-recall patterns like those systems would miss the majority of sparse enterprise entities, while using more low-precision patterns in sparse setting also introduces noise drastically. Second, semantic drift is common in enterprises ("Blue" refers to "Windows Blue"), such that public signals from the web cannot be directly applied on entities. Moreover, many internal entities never appear on the web. Sparse internal signals are the only source for discovering them. To address these challenges, we propose an end-to-end framework for extracting entities in enterprises, taking the input of enterprise corpus and limited seeds to generate a high-quality entity collection as output. We introduce the novel concept of Semantic Pattern Graph to leverage public signals to understand the underlying semantics of lexical patterns, reinforce pattern evaluation using mined semantics, and yield more accurate and complete entities. Experiments on Microsoft enterprise data show the effectiveness of our approach.
Performance Tuning and System Evaluation for Computer Aided Pronunciation Learning

This paper describes the use of a new automatic evaluation technique to evaluate speech-enabled computer aided pronunciation learning (CAPL) systems. The CAPL system is a part of a computer aided automatic training of correct recitation for the holy Qur an for Arabic speakers. The proposed technique evaluates the system by measuring the degree of usefulness of its feedback to learners. Evaluating CAPL systems by this means forces system designers to try to emphasize the system response for confident decisions and make general feedbacks, or no comments for non-confident decisions to reduce deceiving effect of inherent speech recognition systems limited accuracy. Automation of the evaluation process is vital due to complexity of CAPL systems and the existence for many tunable thresholds and parameters.
Random Matchings Which Induce Hamilton Cycles and Hamiltonian Decompositions of Random Regular Graphs

Select four perfect matchings of 2n vertices, independently at random. We find the asymptotic probability that each of the first and second matchings forms a Hamilton cycle with each of the third and fourth. This is generalised to embrace any fixed number of perfect matchings, where a prescribed set of pairs of matchings must each produce Hamilton cycles (with suitable restrictions on the prescribed set of pairs). We also show how the result with four matchings implies that a random d-regular graph for fixed even d? 4 asymptotically almost surely decomposes into d/2 Hamilton cycles. This completes a general result on the edge-decomposition of a random regular graph into regular spanning subgraphs of given degrees together with Hamilton cycles and verifies conjectures of Janson and of Robinson and Wormald.
Increasing the perceived malleability of gender bias using a modified Video Intervention for Diversity in STEM (VIDS)

Scholars are increasingly responding to calls for interventions to address persistent gender disparities in the sciences. Yet, interventions that emphasize the pervasiveness of bias may inadvertently damage efficacy to confront sexism by creating the perception that bias is immutable. We examined this possibility in the context of a successful bias literacy program, Video Interventions for Diversity in STEM (VIDS; Moss-Racusin et al., in press). In two studies with working adults from the general public (N = 343) and science faculty (N = 149), we modified VIDS by developing a module (UNITE) that offers tools for addressing bias and promotes the mindset that bias is malleable. VIDS alone was sufficient to increase awareness of bias, reduce sexism, and improve bias identification. However, UNITE buffered against perceptions that bias is immutable and restored self-efficacy to address bias. We conclude that interventions must aim not only to increase bias literacy but also offer concrete tools and avoid implying that these problems are insurmountable.
Microbial Susceptibility and Plasmid Profiles of Methicillin-Resistant Staphylococcus aureus and Methicillin-Susceptible S. aureus

Background: Today, significant increase in the prevalence and emergence of methicillin-resistant Staphylococcus aureus (MRSA) is a serious public health concern and is likely to have a dramatic negative impact on many current medical practices. Therefore, identification of MRSA strains is important for both clinical and epidemiological implications. Objectives: The present study was carried out to determine the frequency of methicillin resistant; antibiotic susceptibility and plasmid profiles of S. aureus recovered from different types of clinical samples of patients in Zabol, Iran. Material and Methods: Clinical samples from 500 outpatient and hospitalized patients were tested for S. aureus. The susceptibility of 106 S. aureus to 11 antibiotics was evaluated by the disk diffusion method and Etest oxacillin strips. The presence of mecA gene was investigated by polymerase chain reaction (PCR). The plasmid profile patterns of all isolates were determined by a modified alkaline lysis method. Results: A total of 67 (63.20%) strains were found to be MRSA isolates. Most of MRSA isolates showed high level of resistance to ampicillin, erythromycin, nalidixic acid, penicillin, and tetracycline. Twenty-six percent of MRSA isolates showed high level of resistance to oxacillin (minimum inhibitory concentration [MIC] ≥ 256 μg/mL). mecA gene was detected among 62 MRSA isolates. Totally, 75 isolates of both strains harbored plasmid. Conclusions: Resistance to oxacillin and other antibiotics was high, and most of the isolates were found to be multi-drug resistance (MDR). Plasmid analysis of representative S. aureus isolates also demonstrates the presence of a wide range of plasmid sizes, with no consistent relationship between plasmid profiles and resistance phenotypes. Regular surveillance of hospital infections and monitoring of their antibiotic sensitivity patterns are required to reduce MRSA prevalence. High prevalence and multi-drug resistance of MRSA isolates in southeast of Iran could be considered as an urgent warning for public health.
Swift heavy ion irradiation of SrTiO3 under grazing incidence

The irradiation of SrTiO3 single crystals with swift heavy ions leads to modifications of the surface. The details of the morphology of these modifications depend strongly on the angle of incidence and can be characterized by atomic force microscopy. At glancing angles, discontinuous chains of nanosized hillocks appear on the surface. From the variation of the length of the chains with the angle of incidence the latent track radius can be determined. This radius is material specific and allows the calculation of the electron–phonon coupling constant for SrTiO3. We show that a theoretical description of the nanodot creation is possible within a two-temperature model if the spatial electron density is taken into account. The appearance of discontinuous features can be explained easily within this model, but it turns out that the electronic excitation dissipates on a femtosecond timescale, too rapidly to feed sufficient energy into the phonon system in order to induce a thermal melting process. We demonstrate that this can be solved if a temperature-dependent diffusion coefficient is introduced into the model.
Decoding stimulation intensity from evoked ECoG activity using support vector regression

One of the unsolved problems of the application of cortical stimulation for therapeutic means is the selection of optimal stimulation parameters. Using support vector regression, we demonstrate that the intensity of single pulse electrical stimulation can be decoded from the waveform of the evoked electrocorticographic (ECoG) activity, even if in- tensities used for training and testing of the regression model are disjoint. This was most effective when stimulation was applied directly over the mo- tor cortex, less so for premotor and sensory cortex. Thus, if the optimal shape of the evoked neural response to stimulation is known, a regression model trained on the responses to a small set of stimulation intensities could be sufficient to determine the optimal stimulation intensity.
B Lymphocyte Activation by Coinfection Prevents Immune Control of Friend Virus Infection1

Although the adaptive immune response almost invariably fails to completely eliminate retroviral infections, it can exert significant protection from disease and long-term control of viral replication. Friend virus (FV), a mouse retrovirus, causes persistent infection in all strains of mice and erythroleukaemia in susceptible strains, the course of which can be strongly influenced by both genetic and extrinsic factors. In this study we examine the impact of coinfection on the requirements for immune control of FV infection. We show that congenic C57BL/6 mice, in which the introduction of an allele of the Friend virus susceptibility 2 gene provides the potential for FV-induced leukemia development, effectively resist FV infection, and both T cell- and Ab-dependent mechanisms contribute to their resistance. However, we further demonstrate that coinfection with lactate dehydrogenase-elevating virus (LDV) renders these otherwise immunocompetent mice highly susceptible to FV infection and subsequent disease. The presence of LDV delays induction of FV-specific neutralizing Abs and counteracts the protective contribution of adaptive immunity. Importantly, the disease-enhancing effect of LDV coinfection requires the presence of a polyclonal B cell repertoire and is reproduced by direct polyclonal B cell activation. Thus, immune activation by coinfecting pathogens or their products can contribute to the pathogenicity of retroviral infection.
Fake Shadow Detection Based on SIFT Features Matching

Shadow detection is crucial for robust and reliable visual surveillance system. The shadow detection method based on gray level and color information will fail when object parts have very similar properties with real shadow. In this paper, we present a novel shadow detection scheme which can conveniently verify detected shadows utilizing the extracted SIFT (Scale Invariant Feature Transform) features. After candidate shadow regions are detected by utilizing rgb color model, SIFT algorithm is exploited for local feature detection in two consecutive frames. Then location information of SIFT features in moving object and shadow is analyzed. Finally fake shadow regions are successfully identified. Experiments indicate that the proposed algorithm is fast and exact, and improves the accuracy of the moving object detection. The proposed method can be used for shadow detection in SIFT features tracking and will be highly effective.
BIOINFORMATICS ORIGINAL

Motivation: Protein–protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite signiﬁcant progress, mining PPIs from literatures still rely heavily on time-and resource-consuming manual annotations. Results: In this study, we developed a novel methodology based on Bayesian networks (BNs) for extracting PPI triplets (a PPI triplet consists of two protein names and the corresponding interaction word) from unstructured text. The method achieved an overall accuracy of 87% on a cross-validation test using manually annotated dataset. We also showed, through extracting PPI triplets from a large number of PubMed abstracts, that our method was able to complement human annotations to extract large number of new PPIs from literature. Availability: Programs/scripts we developed/used in the study are available at http://stat.fsu. edu/ ∼ jinfeng/datasets/Bio-SI-programs-Bayesian-chowdhary-zhang-liu
Distributed learning: Educating and assessing extended cognitive systems

ABSTRACT Extended and distributed cognition theories argue that human cognitive systems sometimes include non-biological objects. On these views, the physical supervenience base of cognitive systems is thus not the biological brain or even the embodied organism, but an organism-plus-artifacts. In this paper, we provide a novel account of the implications of these views for learning, education, and assessment. We start by conceptualizing how we learn to assemble extended cognitive systems by internalizing cultural norms and practices. Having a better grip on how extended cognitive systems are assembled, we focus on the question: If our cognition extends, how should we educate and assess such extended cognitive systems? We suggest various ways to minimize possible negative effects of extending one’s cognition and to efficiently find and organize (online) information by adopting a virtue epistemology approach. Educational and assessment implications are foregrounded, particularly in the case of Danish students’ use of the internet during exams.