AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz

Numerical simulation of all-normal dispersion visible to near-infrared supercontinuum generation in photonic crystal fibers with core filled chloroform

This study proposes a photonic crystal fiber made of fused silica glass, with the core infiltrated with chloroform as a new source of supercontinuum (SC) spectrum. We numerically study the guiding properties of the fiber structure in terms of characteristic dispersion and mode area of the fundamental mode. Based on the results, we optimized the structural geometries of the CHCl3-core photonic crystal fiber to support the broadband SC generations. The fiber structure with a lattice constant of 1 μm, a filling factor of 0.8, and the diameter of the first-ring air holes equaling 0.5 μm operates in all-normal dispersion. The SC with a broadened spectral bandwidth of 0.64 to 1.80 μm is formed by using a pump pulse with a wavelength of 850 nm, 120 fs duration, and power of 0.833 kW. That fiber would be a good candidate for all-fiber SC sources as cost-effective alternative to glass core fibers

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

Efficient inference of large prokaryotic pangenomes with PanTA

Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705

Enhancing effect of sodium butyrate on phosphatidylserine–liposome-induced macrophage polarization

© 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.Object: Phosphatidylserine-containing liposomes (PSLs) can mimic the immunomodulatory effects of apoptotic cells by binding to the phosphatidylserine receptors of macrophages. Sodium butyrate, an antiinflammatory short-chain fatty acid, is known to facilitate the M2 polarization of macrophages. This study aimed to investigate the effect of sodium butyrate on PSLs-induced macrophage polarization. Methods: PSLs physical properties and cellular uptake tests, reverse transcription–quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, immunofluorescence staining, and flow cytometry analysis were performed to assess the polarization-related indicators of M1/M2 macrophages. Results: The results showed that sodium butyrate did not affect the size and cellular uptake of PSLs. For M1 macrophage polarization, sodium butyrate significantly intensified the antiinflammatory function of PSLs, inhibiting LPS-induced proinflammatory genes expression, cytokines and enzyme release (tumor necrosis factor-alpha, interleukin (IL)-1β, IL-6, and inducible nitric oxide synthase), as well as CD86 (M1 marker) expression. In addition to the enhancing effect of antiinflammation, sodium butyrate also promoted PSL-induced M2 macrophages polarization, especially elevated thymus and activation-regulated chemokine (TARC) and arginase-1 (Arg-1) enzyme levels which are involved in tissue repair. Conclusion: Sodium butyrate enhanced antiinflammatory properties and M2-polarization inducing effect of PSLs. Therefore, sodium butyrate may represent a novel approach to enhance PSL-induced macrophage polarization.N

Optimizing community screening for tuberculosis: Spatial analysis of localized case finding from door-to-door screening for TB in an urban district of Ho Chi Minh City, Viet Nam.

BACKGROUND:Tuberculosis (TB) is the deadliest infectious disease globally. Current case finding approaches may miss many people with TB or detect them too late. DATA AND METHODS:This study was a retrospective, spatial analysis of routine TB surveillance and cadastral data in Go Vap district, Ho Chi Minh City. We geocoded TB notifications from 2011 to 2015 and calculated theoretical yields of simulated door-to-door screening in three concentric catchment areas (50m, 100m, 200m) and three notification window scenarios (one, two and four quarters) for each index case. We calculated average yields, compared them to published reference values and fit a GEE (Generalized Estimating Equation) linear regression model onto the data. RESULTS:The sample included 3,046 TB patients. Adjusted theoretical yields in 50m, 100m and 200m catchment areas were 0.32% (95%CI: 0.27,0.37), 0.21% (95%CI: 0.14,0.29) and 0.17% (95%CI: 0.09,0.25), respectively, in the baseline notification window scenario. Theoretical yields in the 50m-catchment area for all notification window scenarios were significantly higher than a reference yield from literature. Yield was positively associated with treatment failure index cases (beta = 0.12, p = 0.001) and short-term inter-province migrants (beta = 0.06, p = 0.022), while greater distance to the DTU (beta = -0.02, p<0.001) was associated with lower yield. CONCLUSIONS:This study is an example of inter-departmental collaboration and application of repurposed cadastral data to progress towards the end TB objectives. The results from Go Vap showed that the use of spatial analysis may be able to identify areas where targeted active case finding in Vietnam can help improve TB case detection

Climate change in Viet Nam, impacts and adaptation : a COP26 assessment report of the GEMMES Viet Nam project

On the occasion of COP26, this report is proposing an assessment of the socio-economic impacts of climate change in Viet Nam by 2050, based on the intermediary results of the GEMMES Viet Nam research project. MONRE and AFD have undertaken this ambitious collaboration around the GEMMES Viet Nam project with the general objective to support Viet Nam in the implementation of the Paris Climate Agreement. Financed by the Facility 2050, in collaboration with IRD and IMHEN, this report materializes our common wish to develop a long-term vision of the economic, social and territorial issues of a resilient development strategy for Viet Nam

Climate change in Viet Nam, impacts and adaptation : a COP26 assessment report of the GEMMES Viet Nam project

On the occasion of COP26, this report is proposing an assessment of the socio-economic impacts of climate change in Viet Nam by 2050, based on the intermediary results of the GEMMES Viet Nam research project. MONRE and AFD have undertaken this ambitious collaboration around the GEMMES Viet Nam project with the general objective to support Viet Nam in the implementation of the Paris Climate Agreement. Financed by the Facility 2050, in collaboration with IRD and IMHEN, this report materializes our common wish to develop a long-term vision of the economic, social and territorial issues of a resilient development strategy for Viet Nam

Climate change in Viet Nam, impacts and adaptation : a COP26 assessment report of the GEMMES Viet Nam project

On the occasion of COP26, this report is proposing an assessment of the socio-economic impacts of climate change in Viet Nam by 2050, based on the intermediary results of the GEMMES Viet Nam research project. MONRE and AFD have undertaken this ambitious collaboration around the GEMMES Viet Nam project with the general objective to support Viet Nam in the implementation of the Paris Climate Agreement. Financed by the Facility 2050, in collaboration with IRD and IMHEN, this report materializes our common wish to develop a long-term vision of the economic, social and territorial issues of a resilient development strategy for Viet Nam

Moral Economy and the Upper Peasant: The Dynamics of Land Privatization in the Mekong Delta

This paper examines how people mobilize around notions of distributive justice, or ‘moral economies’, to make claims to resources, using the process of post‐socialist land privatization in the Mekong Delta region of southern Vietnam as a case study. First, I argue that the region\u27s history of settlement, production, and political struggle helped to entrench certain normative beliefs around landownership, most notably in its population of semi‐commercial upper peasants. I then detail the ways in which these upper peasants mobilized around notions of distributive justice to successfully press demands for land restitution in the late 1980s, drawing on Vietnamese newspapers and other sources to construct case studies of local land conflicts. Finally, I argue that the successful mobilization of the upper peasants around such a moral economy has helped, over the past two decades, to facilitate the re‐emergence of agrarian capitalism in the Mekong Delta, in contrast to other regions in Vietnam