Evaluating Surveillance Strategies for the Early Detection of Low Pathogenicity Avian Influenza Infections

In recent years, the early detection of low pathogenicity avian influenza (LPAI) viruses in poultry has become increasingly important, given their potential to mutate into highly pathogenic viruses. However, evaluations of LPAI surveillance have mainly focused on prevalence and not on the ability to act as an early warning system. We used a simulation model based on data from Italian LPAI epidemics in turkeys to evaluate different surveillance strategies in terms of their performance as early warning systems. The strategies differed in terms of sample size, sampling frequency, diagnostic tests, and whether or not active surveillance (i.e., routine laboratory testing of farms) was performed, and were also tested under different epidemiological scenarios. We compared surveillance strategies by simulating within-farm outbreaks. The output measures were the proportion of infected farms that are detected and the farm reproduction number (Rh). The first one provides an indication of the sensitivity of the surveillance system to detect within-farm infections, whereas Rh reflects the effectiveness of outbreak detection (i.e., if detection occurs soon enough to bring an epidemic under control). Increasing the sampling frequency was the most effective means of improving the timeliness of detection (i.e., it occurs earlier), whereas increasing the sample size increased the likelihood of detection. Surveillance was only effective in preventing an epidemic if actions were taken within two days of sampling. The strategies were not affected by the quality of the diagnostic test, although performing both serological and virological assays increased the sensitivity of active surveillance. Early detection of LPAI outbreaks in turkeys can be achieved by increasing the sampling frequency for active surveillance, though very frequent sampling may not be sustainable in the long term. We suggest that, when no LPAI virus is circulating yet and there is a low risk of virus introduction, a less frequent sampling approach might be admitted, provided that the surveillance is intensified as soon as the first outbreak is detected

Mining, compressing and classifying with extensible motifs

BACKGROUND: Motif patterns of maximal saturation emerged originally in contexts of pattern discovery in biomolecular sequences and have recently proven a valuable notion also in the design of data compression schemes. Informally, a motif is a string of intermittently solid and wild characters that recurs more or less frequently in an input sequence or family of sequences. Motif discovery techniques and tools tend to be computationally imposing, however, special classes of "rigid" motifs have been identified of which the discovery is affordable in low polynomial time. RESULTS: In the present work, "extensible" motifs are considered such that each sequence of gaps comes endowed with some elasticity, whereby the same pattern may be stretched to fit segments of the source that match all the solid characters but are otherwise of different lengths. A few applications of this notion are then described. In applications of data compression by textual substitution, extensible motifs are seen to bring savings on the size of the codebook, and hence to improve compression. In germane contexts, in which compressibility is used in its dual role as a basis for structural inference and classification, extensible motifs are seen to support unsupervised classification and phylogeny reconstruction. CONCLUSION: Off-line compression based on extensible motifs can be used advantageously to compress and classify biological sequences

Guidelines for the labelling of leucocytes with 111In-oxine

We describe here a protocol for labelling autologous white blood cells with 111In-oxine based on previously published consensus papers and guidelines. This protocol includes quality control and safety procedures and is in accordance with current European Union regulations and International Atomic Energy Agency recommendations

Neglected Tropical Diseases outside the Tropics

Neglected Tropical Diseases (NTDs) have been targeted due to their prevalence and the burden of disease they cause globally, but there has been no significant focus in the literature on the subject of NTDs as a group in immigrants and travelers, and no specific studies on the emerging phenomenon of imported NTDs. We present the experience of a Tropical Medicine Unit in a major European city, over a 19-year period, describing and comparing NTDs diagnosed amongst immigrants, travelers and travelers visiting friends and relatives (VFRs). NTDs were diagnosed outside tropical areas and occurred more frequently in immigrants, followed by VFR travelers and then by other travelers. The main NTDs diagnosed in immigrants were onchocerciasis, Chagas disease and ascariasis; most frequent NTDs in travelers were schistosomiasis, onchocerciasis and ascariasis, and onchocerciasis and schistosomiasis in VFRs. Issues focusing on modes of transmission outside endemic areas and how eradication programs for some NTDs in endemic countries may have an impact in non-tropical Western countries by decreasing disease burden in immigrants, are addressed. Adherence to basic precautions such as safe consumption of food/water and protection against arthropod bites could help prevent many NTDs in travelers

Reversing Melanoma Cross-Resistance to BRAF and MEK Inhibitors by Co-Targeting the AKT/mTOR Pathway

The sustained clinical activity of the BRAF inhibitor vemurafenib (PLX4032/RG7204) in patients with BRAF(V600) mutant melanoma is limited primarily by the development of acquired resistance leading to tumor progression. Clinical trials are in progress using MEK inhibitors following disease progression in patients receiving BRAF inhibitors. However, the PI3K/AKT pathway can also induce resistance to the inhibitors of MAPK pathway.The sensitivity to vemurafenib or the MEK inhibitor AZD6244 was tested in sensitive and resistant human melanoma cell lines exploring differences in activation-associated phosphorylation levels of major signaling molecules, leading to the testing of co-inhibition of the AKT/mTOR pathway genetically and pharmacologically. There was a high degree of cross-resistance to vemurafenib and AZD6244, except in two vemurafenib-resistant cell lines that acquired a secondary mutation in NRAS. In other cell lines, acquired resistance to both drugs was associated with persistence or increase in activity of AKT pathway. siRNA-mediated gene silencing and combination therapy with an AKT inhibitor or rapamycin partially or completely reversed the resistance.Primary and acquired resistance to vemurafenib in these in vitro models results in frequent cross resistance to MEK inhibitors, except when the resistance is the result of a secondary NRAS mutation. Resistance to BRAF or MEK inhibitors is associated with the induction or persistence of activity within the AKT pathway in the presence of these drugs. This resistance can be potentially reversed by the combination of a RAF or MEK inhibitor with an AKT or mTOR inhibitor. These combinations should be available for clinical testing in patients progressing on BRAF inhibitors

Photo-enhanced antinodal conductivity in the pseudogap state of high-T-c cuprates

A major challenge in understanding the cuprate superconductors is to clarify the nature of the fundamental electronic correlations that lead to the pseudogap phenomenon. Here we use ultrashort light pulses to prepare a non-thermal distribution of excitations and capture novel properties that are hidden at equilibrium. Using a broadband (0.5-2 eV) probe, we are able to track the dynamics of the dielectric function and unveil an anomalous decrease in the scattering rate of the charge carriers in a pseudogap-like region of the temperature (T) and hole-doping (p) phase diagram. In this region, delimited by a well-defined T*(neq)(p) line, the photoexcitation process triggers the evolution of antinodal excitations from gapped (localized) to delocalized quasiparticles characterized by a longer lifetime. The novel concept of photo-enhanced antinodal conductivity is naturally explained within the singleband Hubbard model, in which the short-range Coulomb repulsion leads to a k-space differentiation between nodal quasiparticles and antinodal excitations. \ua9 2014 Macmillan Publishers Limited. All rights reserved

Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations