Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a multiplex polymerase chain reaction assay for simultaneous detection of Rhodococcus equi and the vapA gene.

OBJECTIVE To evaluate sensitivity and specificity of a multiplex polymerase chain reaction (PCR) assay for simultaneous detection of Rhodococcus equi and differentiation of strains that contain the virulence-associated gene (vapA) from strains that do not. SAMPLE POPULATION 187 isolates of R equi from equine and nonequine tissue and environmental specimens and 27 isolates of bacterial species genetically or morphologically similar to R equi. PROCEDURE The multiplex PCR assay included 3 gene targets: a universal 311-bp bacterial 16S ribosomal RNA amplicon (positive internal control), a 959-bp R equi-specific target in the cholesterol oxidase gene (choE), and a 564-bp amplicon of the vapA gene. Duplicate multiplex PCR assays for these targets and confirmatory singleplex PCR assays for vapA and choE were performed for each R equi isolate. An additional PCR assay was used to examine isolates for the vapB gene. RESULTS Results of duplicate multiplex and singleplex PCR assays were correlated in all instances, revealing high specificity and reliability (reproducibility) of the vapA multiplex assay. Of the pulmonary isolates from horses with suspected R equi pneumonia, 97.4% (76/78) yielded positive results for vapA. Seven of 50 (14%) human isolates of R equi yielded positive results for vapA. Six human R equi isolates and 1 porcine isolate yielded positive results for vapB. No isolates with vapA and vapB genes were detected. CONCLUSIONS AND CLINICAL RELEVANCE The multiplex PCR assay is a sensitive and specific method for simultaneous confirmation of species identity and detection of the vapA gene. The assay appeared to be a useful tool for microbiologic and epidemiologic diagnosis and research.
Statistical modelling of measles and influenza outbreaks

This paper reviews the application of statistical models to outbreaks of two common respiratory viral diseases, measles and influenza. For each disease, we look first at its epidemiological characteristics and assess the extent to which these either aid or hinder modelling. We then turn to the models that have been developed to simulate geographical spread. For measles, a distinction is drawn between process-based and time series models; for influenza, it is the scale of the communities (from small groups to global populations) which primarily determines modelling style. Applications are provided from work by the authors, largely using Icelandic data. Finally we consider the forecasting potential of the models described.
Three-Dimensional Reconstruction of Optic Nerve Head from Stereo Fundus Images and Its Quantitative Estimation

It is important for diagnosis of glaucoma to grasp 3-D structure of an optic nerve head (ONH). The quantitative 3-D reconstruction of the ONH is required for the diagnosis. We propose a technique to obtain the depth value from stereo image pair of a retinal fundus for the 3-D reconstruction of the ONH. Our technique mainly consists of four steps: (1) cutout of the ONH region from the fundus images, (2) registration of the stereo pair, (3) disparity detection, and (4) depth calculation. For quantitative estimation of the depth value measured by using this method, the depth value was compared with the measurement results determined from the Heidelberg Retina Tomograph (HRT), which is a confocal laser-scanning microscope. As a result, the depth value of the ONH obtained using the stereo retinal image pair was in accordance with that obtained using the HRT (r=0.91). These results indicate that the stereo fundus images could be useful for assessing the depth value of the ONH for the diagnosis of glaucoma.
How Positive Is Their Future? Assessing the Role of Optimism and Social Support in Understanding Mental Health Symptomatology among Homeless Adults

Optimism has been noted as a primary protective factor in understanding mental health symptomatology in clinical and non-clinical settings. Any exploration of optimism has been absent in understanding mental health outcomes among homeless people. This study, using intensive interviews with 168 homeless adults in Northwest Arkansas, examines the role that social support and optimism play in lessening the negative impact of homeless circumstances/experiences on mental health symptomatology. Using OLS, findings support a mediating/protective role that social support and optimism play in lowering the negative effects of childhood life experiences on depressive symptoms among homeless persons. Despite the overwhelming conditions of homelessness, persons with higher levels of optimism and social support report lower depression and anxiety symptoms. The findings are discussed paying particular attention to the importance of developing and maintaining the perception of support and resiliency in preserving a positive outlook for the future among homeless persons facing often-debilitating circumstances. Copyright © 2016 John Wiley & Sons, Ltd.
Rule-based Tagging: Morphological Tagset versus Tagset of Analytical Functions

This work presents a part of a more global study on the problem of parsing of Czech and on the knowledge extraction capabilities of the Rule-based method. It is shown that the successfulness of the Rule-based method for English and its unsuccessfulness for Czech, is not only due to the small cardinality of the English tagset (as it is usually claimed) but mainly depends on its structure (”regularity” of the language information).
Programming in ambience : gearing up for dynamic adaptation to context

In the vision of Ambient Intelligence, people are assisted in their everyday activities through the proactive, opportunistic support of non-intrusive computing devices offering intuitive interaction modalities. The usefulness and quality of delivered services can be improved considerably if the devices are able to adapt their behaviour according to sensed changes in their surrounding environment, both at the physical and logical levels. This interplay between context-awareness and dynamic software adaptability is key to the construction of applications that are smart with respect to user needs. Unfortunately, most current applications do not reach this level of adaptability, due to a lack of appropriate programming technology. Most applications exhibit fixed functionality and seldom do they sense their environment and adapt their services in a context-aware fashion. Many chances of delivering improved services to users and network peers are thus missed. This dissertation presents a programming model to ease the construction of applications that can react to changes in their execution context by adapting their behaviour dynamically. The starting point of our research is the development of novel language abstractions and the adaptation of existing abstractions to render context-aware, self-adaptable applications easier to develop. We demonstrate that a simple yet powerful computation model readily provides the needed support, leading to straightforward application code that is not concerned with context adaptation, behaviour that can be adapted dynamically to different contexts in a non-intrusive fashion, and context-aware applications with software architectures that are not biased towards context adaptation ---rather, they can be designed freely according to their domain. The proposed computation model is realised through the Ambience programming language, and its underlying open implementation, the Ambient Object System. A small-step operational semantics describes it formally. Much in the vein of prototype-based programming, the model has been designed with simplicity and concreteness in mind. It is highly dynamic, featuring dynamic (multiple) dispatch, dynamic inheritance, dynamic typing, and dynamic method scoping. Application logic adaptation is enabled by means of an intuitive, first-class reification of context that is straightforwardly connected to dynamic behaviour selection. We describe needed management techniques for such context, and a few programming guidelines on how to develop context-aware applications using our approach. The approach is validated by showing its application in a number of scenarios inspired on Ambient Intelligence.
Reconstructing Sparticle Mass Spectra using Hadronic Decays

Most sparticle decay cascades envisaged at the Large Hadron Collider (LHC) involve hadronic decays of intermediate particles. We use state-of-the art techniques based on the K⊥ jet algorithm to reconstruct the resulting hadronic final states for simulated LHC events in a number of benchmark supersymmetric scenarios. In particular, we show that a general method of selecting preferentially boosted massive particles such as W ± ,Z 0 or Higgs bosons decaying to jets, using sub-jets found by the K⊥ algorithm, suppresses QCD backgrounds and thereby enhances the observability of signals that would otherwise be indistinct. Consequently, measurements of the supersymmetric mass spectrum at the per-cent level can be obtained from cascades including the hadronic decays of such massive intermediate bosons.
MeMotif: a database of linear motifs in α-helical transmembrane proteins

Membrane proteins are important for many processes in the cell and used as main drug targets. The increasing number of high-resolution structures available makes for the first time a characterization of local structural and functional motifs in α-helical transmembrane proteins possible. MeMotif (http://projects.biotec.tu-dresden.de/memotif) is a database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in α-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable. Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to the improvement of tools for transmembrane protein modeling.
Women’s Leadership

The Problem Women are well prepared to assume leadership roles—They have the education and the will, yet, they do not conform to gendered organizational images of ideal workers. Women often find themselves in a double bind once they advance into a leadership role: They must be cautious not to appear too masculine or too feminine while also personifying the “ideal” (male) worker by exhibiting masculine behaviors and unwavering commitment to the organization. Holding this line is challenging and often at odds with women’s identity and experienced conflicts between life and work. Our understanding of how best to prepare women for careers and create organizations that are hospitable to them is limited by implicit bias, inadequate learning and development strategies, and cultures resilient to change. Current human resource development (HRD) theory inadequately addresses the issues and challenges women leaders face because most leadership theory is based on privileged White males and highly essentialized. The Solution The world is burgeoning with global business, technological innovation, intense competition, and multinational workforces. HRD has a role to play in building effective global business if it can more robustly and broadly address issues related to diversity and inclusion in organizations, particularly the creation of cultures that accept a range of leadership styles and women leaders. It is time to challenge traditional, masculine views of leadership and question how leaders are developed. It is critical to understand women’s leadership if women leaders are to be developed and if persistent gender inequity in organizations is to be addressed. Stakeholders Women are obvious stakeholders, but, ultimately, everyone in organizations is a stakeholder benefiting from women leaders and improved leadership, in general. HRD professionals also benefit by understanding better how to develop women leaders, in particular, and leadership, in general. Globally, elected leaders, nongovernmental organizations, and nations can develop policy that has the potential to influence and create educational, occupational, and economic change for women.
Speech spectrum restoration based on conditional restricted boltzmann machine

Many speech enhancement algorithms have been proposed for speech restoration from distorted speech. However, if some components of the signal are completely missed or distorted, there is no way for those algorithms to restore the clean speech. Considering that the restricted Boltzmann machine (RBM) is a stochastic version of the Hopﬁeld network which can be used as an associative memory, we propose to use its “recall” ability for speech spectrum restoration when some parts of the speech spectrum are completely missed or distorted. Traditionally, in training the RBM, speech spectral patches are randomly selected as input. There is no consideration of the temporal correlation between different input spectral patches. In this study, we further propose to model this temporal correlation by us-ing a conditional RBM (CRBM). The inference on the CRBM is almost the same as that of on the RBM by only modifying the biases as conditional dynamic biases. We did experiments for clean speech reconstruction and distorted speech restoration based on the trained models. Our experimental results showed that both the RBM and CRBM worked well in restoration task. By incorporating temporal correlation in the CRBM, a further improvement on reconstruction and restoration accuracy was achieved
Prevalence of hip dysplasia in dogs according to official radiographic screening in Croatia

The subject of this study was to detect the prevalence of hip dysplasia according to offi cial radiographic screening between 2001 and 2009. The overall number of dogs tested for HD was 5381, belonging to 137 breeds. In 2001 the number of dogs evaluated was 403, and in 2009 this number rose to 856, which is an increase of 212.40%. In 2001 the number of breeds evaluated was 48, and in 2007 this number rose to 79 breeds, which is an increase of 164.58%. In the overall sample there were 2125 (39.5%) males and 3256 (60.5%) females. The mean age was around 24 months. According to the FCI scale, C, D and E grades are interpreted as dysplastic hips. In our sample 4372 (81.25% ) dogs were found to be free of dysplasia (A, B), while HD was found in 1009 (18.75%) dogs. In the period between 2001 and 2009 there was a visible trend of a reduction in the number of dogs with dysplasia. There was a signifi cant difference (P<0.05) between 2001 on the one hand and 2005 and 2006 on the other. In 2001 there were 27.79% of dogs with dysplasia, while in 2005 this number fell to 14.81% and in 2006 to 14.51%. There was no statistical signifi cance in the prevalence of HD in males and in females (P=0.20). The difference in age, however, was signifi cant, and dogs with dysplasia were older on average (P<0.05). The results of our study show that the programme of selection on the basis of radiography of hips should be continued in order to improve the quality of purebred dog breeds in Croatia.
Brain reserve and cognitive decline: a non-parametric systematic review

Background. A previous companion paper to this report (Valenzuela & Sachdev, Psychological Medicine 2006, 36, 441–454) suggests a link between behavioural brain reserve and incident dementia; however, the issues of covariate control and ascertainment bias were not directly addressed. Our aim was to quantitatively review an independent set of longitudinal studies of cognitive change in order to clarify these factors. Method. Cohort studies of the effects of education, occupation, and mental activities on cognitive decline were of interest. Abstracts were identified in MEDLINE (1966–September 2004), CURRENT CONTENTS (to September 2004), PsychINFO (1984–September 2004), Cochrane Library Databases and reference lists from relevant articles. Eighteen studies met inclusion criteria. Key information was extracted by both reviewers onto a standard template with a high level of agreement. Cognitive decline studies were integrated using a non-parametric method after converting outcome data onto a common effect size metric. Results. Higher behavioural brain reserve was related to decreased longitudinal cognitive decline after control for covariates in source studies (ϕ=1·70, p<0·001). This effect was robust to correction for both multiple predictors and multiple outcome measures and was the result of integrating data derived from more than 47000 individuals. Conclusions. This study affirms that the link between behavioural brain reserve and incident dementia is most likely due to fundamentally different cognitive trajectories rather than confound factors.
Immune Optimization of Path Planning for Coal Mine Rescue Robot

In order to further improve the ability of global path planning of coal mine rescue robot in the complex environment, a bacterial foraging algorithm-based polyclonal selection algorithm (BFA-PSA) is proposed. In order to verify the superiority of the BFA-PSA, the proposed algorithm is tested by traveling salesman problem (TSP) and compared with genetic algorithm (GA) and clonal selection algorithm (CSA). Finally, on the basis of grid environment model, the BFA-PSA is used in the optimization of path planning for coal mine rescue robot. The optimization results of the TSP show that the searching ability and efficiency of the BFA-PSA are improved. And the optimization results of path planning for coal mine rescue robot in the grid environment model show the better robustness and validity of the BFA-PSA. ( ( max ) ( max 1 a e f x f  
Energy and time efficient topology control algorithm for underwater acoustic Ad hoc networks

The disadvantages of the current algorithms for the underwater acoustic Ad hoc networks were analyzed. After that, an energy and time efficiency based topology control algorithm was proposed. The networks topology is controlled by a single-hop transmission cost index defined in the algorithm. The index describes the energy consumption, the communication delay and the signal attenuation of the networks. The simulation shows that the new algorithm has better performance on the average node degree, the end-to-end delay and the energy efficiency.
Highly diffusion‐sensitized MRI of brain: Dissociation of gray and white matter

The brains of six healthy volunteers were scanned with a full tensor diffusion MRI technique to study the effect of a high b value on diffusion‐weighted images (DWIs). The b values ranged from 500 to 5000 s/mm2. Isotropic DWIs, trace apparent diffusion coefficient (ADC) maps, and fractional anisotropy (FA) maps were created for each b value. As the b value increased, ADC decreased in both the gray and white matter. Furthermore, ADC of the white matter became lower than that of the gray matter, and, as a result, the white matter became brighter than the gray matter in the isotropic DWIs. Quantitative analysis showed that these changes were due to nonmonoexponential diffusion signal decay of the brain tissue, which was more prominent in white matter than in gray matter. There was no significant change in relation to the b value in the FA maps. High b value appears to have a dissociating effect on gray and white matter in DWIs. Magn Reson Med 45:734–740, 2001. © 2001 Wiley‐Liss, Inc.
On the properties of the deformed consensus protocol

This paper studies a generalization of the standard continuous-time consensus protocol, obtained by replacing the Laplacian matrix of the undirected communication graph with the so-called deformed Laplacian. The deformed Laplacian is a second-degree matrix polynomial in the real variable s which reduces to the standard Laplacian for s equal to unity. The stability properties of the ensuing deformed consensus protocol are studied in terms of parameter s for some special families of undirected graphs, and for graphs of arbitrary topology by leveraging the spectral theory of quadratic eigenvalue problems. Examples and simulation results are provided to illustrate our theoretical findings.
A Similar Place

In 2014, Nishnaabeg scholar Leanne Simpson connected #BlackLivesMatter and #MMIWG2S by highlighting their existence in “a similar place. ” Here, I interpret this as a space of shared emotion and geography, emphasizing the land on which anti-Black and colonial violences occur. I argue that this provides a methodology for the study of multiethnic literature in a way that reckons with the interrelatedness of settler colonialism and anti-Black racism without conflating them under the auspices of “multiculturalism. ” I read memoirs by Deborah Miranda and Jesmyn Ward to explore how they articulate the relationship between personal and spatial history.
Real-time polymerase chain reaction assay for detection of Streptococcus pneumoniae in sputum samples from patients with community-acquired pneumonia.

BACKGROUND AND PURPOSE A quantitative real-time polymerase chain reaction (PCR) method targeting the pneumolysin gene of Streptococcus pneumoniae in sputum specimens from patients with community-acquired pneumonia (CAP) was evaluated for the identification of pneumococci. METHODS The applicability of the assay to clinical samples was evaluated by studying 140 sputum specimens from patients with CAP. Of the specimens, 96 (68.6%) were found to be positive by real-time PCR. The results were compared to culture findings. RESULTS The sensitivity and specificity of the real-time PCR assay developed in this study as compared to those of the culture method were 97.2% and 60.9%, respectively. CONCLUSION Real-time PCR assay was found to be a rapid and sensitive method for the detection of pneumococci.
BIP associates with newly synthesized subunits of the mouse muscle nicotinic receptor

A slow conformational change in newly synthesized acetylcholine receptor subunits is thought to be a requisite step in the biogenesis of this multi-subunit transmembrane glycoprotein. Previously, we demonstrated that this early conformational change within the alpha- subunit was inefficient and dependent upon disulfide bond formation (Blount, P. and J.P. Merlie. 1990. J. Cell Biol. 111:2613-2622). Here we show that newly synthesized acetylcholine receptor subunits and subunit complexes in the muscle-like cell line, BC3H-1, are associated with Bip, a ubiquitous binding protein of the endoplasmic reticulum. Characterization of the Bip/alpha-subunit complex in stably transfected fibroblasts revealed that Bip associates with newly synthesized unassembled alpha-subunit and some alpha gamma and alpha delta subunit complexes. Significantly, Bip does not associate well with the more mature form of the alpha-subunit containing an intramolecular disulfide bridge. Hence, Bip may play an important role in the conformational maturation and/or editing of unassembled AChR subunits and subunit complexes in vivo.
Friends for Free: Self-Organizing Artificial Social Networks for Trust and Cooperation

By harvesting friendship networks from e-mail contacts or instant message “buddy lists” Peer-to-Peer (P2P) applications can improve performance in low trust environments such as the Internet. However, natural social networks are not always suitable, reliable or available. We propose an algorithm (SLACER) that allows peer nodes to create and manage their own friendship networks. We evaluate performance using a canonical test application, requiring cooperation between peers for socially optimal outcomes. The Artificial Social Networks (ASN) produced are connected, cooperative and robust possessing many of the disable properties of human friendship networks such as trust between friends (directly linked peers) and short paths linking everyone via a chain of friends. In addition to new application possibilities, SLACER could supply ASN to P2P applications that currently depend on human social networks thus transforming them into fully autonomous, self-managing systems. 1. Partially supported by the EU within the 6th Framework Programme under contract 001907 “Dynamically Evolving, Large Scale Information Systems” (DELIS). 2. Dept. of Computer Science, The University of Bologna, Mura Anteo Zamboni 7, 40127 Bologna, Italy.