Persistence of hepatic hepatitis B virus after serological clearance of HBsAG with autologous peripheral stem cell transplantation

Delayed clearance of hepatitis B surface antigen was previously reported in a 38 year old woman after high dose chemotherapy with autologous peripheral blood stem cell rescue. Sixteen months later, this patient remained hepatitis B surface antigen negative, hepatitis B surface anti-body positive, and serum hepatitis B DNA negative by polymerase chain reaction. Serial liver biopsies (one at hepatitis B e antigen positive stage, one at hepatitis B e antibody positive stage, and one at hepatitis B surface antigen negative and hepatitis B surface antibody positive stage) showed a gradual resolution of the inflammatory activity with loss of hepatitis B e antigen and then hepatitis B surface antigen in the serum. However, the degree of fibrosis, though mild, remained the same. With the serological clearance of hepatitis B surface antigen, a small amount of hepatitis B virus DNA was still detectable in the nuclei of liver cells.published_or_final_versio

Optimization of fermentation medium for nisin production from Lactococcus lactis subsp. lactis using response surface methodology (RSM) combined with artificial neural network-genetic algorithm (ANN-GA)

Nisin is a bacteriocin approved in more than 50 countries as a safe natural food preservative. Response surface methodology (RSM) combined with artificial neural network-genetic algorithm (ANN-GA) was employed to optimize the fermentation medium for nisin production. Plackett-Burman design (PBD) was used for identifying the significant components in the fermentation medium. After that, the path of steepest ascent method (PSA) was employed to approach their optimal concentrations. Sequentially, Box-Behnken design experiments were implemented for further optimization. RSM combined with ANNGA were used for analysis of data. Specially, a RSM model was used for determining the individual effect and mutual interaction effect of tested variables on nisin titer (NT), an ANN model was used for NT prediction, and GA was employed to search for the optimum solutions based on the ANN model. As the optimal medium obtained by ANN-GA was located at the verge of the test region, a further Box- Behnken design based on the RSM statistical analysis results was implemented. ANN-GA was implemented using the further Box-Behnken design data to locate the optimum solution which was as follow (g/l): Glucose (GLU) 15.92, peptone (PEP) 30.57, yeast extraction powder (YEP) 39.07, NaCl 5.25, KH2PO4 10.00, and MgSO4·7H2O 0.20, with expected NT of 22216 IU/ml. The validation experiments with the optimum solution were implemented in triplicate and the average NT was 21423 IU/ml, which was 2.13 times higher than that without ANN-GA methods and 8.34 times higher than that without optimization.Key words: Response surface methodology, artificial neural network, genetic algorithm, nisin titer

Epigenetic inactivation of the miR-34a in hematological malignancies

miR-34a is a transcriptional target of p53 and implicated in carcinogenesis. We studied the role of miR-34a methylation in a panel of hematological malignancies including acute leukemia [acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL)], chronic leukemia [chronic lymphocytic leukemia (CLL) and chronic myeloid leukemia (CML)], multiple myeloma (MM) and non-Hodgkin's lymphoma (NHL). The methylation status of miR-34a promoter was studied in 12 cell lines and 188 diagnostic samples by methylation-specific polymerase chain reaction. miR-34a promoter was unmethylated in normal controls but methylated in 75% lymphoma and 37% myeloma cell lines. Hypomethylating treatment led to re-expression of pri-miR-34a transcript in lymphoma cells with homozygous miR-34a methylation. In primary samples at diagnosis, miR-34a methylation was detected in 4% CLL, 5.5% MM samples and 18.8% of NHL at diagnosis but none of ALL, AML and CML (P = 0.011). In MM patients with paired samples, miR-34a methylation status remained unchanged at progression. Amongst lymphoid malignancies, miR-34a was preferentially methylated in NHL (P = 0.018), in particular natural killer (NK)/T-cell lymphoma. In conclusion, amongst hematological malignancies, miR-34a methylation is preferentially hypermethylated in NHL, in particular NK/T-cell lymphoma, in a tumor-specific manner, therefore the role of miR-34a in lymphomagenesis warrants further study. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected]

Long-Term Visual Object Tracking Benchmark

We propose a new long video dataset (called Track Long and Prosper - TLP) and benchmark for single object tracking. The dataset consists of 50 HD videos from real world scenarios, encompassing a duration of over 400 minutes (676K frames), making it more than 20 folds larger in average duration per sequence and more than 8 folds larger in terms of total covered duration, as compared to existing generic datasets for visual tracking. The proposed dataset paves a way to suitably assess long term tracking performance and train better deep learning architectures (avoiding/reducing augmentation, which may not reflect real world behaviour). We benchmark the dataset on 17 state of the art trackers and rank them according to tracking accuracy and run time speeds. We further present thorough qualitative and quantitative evaluation highlighting the importance of long term aspect of tracking. Our most interesting observations are (a) existing short sequence benchmarks fail to bring out the inherent differences in tracking algorithms which widen up while tracking on long sequences and (b) the accuracy of trackers abruptly drops on challenging long sequences, suggesting the potential need of research efforts in the direction of long-term tracking.Comment: ACCV 2018 (Oral

A HIV-1 heterosexual transmission chain in Guangzhou, China: a molecular epidemiological study

<p>Abstract</p> <p>Background</p> <p>We conducted molecular analyses to confirm four clustering HIV-1 infections (Patient A, B, C & D) in Guangzhou, China. These cases were identified by epidemiological investigation and suspected to acquire the infection through a common heterosexual transmission chain.</p> <p>Methods</p> <p><it>Env C2V3V4 </it>region, <it>gag p17/p24 </it>junction and partial <it>pol </it>gene of HIV-1 genome from serum specimens of these infected cases were amplified by reverse transcription polymerase chain reaction (RT-PCR) and nucleotide sequenced.</p> <p>Results</p> <p>Phylogenetic analyses indicated that their viral nucleotide sequences were significantly clustered together (bootstrap value is 99%, 98% and 100% in <it>env</it>, <it>gag </it>and <it>pol </it>tree respectively). Evolutionary distance analysis indicated that their genetic diversities of <it>env</it>, <it>gag </it>and <it>pol </it>genes were significantly lower than non-clustered controls, as measured by unpaired <it>t</it>-test (<it>env </it>gene comparison: <it>p </it>< 0.005; <it>gag </it>gene comparison: <it>p </it>< 0.005; <it>pol </it>gene comparison: <it>p </it>< 0.005).</p> <p>Conclusion</p> <p>Epidemiological results and molecular analyses consistently illustrated these four cases represented a transmission chain which dispersed in the locality through heterosexual contact involving commercial sex worker.</p

Understanding the nature of "superhard graphite"

Numerous experiments showed that on cold compression graphite transforms into a new superhard and transparent allotrope. Several structures with different topologies have been proposed for this phase. While experimental data are consistent with these models, the only way to solve this puzzle is to find which structure is kinetically easiest to form. Using state-of-the-art molecular-dynamics transition path sampling simulations, we investigate kinetic pathways of the pressure-induced transformation of graphite to various superhard candidate structures. Unlike hitherto applied methods for elucidating nature of superhard graphite, transition path sampling realistically models nucleation events necessary for physically meaningful transformation kinetics. We demonstrate that nucleation mechanism and kinetics lead to $M$-carbon as the final product. $W$-carbon, initially competitor to $M$-carbon, is ruled out by phase growth. Bct-C$_4$ structure is not expected to be produced by cold compression due to less probable nucleation and higher barrier of formation

The NIH-NIAID Schistosomiasis Resource Center

A bench scientist studying schistosomiasis must make a large commitment to maintain the parasite's life cycle, which necessarily involves a mammalian (definitive) host and the appropriate species of snail (intermediate host). This is often a difficult and expensive commitment to make, especially in the face of ever-tightening funds for tropical disease research. In addition to funding concerns, investigators usually face additional problems in the allocation of sufficient lab space to this effort (especially for snail rearing) and the limited availability of personnel experienced with life cycle upkeep. These problems can be especially daunting for the new investigator entering the field. Over 40 years ago, the National Institutes of Health–National Institute of Allergy and Infectious Diseases (NIH-NIAID) had the foresight to establish a resource from which investigators could obtain various schistosome life stages without having to expend the effort and funds necessary to maintain the entire life cycle on their own. This centralized resource translated into cost savings to both NIH-NIAID and to principal investigators by freeing up personnel costs on grants and allowing investigators to divert more funds to targeted research goals. Many investigators, especially those new to the field of tropical medicine, are only vaguely, if at all, aware of the scope of materials and support provided by this resource. This review is intended to help remedy that situation. Following a short history of the contract, we will give a brief description of the schistosome species provided, provide an estimate of the impact the resource has had on the research community, and describe some new additions and potential benefits the resource center might have for the ever-changing research interests of investigators

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.

BackgroundGeneral translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.ResultsHere, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.ConclusionsOur work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal