Virulence of newcastle disease virus: what is known so far?

In the last decade many studies have been performed on the virulence of Newcastle disease virus (NDV). This is mainly due to the development of reverse genetics systems which made it possible to genetically modify NDV and to investigate the contribution of individual genes and genome regions to its virulence. However, the available information is scattered and a comprehensive overview of the factors and conditions determining NDV virulence is lacking. This review summarises, compares and discusses the available literature and shows that virulence of NDV is a complex trait determined by multiple genetic factors

Physiology-based regularization of the electrocardiographic inverse problem

The inverse problem of electrocardiography aims at noninvasively reconstructing electrical activity of the heart from recorded body-surface electrocardiograms. A crucial step is regularization, which deals with ill-posedness of the problem by imposing constraints on the possible solutions. We developed a regularization method that includes electrophysiological input. Body-surface potentials are recorded and a computed tomography scan is performed to obtain the torso-heart geometry. Propagating waveforms originating from several positions at the heart are simulated and used to generate a set of basis vectors representing spatial distributions of potentials on the heart surface. The real heart-surface potentials are then reconstructed from the recorded body-surface potentials by finding a sparse representation in terms of this basis. This method, which we named 'physiology-based regularization' (PBR), was compared to traditional Tikhonov regularization and validated using in vivo recordings in dogs. PBR recovered details of heart-surface electrograms that were lost with traditional regularization, attained higher correlation coefficients and led to improved estimation of recovery times. The best results were obtained by including approximate knowledge about the beat origin in the PBR basis

Chiral Condensate in Holographic QCD with Baryon Density

We consider the chiral condensate in the baryonic dense medium using the generalized Sakai-Sugimoto model. It is defined as the vacuum expectation value of open Wilson line that is proposed to be calculated by use of the area of world-sheet instanton. We evaluate it in confined as well as deconfined phase. In both phases, the chiral condensate has a minimum as a function of baryon density. In the deconfined phase, taking into account the chiral symmetry restoration, we classify the behavior of chiral condensate into three types. One can set the parameter of the theory such that the results, in low but sufficiently higher density, is in agreement with the expectation from QCD.Comment: 23 pages, 8 figure

How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

BACKGROUND: Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operating Software (MAS or GCOS) from Affymetrix. Recently, more methods to analyse the raw data have become available. Ideally all these methods should come up with more or less the same results. We set out to evaluate the different methods and include work on our own data set, in order to test which method gives the most reliable results. RESULTS: Calculating gene expression with 6 different algorithms (MAS5, dChip PMMM, dChip PM, RMA, GC-RMA and PDNN) using the same (Arabidopsis) data, results in different calculated gene expression levels. Consequently, depending on the method used, different genes will be identified as differentially regulated. Surprisingly, there was only 27 to 36% overlap between the different methods. Furthermore, 47.5% of the genes/probe sets showed good correlation between the mismatch and perfect match intensities. CONCLUSION: After comparing six algorithms, RMA gave the most reproducible results and showed the highest correlation coefficients with Real Time RT-PCR data on genes identified as differentially expressed by all methods. However, we were not able to verify, by Real Time RT-PCR, the microarray results for most genes that were solely calculated by RMA. Furthermore, we conclude that subtraction of the mismatch intensity from the perfect match intensity results most likely in a significant underestimation for at least 47.5% of the expression values. Not one algorithm produced significant expression values for genes present in quantities below 1 pmol. If the only purpose of the microarray experiment is to find new candidate genes, and too many genes are found, then mutual exclusion of the genes predicted by contrasting methods can be used to narrow down the list of new candidate genes by 64 to 73%

Associations between lifestyle factors and an unhealthy diet

BACKGROUND: Unhealthy dietary patterns have been associated with other unhealthy lifestyle factors such as smoking and physical inactivity. Whether these associations are similar in high- and low-educated individuals is currently unknown. METHODS: We used information of the EPIC-NL cohort, a prospective cohort of 39 393 men and women, aged 20-70 years at recruitment. A lifestyle questionnaire and a validated food frequency questionnaire were administered at recruitment (1993-97). Low adherence to a Mediterranean-style diet was used to determine an unhealthy dietary pattern. Lifestyle-related factors included body mass index, waist circumference, smoking status, physical activity level, dietary supplement use and daily breakfast consumption. Multivariate logistic regression analyses were performed for the total population and by strata of educational level. RESULTS: In total 30% of the study population had an unhealthy dietary pattern: 39% in the lowest educated group and 20% in the highest educated group. Physical inactivity, a large waist circumference, no dietary supplement use and skipping breakfast were associated with an unhealthy dietary pattern in both low and high educated participants. Among low educated participants, current smokers had a greater odds of an unhealthy diet compared with never smokers: OR 1.42 (95% CI: 1.25; 1.61). This association was not observed in the high educated group. CONCLUSIONS: Most associations between lifestyle-related factors and unhealthy diet were consistent across educational levels, except for smoking. Only among low educated participants, current smokers reported an unhealthier dietary pattern in comparison to never smokers. These results can be used in the development of targeted health promotion strategies

Evaluation of measurement properties of self-administered PROMs aimed at patients with non-specific shoulder pain and "activity limitations": a systematic review.

To critically appraise and compare the measurement properties of self-administered patient-reported outcome measures (PROMs) focussing on the shoulder, assessing "activity limitations."Systematic review. The study population had to consist of patients with shoulder pain. We excluded postoperative patients or patients with generic diseases. The methodological quality of the selected studies and the results of the measurement properties were critically appraised and rated using the COSMIN checklist.Out of a total of 3427 unique hits, 31 articles, evaluating 7 different questionnaires, were included. The SPADI is the most frequently evaluated PROM and its measurement properties seem adequate apart from a lack of information regarding its measurement error and content validity.For English, Norwegian and Turkish users, we recommend to use the SPADI. Dutch users could use either the SDQ or the SST. In German, we recommend the DASH. In Tamil, Slovene, Spanish and the Danish languages, the evaluated PROMs were not yet of acceptable validity. None of these PROMs showed strong positive evidence for all measurement properties. We propose to develop a new shoulder PROM focused on activity limitations, taking new knowledge and techniques into account

Identification and localization of the structural proteins of anguillid herpesvirus 1

Many of the known fish herpesviruses have important aquaculture species as their natural host, and may cause serious disease and mortality. Anguillid herpesvirus 1 (AngHV-1) causes a hemorrhagic disease in European eel, Anguilla anguilla. Despite their importance, fundamental molecular knowledge on fish herpesviruses is still limited. In this study we describe the identification and localization of the structural proteins of AngHV-1. Purified virions were fractionated into a capsid-tegument and an envelope fraction, and premature capsids were isolated from infected cells. Proteins were extracted by different methods and identified by mass spectrometry. A total of 40 structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. The identification and localization of these proteins allowed functional predictions. Our findings include the identification of the putative capsid triplex protein 1, the predominant tegument protein, and the major antigenic envelope proteins. Eighteen of the 40 AngHV-1 structural proteins had sequence homologues in related Cyprinid herpesvirus 3 (CyHV-3). Conservation of fish herpesvirus structural genes seemed to be high for the capsid proteins, limited for the tegument proteins, and low for the envelope proteins. The identification and localization of the structural proteins of AngHV-1 in this study adds to the fundamental knowledge of members of the Alloherpesviridae family, especially of the Cyprinivirus genus

On semiclassical approximation for correlators of closed string vertex operators in AdS/CFT

We consider the 2-point function of string vertex operators representing string state with large spin in AdS_5. We compute this correlator in the semiclassical approximation and show that it has the expected (on the basis of state-operator correspondence) form of the strong-coupling limit of the 2-point function of single trace minimal twist operators in gauge theory. The semiclassical solution representing the stationary point of the path integral with two vertex operator insertions is found to be related to the large spin limit of the folded spinning string solution by a euclidean continuation, transformation to Poincare coordinates and conformal map from cylinder to complex plane. The role of the source terms coming from the vertex operator insertions is to specify the parameters of the solution in terms of quantum numbers (dimension and spin) of the corresponding string state. Understanding further how similar semiclassical methods may work for 3-point functions may shed light on strong-coupling limit of the corresponding correlators in gauge theory as was recently suggested by Janik et al in arXiv:1002.4613.Comment: 19 pages, 1 figure; minor corrections, references added, footnote below eq. (4.5) adde

Holographic phase transition from dyons in an AdS black hole background

We construct a dyon solution for a Yang-Mills-Higgs theory in a 4 dimensional Schwarzschild-anti-de Sitter black hole background with temperature T. We then apply the AdS/CFT correspondence to describe the strong coupling regime of a 2+1 quantum field theory which undergoes a phase transition exhibiting the condensation of a composite charge operator below a critical temperature $T_c$.Comment: 19 pages, 7 figures. Minor corrections, references added. Version published in JHEP