Blind fluorescence structured illumination microscopy: A new reconstruction strategy

In this communication, a fast reconstruction algorithm is proposed for fluorescence \textit{blind} structured illumination microscopy (SIM) under the sample positivity constraint. This new algorithm is by far simpler and faster than existing solutions, paving the way to 3D and/or real-time 2D reconstruction.Comment: submitted to IEEE ICIP 201

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy

Fluorescence blind structured illumination microscopy: a new reconstruction strategy

International audienceIn this communication, a fast reconstruction algorithm is proposed for fluorescence blind structured illumination mi-croscopy (SIM) under the sample positivity constraint. This new algorithm is by far simpler and faster than existing solutions , paving the way to 3D and real-time 2D reconstruction

Multiple effects of silymarin on the hepatitis C virus lifecycle

Silymarin, an extract from milk thistle (Silybum marianum), and its purified flavonolignans have been recently shown to inhibit hepatitis C virus (HCV) infection, both in vitro and in vivo. In the current study, we further characterized silymarin's antiviral actions. Silymarin had antiviral effects against hepatitis C virus cell culture (HCVcc) infection that included inhibition of virus entry, RNA and protein expression, and infectious virus production. Silymarin did not block HCVcc binding to cells but inhibited the entry of several viral pseudoparticles (pp), and fusion of HCVpp with liposomes. Silymarin but not silibinin inhibited genotype 2a NS5B RNA-dependent RNA polymerase (RdRp) activity at concentrations 5 to 10 times higher than required for anti-HCVcc effects. Furthermore, silymarin had inefficient activity on the genotype 1b BK and four 1b RDRPs derived from HCV-infected patients. Moreover, silymarin did not inhibit HCV replication in five independent genotype 1a, 1b, and 2a replicon cell lines that did not produce infectious virus. Silymarin inhibited microsomal triglyceride transfer protein activity, apolipoprotein B secretion, and infectious virion production into culture supernatants. Silymarin also blocked cell-to-cell spread of virus. CONCLUSION: Although inhibition of in vitro NS5B polymerase activity is demonstrable, the mechanisms of silymarin's antiviral action appear to include blocking of virus entry and transmission, possibly by targeting the host cell

A New Approach for Designing Orthogonal Wavelets for Multicarrier Applications

yesThe Daubechies, coiflet and symlet wavelets, with properties of orthogonal wavelets are suitable for multicarrier transmission over band-limited channels. It has been shown that similar wavelets can be constructed by Lagrange approximation interpolation. In this work and using established wavelet design algorithms, it is shown that ideal filters can be approximated to construct new orthogonal wavelets. These new wavelets, in terms of BER behave slightly better than the wavelets mentioned above, and much better than biorthogonal wavelets, in multipath channels with additive white Gaussian noise (AWGN). It is shown that the construction, which uses a simple simultaneous solution to obtain the wavelet filters from the ideal filters based on established wavelet design algorithms, is simple and can easily be reproduced

Prevalence of HIV/AIDS: A report based on a survey in women attending ANC services in Eritrea in 2005

Study objective: To determine the prevalence and socio-demographic factors of HIV in ANC attendees in Eritrea. Methods: Cross sectional anonymous unlinked sentinel surveillance of HIV prevalence in ANC attendee pregnant women frpm March 2005 to May 2006. The study was conducted in 15 clusters; 10 urban and 5 rural clusters with a total of 19 urban and 26 rural sentinel sites that includes all six capital cities and a number of semi urban and rural sentinel sites from all six zones of Eritrea. Cluster sampling, non probability consecutive sampling of pregnant women who came to attend their first ANC in the study sites. Result: The total sample size was 5033. The over all HIV prevalence in pregnant women attending ANC was 2.38%. The highest prevalence was observed in Southern Red Sea zone (5.9%) followed by central zone (3.48%). Lowest prevalence was seen in Anseba zone (1.3%), South zone (1.65%), Northern Red Sea zone (1.77%), and Gash Barka zone (2.06%). It was found to be 3.04% in urban women and 0.9% in rural women. It was also higher in single women 7.2% than in married women 2%. HIV prevalence increased with age (1.3%) in women aged 15-19, 2% in 20-24, 3.8% in 25-29, 2.5% in 30-34, 1.5% in 35-39, 2.7% in 40-44 and 1.8% in 15-24 years age group women. Further the prevalence fluctuated with level of formal education and occupation; 0.9% in illiterate and 4% in women with secondary school education, 1.94% in house wives, 5.9% in women daily labourers, 5.6% in unemployed unmarried women, and 8.5% in commercial sexual workers. 5.4% in women whose partners are truck/bus drivers, 3.8%% in women whose partners are merchants and 2.6% in women whose partner’s are in the military/national service. Conclusion: HIV prevalence in Eritrea is low and declining from the highest 4.2% in 1999 to 2.38% in 2005 ANS sentinel surveillance. HIV prevalence was more prevalent in urban areas, in single, young women and increased with increasing age and educational level and was influenced by the women’s and partners occupation

IL-1β Production through the NLRP3 Inflammasome by Hepatic Macrophages Links Hepatitis C Virus Infection with Liver Inflammation and Disease

Chronic hepatitis C virus (HCV) infection is a leading cause of liver disease. Liver inflammation underlies infection-induced fibrosis, cirrhosis and liver cancer but the processes that promote hepatic inflammation by HCV are not defined. We provide a systems biology analysis with multiple lines of evidence to indicate that interleukin-1β (IL-1β) production by intrahepatic macrophages confers liver inflammation through HCV-induced inflammasome signaling. Chronic hepatitis C patients exhibited elevated levels of serum IL-1β compared to healthy controls. Immunohistochemical analysis of healthy control and chronic hepatitis C liver sections revealed that Kupffer cells, resident hepatic macrophages, are the primary cellular source of hepatic IL-1β during HCV infection. Accordingly, we found that both blood monocyte-derived primary human macrophages, and Kupffer cells recovered from normal donor liver, produce IL-1β after HCV exposure. Using the THP-1 macrophage cell-culture model, we found that HCV drives a rapid but transient caspase-1 activation to stimulate IL-1β secretion. HCV can enter macrophages through non-CD81 mediated phagocytic uptake that is independent of productive infection. Viral RNA triggers MyD88-mediated TLR7 signaling to induce IL-1β mRNA expression. HCV uptake concomitantly induces a potassium efflux that activates the NLRP3 inflammasome for IL-1β processing and secretion. RNA sequencing analysis comparing THP1 cells and chronic hepatitis C patient liver demonstrates that viral engagement of the NLRP3 inflammasome stimulates IL-1β production to drive proinflammatory cytokine, chemokine, and immune-regulatory gene expression networks linked with HCV disease severity. These studies identify intrahepatic IL-1β production as a central feature of liver inflammation during HCV infection. Thus, strategies to suppress NLRP3 or IL-1β activity could offer therapeutic actions to reduce hepatic inflammation and mitigate disease

The burden of neglected tropical diseases in Ethiopia, and opportunities for integrated control and elimination

Background: Neglected tropical diseases (NTDs) are a group of chronic parasitic diseases and related conditions that are the most common diseases among the 2·7 billion people globally living on less than US$2 per day. In response to the growing challenge of NTDs, Ethiopia is preparing to launch a NTD Master Plan. The purpose of this review is to underscore the burden of NTDs in Ethiopia, highlight the state of current interventions, and suggest ways forward. Results: This review indicates that NTDs are significant public health problems in Ethiopia. From the analysis reported here, Ethiopia stands out for having the largest number of NTD cases following Nigeria and the Democratic Republic of Congo. Ethiopia is estimated to have the highest burden of trachoma, podoconiosis and cutaneous leishmaniasis in sub-Saharan Africa (SSA), the second highest burden in terms of ascariasis, leprosy and visceral leishmaniasis, and the third highest burden of hookworm. Infections such as schistosomiasis, trichuriasis, lymphatic filariasis and rabies are also common. A third of Ethiopians are infected with ascariasis, one quarter is infected with trichuriasis and one in eight Ethiopians lives with hookworm or is infected with trachoma. However, despite these high burdens of infection, the control of most NTDs in Ethiopia is in its infancy. In terms of NTD control achievements, Ethiopia reached the leprosy elimination target of 1 case/10,000 population in 1999. No cases of human African trypanosomiasis have been reported since 1984. Guinea worm eradication is in its final phase. The Onchocerciasis Control Program has been making steady progress since 2001. A national blindness survey was conducted in 2006 and the trachoma program has kicked off in some regions. Lymphatic Filariasis, podoconiosis and rabies mapping are underway. Conclusion: Ethiopia bears a significant burden of NTDs compared to other SSA countries. To achieve success in integrated control of NTDs, integrated mapping, rapid scale up of interventions and operational research into co implementation of intervention packages will be crucial