Molecular Epidemiology of HCV RNA Genotype-3 in Dhaka City, Bangladesh.

Hepatitis C virus (HCV) is a causative agent that causes chronic liver diseases worldwide. It is a little, enclosed, single-stranded ribonucleic acid (RNA) virus. The recognition of the pathogenic HCV genotype is critical for the remedy of its sufferers. The aim of this study was to identify the HCV RNA genotype to decide the correct treatment of hepatitis C positive sufferers in Bangladesh. Blood samples were collected from 390 individuals and isolated RNA (60 µg) from blood plasma. Extracted RNA was used for quantitative HCV RNA, and complementary DNA (cDNA) was prepared by polymerase chain reaction (PCR) conducted by reverse transcriptase enzyme. This cDNA amplified in multiplex by RT-PCR, which was performed with specific set of primers. The HCV RNA genotype was detected 297 of 390 patients. Of the 390 test samples, 200 (51.28%) samples were from males and 190 (48.71%) were from females, with age ranging from 5 to 78 years. In all, 166 of 200 male samples and 131/190 female samples were found positive for HCV. Of these 390 participants included in the study, 213 (54.61%) were identified as genotype 3 positive, 78 (20%) as genotype 1 positive, 6 (1.53%) as genotype 6 positive, and the remaining 93 (23.85%) samples were unclassified due to low/undetected viral load. In this study, we detected the highest percentage (30.89%) of genotype 3 HCV in patients aged 51 to 60 years. The results suggested that genotype 3 HCV is frequently present in Bangladesh and it is usually responses better to interferon therapy. However, genotype 1 and 6 HCV have also been found circulating in this country, which demands longer treatments and effective control measures.

TEsoNet: knowledge transfer in surgical phase recognition from laparoscopic sleeve gastrectomy to the laparoscopic part of Ivor-Lewis esophagectomy.

BACKGROUND: Surgical phase recognition using computer vision presents an essential requirement for artificial intelligence-assisted analysis of surgical workflow. Its performance is heavily dependent on large amounts of annotated video data, which remain a limited resource, especially concerning highly specialized procedures. Knowledge transfer from common to more complex procedures can promote data efficiency. Phase recognition models trained on large, readily available datasets may be extrapolated and transferred to smaller datasets of different procedures to improve generalizability. The conditions under which transfer learning is appropriate and feasible remain to be established. METHODS: We defined ten operative phases for the laparoscopic part of Ivor-Lewis Esophagectomy through expert consensus. A dataset of 40 videos was annotated accordingly. The knowledge transfer capability of an established model architecture for phase recognition (CNN + LSTM) was adapted to generate a "Transferal Esophagectomy Network" (TEsoNet) for co-training and transfer learning from laparoscopic Sleeve Gastrectomy to the laparoscopic part of Ivor-Lewis Esophagectomy, exploring different training set compositions and training weights. RESULTS: The explored model architecture is capable of accurate phase detection in complex procedures, such as Esophagectomy, even with low quantities of training data. Knowledge transfer between two upper gastrointestinal procedures is feasible and achieves reasonable accuracy with respect to operative phases with high procedural overlap. CONCLUSION: Robust phase recognition models can achieve reasonable yet phase-specific accuracy through transfer learning and co-training between two related procedures, even when exposed to small amounts of training data of the target procedure. Further exploration is required to determine appropriate data amounts, key characteristics of the training procedure and temporal annotation methods required for successful transferal phase recognition. Transfer learning across different procedures addressing small datasets may increase data efficiency. Finally, to enable the surgical application of AI for intraoperative risk mitigation, coverage of rare, specialized procedures needs to be explored.

The degradation of textile industry dyes using the effective bacterial consortium.

The effluents from textile industries without proper treatment contains a remarkable amount of synthetic dyes which are harmful to the environment and a big challenge globally to degrade it with a eco-friendly way. Conventional methods are extremely energy-consuming, non-effective and generate a toxic sludge impacting the environment. Several microorganisms can be utilized to treat these effluents. The research deals with five bacteria isolated from textile effluent and their consortium for the biodegradation ability of Novacron dyes. The isolates were identified through the Biolog™ identification system and molecular technique. Biodegradation was confirmed by measuring optical density (OD) optimizing conditions (pH 7.0, temperature 37 °C, 10 % inoculums and 100 mg/L dye) under static condition. The isolates started decolourization at 24 h whereas, the consortium started decolourization at 18 h and exhibited a maximum after 72 h. The presence of low molecular weight protein as metabolite supported the biodegradation and non hazardous to environment. This study revealed that these bacteria might have degradation potentials, and research results will help to set up dye removal eco-friendly methods to expose the dye effulents to environment in future.

In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism.

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

Applied origami. A method for building self-folding machines.

Origami can turn a sheet of paper into complex three-dimensional shapes, and similar folding techniques can produce structures and mechanisms. To demonstrate the application of these techniques to the fabrication of machines, we developed a crawling robot that folds itself. The robot starts as a flat sheet with embedded electronics, and transforms autonomously into a functional machine. To accomplish this, we developed shape-memory composites that fold themselves along embedded hinges. We used these composites to recreate fundamental folded patterns, derived from computational origami, that can be extrapolated to a wide range of geometries and mechanisms. This origami-inspired robot can fold itself in 4 minutes and walk away without human intervention, demonstrating the potential both for complex self-folding machines and autonomous, self-controlled assembly.

Programmable matter by folding.

Programmable matter is a material whose properties can be programmed to achieve specific shapes or stiffnesses upon command. This concept requires constituent elements to interact and rearrange intelligently in order to meet the goal. This paper considers achieving programmable sheets that can form themselves in different shapes autonomously by folding. Past approaches to creating transforming machines have been limited by the small feature sizes, the large number of components, and the associated complexity of communication among the units. We seek to mitigate these difficulties through the unique concept of self-folding origami with universal crease patterns. This approach exploits a single sheet composed of interconnected triangular sections. The sheet is able to fold into a set of predetermined shapes using embedded actuation. To implement this self-folding origami concept, we have developed a scalable end-to-end planning and fabrication process. Given a set of desired objects, the system computes an optimized design for a single sheet and multiple controllers to achieve each of the desired objects. The material, called programmable matter by folding, is an example of a system capable of achieving multiple shapes for multiple functions.

Rac GTPases are involved in development, survival and homeostasis of T cells.

Rac GTPases consist of Rac1, 2 and 3, and each of them have redundant and differential functions. Rac1 is the most ubiquitously and abundantly expressed of the three and has been shown to work as a "molecular switch" in various signal transduction pathways. Although Rac1 and Rac2 are both activated by TCR ligation, little is known about the function of Rac GTPases in the development and activation of T cells. In order to investigate the precise function of Rac GTPases in T cells in vivo, we established dominant negative Rac1 transgenic (dnRac1-Tg) mice controlled by the human CD2 promoter. Total numbers of thymocytes of dnRac1-Tg mice were significantly decreased because of impaired transition from the CD4CD8 double negative stage to the CD4CD8 double positive (DP) stage. Although positive selection of CD4 single positive (SP) was not altered, positive selection of CD8-SP was slightly increased. On the contrary, the number of mature CD4-SP and CD8-SP cells in the spleen, mesenteric lymph nodes and peripheral blood was severely decreased in dnRac1-Tg mice. Proliferation of splenic CD4-SP cells upon TCR stimulation in vitro was unaltered, however, homeostatic proliferation of dnRac1-Tg splenic CD4-SP cells in lymphopenic mice was severely reduced. Finally, we found increased spontaneous apoptosis of DP thymocytes and mature T cells in dnRac1-Tg mice, possibly because of reduced phosphorylation of Akt with or without TCR stimulation. Collectively, the current results indicate that Rac GTPases are important in survival of DP thymocytes and mature T cells in vivo by regulating Akt activation.

Fusion of family 2b carbohydrate-binding module increases the catalytic activity of a xylanase from Thermotoga maritima to soluble xylan.

A family 2b carbohydrate-binding module from Streptomyces thermoviolaceus STX-II was fused at the carboxyl-terminus of XynB, a thermostable and single domain family 10 xylanase from Thermotoga maritima, to create a chimeric xylanase. The chimeric enzyme (XynB-CBM2b) was purified and characterized. It displayed a pH-activity profile similar to that of XynB and was stable up to 90 degrees C. XynB-CBM2b bound to insoluble birchwood and oatspelt xylan. Whereas its hydrolytic activities toward insoluble xylan and p-nitrophenyl-beta-xylopyranoside were similar to those of XynB, its activity toward soluble xylan was moderately higher than that of XynB.

Evidence that the putative alpha-glucosidase of Thermotoga maritima MSB8 is a pNP alpha-D-glucuronopyranoside hydrolyzing alpha-glucuronidase.

The gene (agu) encoding p-nitrophenyl alpha-D-glucuronopyranoside (pNP-GUA) hydrolyzing alpha-glucuronidase of the hyperthermophilic bacterium Thermotoga maritima was cloned and expressed in Escherichia coli. The recombinant enzyme was purified and characterized. The gene previously designated as putative alpha-glucosidase was found to code for a protein that had no alpha-glucosidase activity. It showed a rare activity profile with its ability to hydrolyze pNP-GUA, an activity not known in the alpha-glucuronidases from microbial sources. This is the first report on the occurrence of an alpha-glucuronidase which belongs to the family 4 of glycosyl hydrolases.

Comparison of instream methods for measuring hydraulic conductivity in sandy streambeds.

Streambed hydraulic conductivity (K) values were determined at seven stream transects in the Platte River Basin in Nebraska using different instream measurement techniques. Values were compared to determine the most appropriate technique(s) for use in sandy streambeds. Values of K determined from field falling- and constant-head permeameter tests analyzed using the Darcy equation decreased as permeameter diameter increased. Seepage meters coupled with hydraulic gradient measurements failed to yield K values in 40% of the trials. Consequently, Darcy permeameter and seepage meter tests were not preferred approaches. In the upper 0.25 m of the streambed, field falling- and constant-head permeameter tests analyzed with the Hvorslev solution generally had similar K values that were significantly greater than those determined using the Hazen grain-size, Bouwer and Rice slug test for anisotropic and isotropic conditions, and Alyamani and Sen grain-size methods; median differences between these tests and the Hvorslev falling-head 60 cm diameter permeameter were about 8, 9, 17, and 35 m/day, respectively. The Hvorslev falling-head permeameter test is considered the most robust method for measuring K of the upper 0.25 m of the streambed because of the inherent limitations of the empirical grain-size methods and less sediment disturbance for permeameter than slug tests. However, lateral variability in K along transects on the Platte, North Platte, and Wood Rivers was greater than variability in K between valid permeameter, grain-size, or slug tests, indicating that the method used may matter less than making enough measurements to characterize spatial variability adequately. At the Platte River tributary sites, the upper 0.3 m of the streambed typically had greater K than sediment located 0.3 to 2.5 m below the streambed surface, indicating that deposits below the streambed may limit ground water/surface water fluxes. The Hvorslev permeameter tests are not a practical measurement approach for these greater depths. Thus, selection of a method for measuring streambed K needs to consider the vertical location of the sediments that are most likely to limit the rate of ground water/surface water interaction.

The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies.

The Functional Magnetic Resonance Imaging Data Center (fMRIDC) (http://www.fmridc.org) was established in the Autumn of 1999 with the objective of creating a mechanism by which members of the neuroscientific community may more easily share functional neuroimaging data. Examples in other sciences offer proof of the usefulness and benefit that sharing data provides through encouraging growth and development in those fields. By building a publicly accessible repository of raw data from peer-reviewed studies, the Data Center hopes to create a similarly successful environment for the neurosciences. In this article, we discuss the continuum of data-sharing efforts and provide an overview of the scientific and practical difficulties inherent in managing various fMRI data-sharing approaches. Next, we detail the organization, design and foundation of the fMRIDC, ranging from its current capabilities to the issues involved in the submitting and requesting of data. We discuss how a publicly accessible database enables other fields to develop relevant tools that can aid in the growth of understanding of cognitive processes. Information retrieval and meta-analytic techniques can be used to search, sort and categorize study information with a view towards subjecting study data to secondary 'meta-' and 'mega-analyses'. In addition, we detail the technical and policy challenges that have had to be addressed in the formation of the Data Center. Among others, these include: human subject confidentiality issues; ensuring investigator's rights; heterogeneous data description and organization; development of search tools; and data transfer issues. We conclude with comments concerning the future of the fMRIDC effort, its role in promoting the sharing of neuroscientific data, and how this may alter the manner in which studies are published.

Molecular cloning of cDNAs of mouse peptidylarginine deiminase type I, type III and type IV, and the expression pattern of type I in mouse.

Peptidylarginine deiminases (PADs), a group of post-translational enzymes, catalyze the conversion of protein-bound arginine residues to citrulline residues in a calcium ion-dependent manner and are widely distributed in various organs of vertebrates. Although the existence of four isoforms of PAD (types I, II, III, and IV) is reported in rodents, the relative functions of the isoforms with respect to their colocation in the tissues have yet to be explored. In this study, we cloned the full-length cDNA encoding mouse PAD type I by screening a uterine cDNA library and using the RACE method. This cDNA consists of an open reading frame of 1989 bases encoding 662 amino acids (73,823 Da), a 5'-untranslated region of 127 bases and a 3'-untranslated region of 1639 bases. Comparative reverse transcription-PCR and Northern-blot analyses detected PAD type I mRNA only in the epidermis and uterus. Administration of estrogen to adult ovariectomized mice increased the content of PAD type I mRNA in the uterus, providing evidence that its expression is under the control of the sex steroid hormone. We also cloned the full-length cDNAs of mouse PAD type III and type IV by the reverse transcription-PCR and RACE methods. The primary structure of PAD type III contains 664 amino acids (75,098 Da) deduced from the coding region of 1995 bases, and the primary structure of PAD type IV consists of 666 amino acids (74,475 Da) deduced from the coding region of 2001 bases. Comparison of the deduced amino acid sequences of all four isoforms of PAD showed about 50% identity with each other, the 3' regions being highly homologous compared with the 5' regions.