Homology sequence analysis using GPU acceleration

A number of problems in bioinformatics, systems biology and computational biology field require abstracting physical entities to mathematical or computational models. In such studies, the computational paradigms often involve algorithms that can be solved by the Central Processing Unit (CPU). Historically, those algorithms benefit from the advancements of computing power in the serial processing capabilities of individual CPU cores. However, the growth has slowed down over recent years, as scaling out CPU has been shown to be both cost-prohibitive and insecure. To overcome this problem, parallel computing approaches that employ the Graphics Processing Unit (GPU) have gained attention as complementing or replacing traditional CPU approaches. The premise of this research is to investigate the applicability of various parallel computing platforms to several problems in the detection and analysis of homology in biological sequence. I hypothesize that by exploiting the sheer amount of computation power and sequencing data, it is possible to deduce information from raw sequences without supplying the underlying prior knowledge to come up with an answer. I have developed such tools to perform analysis at scales that are traditionally unattainable with general-purpose CPU platforms. I have developed a method to accelerate sequence alignment on the GPU, and I used the method to investigate whether the Operational Taxonomic Unit (OTU) classification problem can be improved with such sheer amount of computational power. I have developed a method to accelerate pairwise k-mer comparison on the GPU, and I used the method to further develop PolyHomology, a framework to scaffold shared sequence motifs across large numbers of genomes to illuminate the structure of the regulatory network in yeasts. The results suggest that such approach to heterogeneous computing could help to answer questions in biology and is a viable path to new discoveries in the present and the future.Includes bibliographical reference

LAKESCAPE UNDER URBAN DEVELOPMENT IN DONG DA DISTRICT, HANOI CITY

Joint Research on Environmental Science and Technology for the Eart

THE INFRASTRUCTURE AND ENVIRONMENT IN THE OLD TENEMENTS IN HANOI

Joint Research on Environmental Science and Technology for the Eart

LAND USE CHANGE AND RELATED PROBLEMS UNDER URBANIZATION IN SUBURBAN AREA OF HANOI CITY (A CASE STUDY OF HOANG LIET COMMUNE, THANH TRI DISTRICT)

Joint Research on Environmental Science and Technology for the Eart

TÍNH TOÁN CÁC ĐẶC TRƯNG SÓNG Ở KHU VỰC NINH THUẬN - BÌNH THUẬN BẰNG MÔ HÌNH SWAN TRÊN LƯỚI PHI CẤU TRÚC

The wave model SWAN (version 41.01A) with unstructured grid has been applied for Ninh Thuan - Binh Thuan waters. This model is SWAN Cycle III using a vertex-based, fully implicit finite difference method. It can accommodate unstructured meshes with a high variability in geographic resolution suitable for representing complicated bottom topography in shallow areas and irregular shoreline. In particular, the unstructured meshes (triangular meshes) can be used to calculate the flow by finite element method. This is very helpful in solving the problems of interactions between wave-current and wave-wave. The initial results indicate that the approach to SWAN model is reasonable, stable for any time step while permitting local mesh refinements in interested areas. A lot of applications are shown to verify the correctness and numerical accuracy of the unstructured version of SWAN.Mô hình sóng SWAN (phiên bản 41.01A) với lưới phi cấu trúc đã được áp dụng thử nghiệm vào tính sóng tại vùng biển Ninh Thuận - Bình Thuận. Đây là mô hình sóng thế hệ thứ ba, sử dụng phương pháp sai phân hữu hạn, ẩn hoàn toàn dựa trên các cạnh của điểm lưới phần tử phi cấu trúc với một sự khác nhau lớn về độ phân giải không gian nhằm phù hợp với một địa hình đáy phức tạp đại diện cho vùng nước nông và đường bờ khúc khuỷu. Đặc biệt, có thể sử dụng cùng mạng lưới tam giác phi cấu trúc trong tính toán dòng chảy bằng phương pháp phần tử hữu hạn. Điều này rất hữu ích trong giải quyết bài toán tương tác sóng - dòng và sóng - sóng. Những kết quả bước đầu cho thấy, cách tiếp cận ứng dụng mô hình tính sóng này là hợp lý, ổn định cho bước thời gian bất kỳ cho mạng lưới làm mịn, mang đặc trưng địa phương trong vùng nghiên cứu. Một số ứng dụng được chứng minh tính hợp lý của phiên bản lưới phi cấu trúc trong mô hình SWAN

One-pot preparation of alumina-modified polysulfone-graphene oxide nanocomposite membrane for separation of emulsion-oil from wastewater

In recent years, polysulfone-based nanocomposite membranes have been widely used for contaminated water treatment because they comprise properties such as high thermal stability and chemical resistance. In this study, a polysulfone (PSf) nanocomposite membrane was fabricated using the wet-phase inversion method with the fusion of graphene oxide (GO) and alumina (Al2O3) nanoparticles. We also showed that GO-Al2O3 nanoparticles were synthesised successfully by using a one-pot hydrothermal method. The nanocomposite membranes were characterised by Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), nitrogen adsorption-desorption isotherms, energy-dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), and water contact angle. The loading of GO and Al2O3 was investigated to improve the hydrophilic and oil rejection of the matrix membrane. It was shown that by using 1.5 wt.% GO-Al2O3 loaded in polysulfone, ~74% volume of oil was separated from the oil/water emulsion at 0.87 bar and 30 min. This figure was higher than that of the process using the unmodified membrane (PSf/GO) at the same conditions, in which only ~60% volume of oil was separated. The pH, oil/water emulsion concentration, separation time, and irreversible fouling coefficient (FRw) were also investigated. The obtained results suggested that the GO-Al2O3 nanoparticles loaded in the polysulfone membrane might have potential use in oily wastewater treatment applications

BIẾN ĐỘNG CỦA TRƯỜNG NHIỆT ĐỘ VÀ MỐI QUAN HỆ CỦA NÓ VỚI ENSO TRONG VÙNG BIỂN NINH THUẬN - BÌNH THUẬN

In this paper, our aim was to examine the role of ENSO in the recent climate variations. Analyzed results on temporal variability of thermal fields in period of 38 years (Jan. 1979-Aug. 2016) showed that Ninh Thuan - Binh Thuan waters were subjected to the significant impact of the ENSO phases (warming and cooling) as well as other processes related to seasonal, inter-seasonal, yearly and mutlti-yearly variations such as in the periods 1986-1989, 1996-2000 and 2009-2011. In order to clarify above issues, authors carried out the analysis of the temporal -spatial changes of temperature fields (include air temperature and sea surface temperature) in Ninh Thuan - Binh Thuan region. The temperature data were exploited from The National Centers for Environmental Prediction (NCEP) and Climate Forecast System Reanalysis (CFSR) in the form of hourly time-series products with spatial resolution of 0.3o (1979-2010) and 0.20o (2011-8/2016). The results showed that 2016 was quite similar to 1998 and 2010 when the coral bleaching occurred in the study area.Các kết quả phân tích trường nhiệt độ trong 38 năm (1/1979 - 8/2016) đã cho thấy vùng biển Ninh Thuận - Bình Thuận chịu sự tác động không nhỏ của các pha ENSO (ấm, lạnh) mà còn có liên quan đến các quá trình khác có chu kỳ mùa, liên mùa, năm, nhiều năm thể hiện tại các giai đoạn 1986-1989; 1996-2000 và 2009-2011. Để góp phần làm sáng tỏ vấn đề trên, chúng tôi đã tiến hành phân tích sự thay đổi nền nhiệt độ của nhiệt độ không khí, nhiệt độ nước bề mặt biển. Các số liệu nhiệt độ sử dụng trong nghiên cứu này được khai thác từ Hệ thống Dự đoán Khí hậu Phân tích lại (CFSR) theo bước thời gian 1 giờ với độ phân giải ngang 0,3° (1979-2010) và 0,2o (2011-8/2016) của Trung tâm Dự báo Môi trường Quốc gia Hoa Kỳ (NCEP). Kết quả phân tích cho thấy năm 2016 có nét khá tương đồng với năm 1998 và 2010, các năm được phát hiện đã xảy ra hiện tượng tẩy trắng san hô tại khu vực nghiên cứu

Sintering behavior and physical properties of Bi0.5(Na1–xKx)0.5SnO3 lead-free ceramics

In this study, Bi0.5(Na1–xKx)0.5SnO3 (BNKS) ceramics (x = 0, 0.1, 0.2, 0.3, and 0.4) were fabricated via ultrasound wave before milling. The time of ball milling decreased from 20 to 1 h. The X-ray diffraction patterns show that the BNKS has a single-phase structure. When the potassium content increases, the phase structure of the ceramics changes from rhombohedral to tetragonal. When sintered at 1100 °C and x = 0.2, the ceramics’ physical properties are the best with the mass density of 5.59 g/cm3, the electromechanical coupling constants kp of 0,31 and kt of 0.27, the remanent polarization of      11.9 µC/cm; the dielectric constant εr of 1131, and the highest dielectric constant emax of 4800

Engineered CD4 T cells expressing a membrane anchored viral inhibitor restrict HIV-1 through cis and trans mechanisms

HIV-1 infection of target cells can occur through either cell-free virions or cell-cell transmission in a virological synapse, with the latter mechanism of infection reported to be 100- to 1,000-fold more efficient. Neutralizing antibodies and entry inhibitors effectively block cell-free HIV-1, but with few exceptions, they display much less inhibitory activity against cell-mediated HIV-1 transmission. Previously, we showed that engineering HIV-1 target cells by genetically linking single-chain variable fragments (scFvs) of antibodies to glycosyl phosphatidylinositol (GPI) potently blocks infection by cell-free virions and cell-mediated infection by immature dendritic cell (iDC)-captured HIV-1. Expression of scFvs on CD4+ cell lines by transduction with X5 derived anti-HIV-1 Env antibody linked to a GPI attachment signal directs GPI-anchored scFvs into lipid rafts of the plasma membrane. In this study, we further characterize the effect of GPI-scFv X5 on cell-cell HIV-1 transmission from DCs to target cells. We report that expression of GPI-scFv X5 in transduced CD4+ cell lines and human primary CD4+ T cells potently restricts viral replication in iDC- or mDC-captured HIV-1 in trans. Using live-cell imaging, we observed that when GPI-GFP or GPI-scFv X5 transduced T cells are co-cultured with iDCs, GPI-anchored proteins enrich in contact zones and subsequently migrate from T cells into DCs, suggesting that transferred GPI-scFv X5 interferes with HIV-1 infection of iDCs. We conclude that GPI-scFv X5 on the surface of transduced CD4+ T cells not only potently blocks cell-mediated infection by DCs, but it transfers from transduced cells to the surface of iDCs and neutralizes HIV-1 replication in iDCs. Our findings have important implications for HIV-1 antibody-based immunotherapies as they demonstrate a viral inhibitory effect that extends beyond the transduced CD4+ T cells to iDCs which can enhance HIV-1 replication