Vietnam Academy of Science and Technology

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Electrodeposition of CuAg alloy films from plating baths containing 3,5-diamino-1,2,4-triazole (DAT) as an inhibitor yields high surface area catalysts for the active and selective electroreduction of CO2 to multicarbon hydrocarbons and oxygenates. EXAFS shows the co-deposited alloy film to be homogeneously mixed. The alloy film containing 6% Ag exhibits the best CO2 electroreduction performance, with the Faradaic efficiency for C2H4 and C2H5OH production reaching nearly 60 and 25%, respectively, at a cathode potential of just −0.7 V vs RHE and a total current density of ∼ – 300 mA/cm2. Such high levels of selectivity at high activity and low applied potential are the highest reported to date. In situ Raman and electroanalysis studies suggest the origin of the high selectivity toward C2 products to be a combined effect of the enhanced stabilization of the Cu2O overlayer and the optimal availability of the CO intermediate due to the Ag incorporated in the alloy.

Abstract Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action 1,2 . Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment 3,4 . Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

Strongly luminescent CuInS2/ZnS core/shell nanocrystals were synthesized from copper iodide, indium acetate, zinc stearate, and dodecanethiol as starting compounds in octadecene solvent. The as-prepared core/shell nanocrystals exhibit a low size distribution (<10%), and present photoluminescence in the range of 550−815 nm with a maximum fluorescence quantum yield (QY) of 60%. Time-resolved fluorescence spectroscopy revealed that the lifetimes of the different spectral components are on the order of hundreds of nanoseconds, indicating that donor−acceptor pair recombinations are at the origin of the observed emission bands. The CuInS2/ZnS nanocrystals were subsequently transferred to the aqueous phase via surface ligand exchange with dihydrolipoic acid and used as fluorescent labels for in vivo imaging. After tail vein injection into nude mice, the biodistribution of the quantum dots was monitored during 24 h using fluorescence reflectance imaging.

Since Zadeh introduced fuzzy sets in 1965, a lot of new theories treating imprecision and uncertainty have been introduced. Some of these theories are extensions of fuzzy set theory, other try to handle imprecision and uncertainty in different way. In this paper, we introduce a new notion of picture fuzzy sets (PFS), which are directly extensions of fuzzy sets and of intuitonistic fuzzy sets (Atanassov). Then some operations on picture fuzzy sets are defined and some properties of these operations are considered. Here the basic preliminaries of PFS theory are presented.

As concern regarding the toxic effects of bisphenol A (BPA) grows, BPA in many consumer products is gradually being replaced with compounds such as bisphenol S (BPS). Nevertheless, data on the occurrence of BPS in human specimens are limited. In this study, 315 urine samples, collected from the general populations in the United States, China, India, Japan, Korea, Kuwait, Malaysia, and Vietnam, were analyzed for the presence of total BPS (free plus conjugated) concentrations by high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). BPS was detected in 81% of the urine samples analyzed at concentrations ranging from below the limit of quantitation (LOQ; 0.02 ng/mL) to 21 ng/mL (geometric mean: 0.168 ng/mL). The urinary BPS concentration varied among countries, and the highest geometric mean concentration [1.18 ng/mLor 0.933 μg/g creatinine (Cre)] of BPS was found in urine samples from Japan, followed by the United States (0.299 ng/mL, 0.304 μg/g Cre), China (0.226 ng/mL, 0.223 μg/g Cre), Kuwait (0.172 ng/mL, 0.126 μg/g Cre), and Vietnam (0.160 ng/mL, 0.148 μg/g Cre). Median concentrations of BPS in urine samples from the Asian countries were 1 order of magnitude lower than the median concentrations reported earlier for BPA in the same set of samples, with the exception of samples from Japan. There were no significant differences in BPS concentrations between genders (male versus female), or among age groups (categorized as ≤ 19, 20-29, 30-39, 40-49, and ≥ 50 years), or races (Caucasian versus Asian). The daily intake (EDI) of BPS was estimated on the basis of urinary concentrations using a simple pharmacokinetic approach. The median EDI values of BPS in Japan, China, United States, Kuwait, Vietnam, Malaysia, India, and Korea were 1.67, 0.339, 0.316, 0.292, 0.217, 0.122, 0.084, and 0.023 μg/person, respectively. This is the first study to report the occurrence of BPS in human urine.

Poly(ethylene glycol) (PEG) is widely used as a gold standard in bioconjugation and nanomedicine to prolong blood circulation time and improve drug efficacy. The conjugation of PEG to proteins, peptides, oligonucleotides (DNA, small interfering RNA (siRNA), microRNA (miRNA)) and nanoparticles is a well-established technique known as PEGylation, with PEGylated products have been using in clinics for the last few decades. However, it is increasingly recognized that treating patients with PEGylated drugs can lead to the formation of antibodies that specifically recognize and bind to PEG (i.e., anti-PEG antibodies). Anti-PEG antibodies are also found in patients who have never been treated with PEGylated drugs but have consumed products containing PEG. Consequently, treating patients who have acquired anti-PEG antibodies with PEGylated drugs results in accelerated blood clearance, low drug efficacy, hypersensitivity, and, in some cases, life-threatening side effects. In this succinct review, we collate recent literature to draw the attention of polymer chemists to the issue of PEG immunogenicity in drug delivery and bioconjugation, thereby highlighting the importance of developing alternative polymers to replace PEG. Several promising yet imperfect alternatives to PEG are also discussed. To achieve asatisfactory alternative, further joint efforts of polymer chemists and scientists in related fields are urgently needed to design, synthesize and evaluate new alternatives to PEG.

As international concern for the survival of deltas grows, the Mekong River delta, the world's third largest delta, densely populated, considered as Southeast Asia's most important food basket, and rich in biodiversity at the world scale, is also increasingly affected by human activities and exposed to subsidence and coastal erosion. Several dams have been constructed upstream of the delta and many more are now planned. We quantify from high-resolution SPOT 5 satellite images large-scale shoreline erosion and land loss between 2003 and 2012 that now affect over 50% of the once strongly advancing >600 km-long delta shoreline. Erosion, with no identified change in the river's discharge and in wave and wind conditions over this recent period, is consistent with: (1) a reported significant decrease in coastal surface suspended sediment from the Mekong that may be linked to dam retention of its sediment, (2) large-scale commercial sand mining in the river and delta channels, and (3) subsidence due to groundwater extraction. Shoreline erosion is already responsible for displacement of coastal populations. It is an additional hazard to the integrity of this Asian mega delta now considered particularly vulnerable to accelerated subsidence and sea-level rise, and will be exacerbated by future hydropower dams.

In the original version of this manuscript, an error was introduced on pp352. '2.7nb:1.6nb' has been corrected to '2.4nb:1.3nb' in the current online and printed version. doi:10.1093/ptep/ptz106.

Emerging infectious diseases are reducing biodiversity on a global scale. Recently, the emergence of the chytrid fungus Batrachochytrium salamandrivorans resulted in rapid declines in populations of European fire salamanders. Here, we screened more than 5000 amphibians from across four continents and combined experimental assessment of pathogenicity with phylogenetic methods to estimate the threat that this infection poses to amphibian diversity. Results show that B. salamandrivorans is restricted to, but highly pathogenic for, salamanders and newts (Urodela). The pathogen likely originated and remained in coexistence with a clade of salamander hosts for millions of years in Asia. As a result of globalization and lack of biosecurity, it has recently been introduced into naïve European amphibian populations, where it is currently causing biodiversity loss.

COVID-19 vaccines have been developed with unprecedented speed which would not have been possible without decades of fundamental research on delivery nanotechnology. Lipid-based nanoparticles have played a pivotal role in the successes of COVID-19 vaccines and many other nanomedicines, such as Doxil® and Onpattro®, and have therefore been considered as the frontrunner in nanoscale drug delivery systems. In this review, we aim to highlight the progress in the development of these lipid nanoparticles for various applications, ranging from cancer nanomedicines to COVID-19 vaccines. The lipid-based nanoparticles discussed in this review are liposomes, niosomes, transfersomes, solid lipid nanoparticles, and nanostructured lipid carriers. We particularly focus on the innovations that have obtained regulatory approval or that are in clinical trials. We also discuss the physicochemical properties required for specific applications, highlight the differences in requirements for the delivery of different cargos, and introduce current challenges that need further development. This review serves as a useful guideline for designing new lipid nanoparticles for both preventative and therapeutic vaccines including immunotherapies.

Abstract Risk management has reduced vulnerability to floods and droughts globally 1,2 , yet their impacts are still increasing 3 . An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data 4,5 . On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change 3 .

The binding pose and affinity between a ligand and enzyme are very important pieces of information for computer-aided drug design. In the initial stage of a drug discovery project, this information is often obtained by using molecular docking methods. Autodock4 and Autodock Vina are two commonly used open-source and free software tools to perform this task, and each has been cited more than 6000 times in the last ten years. It is of great interest to compare the success rate of the two docking software programs for a large and diverse set of protein–ligand complexes. In this study, we selected 800 protein–ligand complexes for which both PDB structures and experimental binding affinity are available. Docking calculations were performed for these complexes using both Autodock4 and Autodock Vina with different docking options related to computing resource consumption and accuracy. Our calculation results are in good agreement with a previous study that the Vina approach converges much faster than AD4 one. However, interestingly, AD4 shows a better performance than Vina over 21 considered targets, whereas the Vina protocol is better than the AD4 package for 10 other targets. There are 16 complexes for which both the AD4 and Vina protocols fail to produce a reasonable correlation with respected experiments so both are not suitable to use to estimate binding free energies for these cases. In addition, the best docking option for performing the AD4 approach is the long option. However, the short option is the best solution for carrying out Vina docking. The obtained results probably will be useful for future docking studies in deciding which program to use.

MOTIVATION: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. MAIN TYPES OF VARIABLES INCLUDED: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. SPATIAL LOCATION AND GRAIN: ). TIME PERIOD AND GRAIN: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. MAJOR TAXA AND LEVEL OF MEASUREMENT: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. SOFTWARE FORMAT: .csv and .SQL.

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases. Various novel bioinformatics approaches such as molecular networking (MN) and in-silico fragmentation tools have emerged recently and provide new perspective for early metabolite identification in natural products (NPs) research. Here we propose an innovative dereplication strategy based on the combination of MN with an extensive in-silico MS/MS fragmentation database of NPs. Using two case studies, we demonstrate that this combined approach offers a powerful tool to navigate through the chemistry of complex NPs extracts, dereplicate metabolites, and annotate analogues of database entries.

We present a comprehensive review of keV-scale sterile neutrino Dark Matter, collecting views and insights from all disciplines involved—cosmology, astrophysics, nuclear, and particle physics—in each case viewed from both theoretical and experimental/observational perspectives. After reviewing the role of active neutrinos in particle physics, astrophysics, and cosmology, we focus on sterile neutrinos in the context of the Dark Matter puzzle. Here, we first review the physics motivation for sterile neutrino Dark Matter, based on challenges and tensions in purely cold Dark Matter scenarios. We then round out the discussion by critically summarizing all known constraints on sterile neutrino Dark Matter arising from astrophysical observations, laboratory experiments, and theoretical considerations. In this context, we provide a balanced discourse on the possibly positive signal from X-ray observations. Another focus of the paper concerns the construction of particle physics models, aiming to explain how sterile neutrinos of keV-scale masses could arise in concrete settings beyond the Standard Model of elementary particle physics. The paper ends with an extensive review of current and future astrophysical and laboratory searches, highlighting new ideas and their experimental challenges, as well as future perspectives for the discovery of sterile neutrinos.

Formation of acid mine drainage (AMD) is a widespread environmental issue that has not subsided throughout decades of continuing research. Highly acidic and highly concentrated metallic streams are characteristics of such streams. Humans, plants and surrounding ecosystems that are in proximity to AMD producing sites face immediate threats. Remediation options include active and passive biological treatments which are markedly different in many aspects. Sulfate reducing bacteria (SRB) remove sulfate and heavy metals to generate non-toxic streams. Passive systems are inexpensive to operate but entail fundamental drawbacks such as large land requirements and prolonged treatment period. Active bioreactors offer greater operational predictability and quicker treatment time but require higher investment costs and wide scale usage is limited by lack of expertise. Recent advancements include the use of renewable raw materials for AMD clean up purposes, which will likely achieve much greener mitigation solutions.

Schistosomes are digenean flukes, parasitic of birds, mammals and crocodiles. The family Schistosomatidae contains species of considerable medical and veterinary importance, which cause the disease schistosomiasis. Previous studies, both morphological and molecular, which have provided a good deal of information on the phylogenetics of this group, have been limited in the number of species investigated or the type or extent of molecular data used. This paper presents the most comprehensive phylogeny to date, based on the sequences of 3 genes, complete ribosomal small subunit rRNA and large ribosomal subunit rRNA, and mitochondrial cytochrome oxidase 1, sequenced from 30 taxa including at least 1 representative from 10 of the 13 known genera of the Schistosomatidae and 17 of the 20 recognized Schistosoma species. The phylogeny is examined using morphological characters, intermediate and definitive host associations and biogeography. Theories as to the origins and spread of Schistosoma are also explored. The principal findings are that Ornithobilharzia and Austrobilharzia form a sister group to the Schistosoma; mammalian schistosomes appear paraphyletic and 2 Trichobilharzia species, T. ocellata and T. szidati, seem to be synonymous. The position of Orientobilharzia within the Schistosoma is confirmed, as is an Asian origin for the Schistosoma, followed by subsequent dispersal through India and Africa.

We report here on a new series of CO2-reducing molecular catalysts based on Earth-abundant elements that are very selective for the production of formic acid in dimethylformamide (DMF)/water mixtures (Faradaic efficiency of 90 ± 10%) at moderate overpotentials (500–700 mV in DMF measured at the middle of the catalytic wave). The [CpCo(PR2NR′2)I]+ compounds contain diphosphine ligands, PR2NR′2, with two pendant amine residues that act as proton relays during CO2-reduction catalysis and tune their activity. Four different PR2NR′2 ligands with cyclohexyl or phenyl substituents on phosphorus and benzyl or phenyl substituents on nitrogen were employed, and the compound with the most electron-donating phosphine ligand and the most basic amine functions performs best among the series, with turnover frequency >1000 s–1. State-of-the-art benchmarking of catalytic performances ranks this new class of cobalt-based complexes among the most promising CO2-to-formic acid reducing catalysts developed to date; addressing the stability issues would allow further improvement. Mechanistic studies and density functional theory simulations confirmed the role of amine groups for stabilizing key intermediates through hydrogen bonding with water molecules during hydride transfer from the Co center to the CO2 molecule.