Modal decomposition technique for multimode fibers

International audienceWe propose a new solution for modal decomposition in multimode fibers, based on a spectral and spatial imaging technique. The appearance of spurious modes in the spectral and spatial processing of the images at the output of the fiber under test when it has more than two modes is demonstrated theoretically. The new method, which allows us to identify spurious modes, is more accurate, simpler, and faster than previously reported methods. For demonstration, measurements in a standard step-index multimode fiber and a small-core microstructured fiber are carried out successfully

AMRomics: a scalable workflow to analyze large microbial genome collections

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license

Mangrove Mapping and Above-Ground Biomass Change Detection using Satellite Images in Coastal Areas of Thai Binh Province, Vietnam

Mangroves are recognized as a highly valuable resource due to their provision of multiple ecosystem services. Therefore, mangrove ecosystems mapping and monitoring is a crucial objective, especially for tropical regions. Thai Binh province is one of the most important mangrove ecosystems in Vietnam. The mangrove ecosystem in this province has faced threats of deforestation from urban development, land reclamation, tourism activities, and natural disasters. Recently, to maintain the fundamental functions of the ecosystems, a large mangrove area was planted in Thai Binh. The aim of this research is to detect the change in the mangrove areas and to create an aboveground biomass map for mangrove forests in Thai Binh province. Landsat and Sentinel-2 satellite images from 1998 to 2018 were analysed using the supervised classification method to detect mangrove area change. Mangrove Above-ground Biomass (AGB) was estimated using linear regression between vegetation indices and field AGB survey. The accuracy assessment for the classified images of 1998, 2003 and 2007, 2013 and 2018 are 93%, 86%, 96%, 94% and 91% respectively with kappa of 0.8881, 0.7953, 0.9357, 0.9114 and 0.8761. The mangrove cover in the study area was estimated at 5874.93 ha in 1998. This figure decreased significantly to 4433.85 ha in 2007, before recovery began to take place in the study area, which was estimated at 6587.88 ha in 2018. In 1998, the average AGB in this study area was 22.57 ton/ha, and in 2018 it was 37.74 ton/ha with a standard error of 12.41 ton/ha and the root mean square error (RMSE) was ±12.08 ton/ha

A comparison for donor-acceptor interactions between E(PH3)2 and NHEMe ligands (E = C to Pb) of W(CO)5 complexes using energy decomposition analysis method with natural orbitals for chemical valence theory

Quantum chemical calculations at the BP86/TZ2P+ level of theory are performed for a comparison of density functional theory (DFT) between tetrylones [(CO)5W-{E(PH3)2}] (W5-EP2) and tetrylenes [(CO)5W-{NHEMe}] (W5-NHEMe) when E = C to Pb. The EDA-NOCV results suggest that the W-E bond dissociation energies (BDEs) in tetrylone complexes increase from the lighter to the heavier homologues. The W-E bond dissociation energies (BDEs) trend in W5-EP2 comes from the increase in (CO)5W←E(PH3)2 donation and strong electrostatic attraction, and that the ligands E(PH3)2 (EP2) are strong s-donors and very weak π-donors. The W-E BDEs trend in tetrylene complexes W5-NHEMe is opposite to that of the W5-EP2 complexes which decrease from the lighter to the heavier homologues. The NHEMe ligands are strong s-donors and weak π-acceptors. NOCV pairs were used in a description of the chemical bond between the W(CO)5 fragment and the ligands in the transition-metal complexes and the results indicated that the NOCV pairs lead to very valuable description of the bonding situation of the fragment-ligand bond in complexes. Keywords. Density functional theory; Bond dissociation energies (BDEs); Energy decomposition analysis (EDA); Natural Orbitals for Chemical Valence (NOCV)

Petrography and geochemistry of Permian basalts of the Cam Thuy formation and their relation to Song Da and Emeishan magmatic rocks

Cam Thuy Permian basalts consisting of thick lava flows and pyroclastic layers appear along both sides of the Song Ma fault zone in Thanh Hoa and in Son La and Ninh Binh provinces, NW Vietnam. The magmatism has been thought to have genetic relationship with Permian volcanism in the Song Da rift zone, which is believed to be part of the Emeishan large igneous province, having been extruded along the Red River shear zone following Paleogene India-Eurasian collision. A set of Cam Thuy volcanic samples including olivine and alkaline basalts was collected in the Lam Son area (Tho Xuan, Thanh Hoa province) to analyze for geochemical major, trace element and Sr-Nd-Pb isotopic composition. The Cam Thuy basalts are high-TiO2, CaO, FeO*, moderate MgO and SiO2 that plot between the Song Da and Emeishan high- and low-Ti basalt distribution fields and closely overlap that of Song Da’s high-Ti field. The primitive mantle and chondrite normalized trace element patterns of Cam Thuy basalts are essentially enriched oceanic island basalt (OIB)-like; this feature, together with crustal contamination-free, chondritic Sr, Nd and Pb initial (255Ma) isotopic composition are certainly of asthenospheric origin. These geochemical and isotopic characteristics are closely analogous to those features observed for the Song Da high-Ti basalts, suggesting similarity in their source of origin. Nevertheless, while the Song Da (and Emeishan) magmatism is signified by the presence of both high- and low-Ti basalts, with the latter being derived from heterogeneous and partially crustal-material contaminated sources in the lithospheric mantle, this low-Ti volcanic rock type has yet to be discovered in the Cam Thuy formation.ReferencesAnders, E., Grevesse, N., 1989. Abundances of the elements: meteorite and solar. 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NGHIÊN CỨU SỬ DỤNG DỮ LIỆU CÁC AXIT BÉO TRONG PHÂN LOẠI HOÁ HỌC THỰC VẬT (CHEMOTAXONOMY) ĐỐI VỚI CÁC LOÀI RONG ĐỎ

In this paper, the compositions and contents of fatty acids in the total lipid extracts of 69 red seaweed samples belonging to 9 families (Gracilariaceae, Hypneaceae, Ceramiaceae, Bangiaceae, Hylamaniaceae, Bonnemaisoniaceae, Phyllophoraceae, Rhodymeniaceae and Halymeniaceae) are studied. According to the results, 56 fatty acids are identified, in which 12 fatty acids were considered “fatty acid markers” for the botanical classification (Chemotaxonomy) of red seaweed species such as C14:0, C15:0, C16:0, C16:1n-7, C18:0, C18:1n-9, C18:1n-7, C18:2n-6, C20:3n-6, C20:4n-6, C20:5n-3 and C22:0. By using principal component analysis method (PCA), the analysis result on two-dimensional chart showed that families of red seaweed are distributed into separate regions. Classification tree diagram of the red seaweed species based on essential fatty acid composition is also given.Chúng tôi đã tiến hành nghiên cứu thành phần và hàm lượng các axit béo trong dịch chiết lipit tổng của 69 mẫu rong đỏ Rhodophyta thuộc 9 họ Gracilariaceae, Hypneaceae, Ceramiaceae, Bangiaceae, Hylamaniaceae, Phyllophoraceae, Rhodymeniaceae, họ Halymeniaceae. Kết quả đã xác định được 56 axit béo trong đó có 12 axit béo là C14:0, C15:0, C16:0, C16:1n-7, C18:0, C18:1n-9, C18:1n-7, C18:2n-6, C20:3n-6, C20:4n-6, C20:5n-3 và C22:0 được sử dụng là những chất đánh dấu cho việc phân loại hoá học thực vật (Chemotaxonomy) đối với các loài rong đỏ. Sử dụng phương pháp phân tích cấu tử chính (PCA), kết quả thể hiện qua giản đồ hai chiều, các họ rong đỏ phân định thành các vùng riêng rẽ. Chúng tôi cũng đưa ra sơ đồ cây phân loại của các loài rong đỏ theo thành phần axit béo chính yếu

Association between ACE I/D genetic polymorphism and the severity of coronary artery disease in Vietnamese patients with acute myocardial infarction

BackgroundThe severity of coronary artery disease is a prognostic factor for major adverse cardiovascular events in patients diagnosed with acute myocardial infarction. ACE I/D polymorphism is one of the genetic factors that may affect the severity of coronary artery disease. This study aimed to investigate the association between ACE I/D genotypes and the severity of coronary artery disease in patients with acute myocardial infarction.Materials and methodsA single-center, prospective, observational study was conducted at the Department of Cardiology and Department of Interventional Cardiology, Cho Ray Hospital, Ho Chi Minh City, Vietnam from January 2020 to June 2021. All participants diagnosed with acute myocardial infarction underwent contrast-enhanced coronary angiography. The severity of coronary artery disease was determined by Gensini score. ACE I/D genotypes were identified in all subjects by using the polymerase chain reaction method.ResultsA total of 522 patients diagnosed with first acute myocardial infarction were recruited. The patients' median Gensini score was 34.3. The II, ID, and DD genotype rates of ACE I/D polymorphism were 48.9%, 36.4%, and 14.7%, respectively. After adjusting for confounding factors, multivariable linear regression analysis showed that the ACE DD genotype was independently associated with a higher Gensini score compared with the II or ID genotypes.ConclusionThe DD genotype of the ACE I/D polymorphism was associated with the severity of coronary artery disease in Vietnamese patients diagnosed with first acute myocardial infarction

ĐẶC ĐIỂM DÒNG CHẢY VEN BỜ BẮC TRUNG BỘ (HÀ TĨNH - THỪA THIÊN-HUẾ) THỜI KỲ 4/2016

This paper presents the modeled results of general current pattern (daily average value) in Northern Central Vietnam Coast (Ha Tinh - Thua Thien-Hue) during April 2016. Study results show that in general, current flowed from the North to the South with small and instable velocity (V ≈ 0.1 - 0.2 m/s). From 2nd to 6th April current flowed from the South to the North. From 7th to 29th April current flowed from the North to the South. During 13rd to 16th April current velocity was weak (V ≤ 0.1 m/s). In the southern region of Thua Thien-Hue province, the direction of current was instable (from 6th to 9th and from 20th to 22nd April current flowed from the South to the North). Current distribution pattern from modeled results was in accordance with the propagation characteristics of surface water temperatures in the studied area through data analysis of satellite images.Bài báo trình bày kết quả tính toán trường dòng chảy tổng hợp trung bình ngày cho khu vực ven bờ Bắc Trung Bộ (Hà Tĩnh - Thừa Thiên-Huế) thời kỳ 4/2016. Kết quả nghiên cứu cho thấy trong thời gian nghiên cứu nhìn chung dòng chảy tổng hợp trung bình ngày có hướng từ bắc xuống nam, tốc độ tương đối nhỏ V ≈ 0,1 - 0,2 m/s và không ổn định. Từ 2-6/4/2016 dòng chảy tổng hợp trung bình ngày ven bờ có hướng từ nam lên bắc. Từ 7-29/4/2016 dòng chảy ven bờ có hướng từ bắc xuống nam. Các ngày 13-16/4/2016 dòng chảy tổng hợp trung bình ngày có tốc độ nhỏ (V ≤ 0,1 m/s). Khu vực phía nam Thừa Thiên-Huế dòng chảy tổng hợp trung bình ngày có hướng bị biến động mạnh nhất (các ngày 6-9/4 và 20-22/4 hướng dòng từ nam lên bắc). Đặc điểm phân bố dòng chảy tính toán tương đối phù hợp với đặc điểm lan truyền nhiệt độ nước tầng mặt tại khu vực nghiên cứu qua số liệu phân tích ảnh vệ tinh

De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene–which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management

Predicting range shifts of African apes under global change scenarios

Aim: Modelling African great ape distribution has until now focused on current or past conditions, while future scenarios remain scarcely explored. Using an ensemble forecasting approach, we predicted changes in taxon-specific distribution under future scenarios of climate, land use and human populations for (1) areas outside protected areas (PAs) only (assuming complete management effectiveness of PAs), (2) the entire study region and (3) interspecies range overlap. Location: Tropical Africa. Methods: We compiled occurrence data (n = 5,203) on African apes from the IUCN A.P.E.S. database and extracted relevant climate-, habitat- and human-related predictors representing current and future (2050) conditions to predict taxon-specific range change under a best- and a worst-case scenario, using ensemble forecasting. Results The predictive performance of the models varied across taxa. Synergistic interactions between predictors are shaping African ape distribution, particularly human-related variables. On average across taxa, a range decline of 50% is expected outside PAs under the best scenario if no dispersal occurs (61% in worst scenario). Otherwise, an 85% range reduction is predicted to occur across study regions (94% worst). However, range gains are predicted outside PAs if dispersal occurs (52% best, 21% worst), with a slight increase in gains expected across study regions (66% best, 24% worst). Moreover, more than half of range losses and gains are predicted to occur outside PAs where interspecific ranges overlap. Main Conclusions: Massive range decline is expected by 2050, but range gain is uncertain as African apes will not be able to occupy these new areas immediately due to their limited dispersal capacity, migration lag and ecological constraints. Given that most future range changes are predicted outside PAs, Africa's current PA network is likely to be insufficient for preserving suitable habitats and maintaining connected ape populations. Thus, conservation planners urgently need to integrate land use planning and climate change mitigation measures at all decision-making levels both in range countries and abroad