Displaying publications 21 - 36 of 36 in total

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  1. Fulltext Functionality of the putative surface glycoproteins of the Wuhan spiny eel influenza virus
    Arunkumar GA, Bhavsar D, Li T, Strohmeier S, Chromikova V, Amanat F, et al.
    Nat Commun, 2021 10 25;12(1):6161.
    PMID: 34697321 DOI: 10.1038/s41467-021-26409-2
    A panel of influenza virus-like sequences were recently documented in fish and amphibians. Of these, the Wuhan spiny eel influenza virus (WSEIV) was found to phylogenetically cluster with influenza B viruses as a sister clade. Influenza B viruses have been documented to circulate only in humans, with certain virus isolates found in harbor seals. It is therefore interesting that a similar virus was potentially found in fish. Here we characterize the putative hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins of the WSEIV. Functionally, we show that the WSEIV NA-like protein has sialidase activity comparable to B/Malaysia/2506/2004 influenza B virus NA, making it a bona fide neuraminidase that is sensitive to NA inhibitors. We tested the functionality of the HA by addressing the receptor specificity, stability, preferential airway protease cleavage, and fusogenicity. We show highly specific binding to monosialic ganglioside 2 (GM2) and fusogenicity at a range of different pH conditions. In addition, we found limited antigenic conservation of the WSEIV HA and NA relative to the B/Malaysia/2506/2004 virus HA and NA. In summary, we perform a functional and antigenic characterization of the glycoproteins of WSEIV to assess if it is indeed a bona fide influenza virus potentially circulating in ray-finned fish.
  2. Oilfield-produced water treatment using conventional and membrane-based technologies for beneficial reuse: A critical review
    Samuel O, Othman MHD, Kamaludin R, Sinsamphanh O, Abdullah H, Puteh MH, et al.
    J Environ Manage, 2022 Feb 03;308:114556.
    PMID: 35124308 DOI: 10.1016/j.jenvman.2022.114556
    Oilfield produced water (OPW) is one of the most important by-products, resulting from oil and gas exploration. The water contains a complex mixture of organic and inorganic compounds such as grease, dissolved salt, heavy metals as well as dissolved and dispersed oils, which can be toxic to the environment and public health. This article critically reviews the complex properties of OPW and various technologies for its treatment. They include the physico-chemical treatment process, biological treatment process, and physical treatment process. Their technological strengths and bottlenecks as well as strategies to mitigate their bottlenecks are elaborated. A particular focus is placed on membrane technologies. Finally, further research direction, challenges, and perspectives of treatment technologies for OPW are discussed. It is conclusively evident from 262 published studies (1965-2021) that no single treatment method is highly effective for OPW treatment as a stand-alone process however, conventional membrane-based technologies are frequently used for the treatment of OPW with the ultrafiltration (UF) process being the most used for oil rejection form OPW and oily waste water. After membrane treatment, treated effluents of the OPW could be reused for irrigation, habitant and wildlife watering, microalgae production, and livestock watering. Overall, this implies that target pollutants in the OPW samples could be removed efficiently for subsequent use, despite its complex properties. In general, it is however important to note that feed quality, desired quality of effluent, cost-effectiveness, simplicity of process are key determinants in choosing the most suitable treatment process for OPW treatment.
  3. Fulltext APOE, TOMM40, and sex interactions on neural network connectivity
    Li T, Pappas C, Le ST, Wang Q, Klinedinst BS, Larsen BA, et al.
    Neurobiol Aging, 2022 Jan;109:158-165.
    PMID: 34740077 DOI: 10.1016/j.neurobiolaging.2021.09.020
    The Apolipoprotein E ε4 (APOE ε4) haplotype is the strongest genetic risk factor for late-onset Alzheimer's disease (AD). The Translocase of Outer Mitochondrial Membrane-40 (TOMM40) gene maintains cellular bioenergetics, which is disrupted in AD. TOMM40 rs2075650 ('650) G versus A carriage is consistently related to neural and cognitive outcomes, but it is unclear if and how it interacts with APOE. We examined 21 orthogonal neural networks among 8,222 middle-aged to aged participants in the UK Biobank cohort. ANOVA and multiple linear regression tested main effects and interactions with APOE and TOMM40 '650 genotypes, and if age and sex acted as moderators. APOE ε4 was associated with less strength in multiple networks, while '650 G versus A carriage was related to more language comprehension network strength. In APOE ε4 carriers, '650 G-carriage led to less network strength with increasing age, while in non-G-carriers this was only seen in women but not men. TOMM40 may shift what happens to network activity in aging APOE ε4 carriers depending on sex.
  4. Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise
    Kim HL, Li T, Kalsi N, Nguyen HTT, Shaw TA, Ang KC, et al.
    Commun Biol, 2023 Feb 04;6(1):150.
    PMID: 36739308 DOI: 10.1038/s42003-023-04510-0
    Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500-14,000 years ago) and 1B (MWP1B, ~11,500-11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise.
  5. Sustainable Approach for the Synthesis of a Semicrystalline Polymer with a Reversible Shape-Memory Effect
    Wong JW, Yang X, Zhao Q, Xue Y, Lok TJ, Wang L, et al.
    ACS Macro Lett, 2023 Apr 13.
    PMID: 37052196 DOI: 10.1021/acsmacrolett.3c00017
    Shape-memory polymers (SMPs) have demonstrated potential for use in automotive, biomedical, and aerospace industries. However, ensuring the sustainability of these materials remains a challenge. Herein, a sustainable approach to synthesize a semicrystalline polymer using biomass-derivable precursors via catalyst-free polyesterification is presented. The synthesized biodegradable polymer, poly(1,8-octanediol-co-1,12-dodecanedioate-co-citrate) (PODDC), exhibits excellent shape-memory properties, as evidenced by good shape fixity and shape recovery ratios of 98%, along with a large reversible actuation strain of 28%. Without the use of a catalyst, the mild polymerization enables the reconfiguration of the partially cured two-dimensional (2D) film to a three-dimensional (3D) geometric form in the middle process. This study appears to be a step forward in developing sustainable SMPs and a simple way for constructing a 3D structure of a permanent shape.
  6. Intrinsic Permanent Shape Reconfigurable Semicrystalline Biopolyester Thermoset
    Chen X, Wong JW, Low JT, Lok TJ, Xue Y, Zeng Z, et al.
    ACS Macro Lett, 2024 Aug 20;13(8):1037-1042.
    PMID: 39078044 DOI: 10.1021/acsmacrolett.4c00266
    Catalyst-free, volatile organic solvent (VOC)-free synthesis of biobased cross-linked polymers is an important sustainable feature in polyesterification. To date, these polyesters have been extensively studied for their fundamental sustainability across various uses. The ultimate potential sustainability for these materials, however, is constrained to static structural parts due to their intractable rigid three-dimensional (3D) network. Here, we reveal intrinsic dynamic exchangeable bonds within this type of cross-linked semicrystalline network, poly(1,8-octanediol-co-1,12-docanedioate-co-citrate) (PODDC), enabling permanent shape reconfigurability. Annealing at slightly above melting-transition temperature (Tm) allows for shape reconfigurability up to nine times, comparable in performance to the existing bond-exchange systems. No reagents are involved from synthesis to shape reconfiguration, suggesting an exciting feature exhibited by this sustainable cross-linked material without the need for further chemical modification. We further extend this benefit of reconfigurability to enable flexible shape design in a smart shape-memory polymer (SMP), showing it as one of its potential applications. After its applications, it can undergo hydrolytic degradation. We envision that such multifaceted sustainability for the material will attract interest in environmentally friendly applications such as fabricating external part of soft robots and shape-morphing devices with reduced environmental impact.
  7. Fulltext Design of next-generation ceramic fuel cells and real-time characterization with synchrotron X-ray diffraction computed tomography
    Li T, Heenan TMM, Rabuni MF, Wang B, Farandos NM, Kelsall GH, et al.
    Nat Commun, 2019 04 02;10(1):1497.
    PMID: 30940801 DOI: 10.1038/s41467-019-09427-z
    Ceramic fuel cells offer a clean and efficient means of producing electricity through a variety of fuels. However, miniaturization of cell dimensions for portable device application remains a challenge, as volumetric power densities generated by readily-available planar/tubular ceramic cells are limited. Here, we demonstrate a concept of 'micro-monolithic' ceramic cell design. The mechanical robustness and structural integrity of this design is thoroughly investigated with real-time, synchrotron X-ray diffraction computed tomography, suggesting excellent thermal cycling stability. The successful miniaturization results in an exceptional power density of 1.27 W cm-2 at 800 °C, which is among the highest reported. This holistic design incorporates both mechanical integrity and electrochemical performance, leading to mechanical property enhancement and representing an important step toward commercial development of portable ceramic devices with high volumetric power (>10 W cm-3), fast thermal cycling and marked mechanical reliability.
  8. Bictegravir, emtricitabine, and tenofovir alafenamide versus dolutegravir, emtricitabine, and tenofovir disoproxil fumarate for initial treatment of HIV-1 and hepatitis B coinfection (ALLIANCE): a double-blind, multicentre, randomised controlled, phase 3 non-inferiority trial
    Avihingsanon A, Lu H, Leong CL, Hung CC, Koenig E, Kiertiburanakul S, et al.
    Lancet HIV, 2023 Oct;10(10):e640-e652.
    PMID: 37494942 DOI: 10.1016/S2352-3018(23)00151-0
    BACKGROUND: For most adults with HIV-1 and hepatitis B virus (HBV) coinfection, initial recommended treatment is a tenofovir-containing antiretroviral regimen, but no randomised studies have compared tenofovir disoproxil fumarate with tenofovir alafenamide. We aimed to investigate whether bictegravir, emtricitabine, and tenofovir alafenamide is non-inferior to dolutegravir, emtricitabine, and tenofovir disoproxil fumarate for viral suppression in individuals with HIV-1 and HBV coinfection at 48 and 96 weeks.

    METHODS: We did this randomised, double-blind, active-controlled, phase 3, non-inferiority trial at 46 outpatient centres in China, Dominican Republic, Hong Kong, Japan, Malaysia, South Korea, Spain, Taiwan, Thailand, Turkey, and the USA. Eligible participants were treatment-naive adults (aged ≥18 years) with plasma HIV-1 RNA of at least 500 copies per mL and plasma HBV DNA of at least 2000 IU/mL. Participants were randomly assigned (1:1) to receive daily oral bictegravir 50 mg, emtricitabine 200 mg, and tenofovir alafenamide 25 mg, or dolutegravir 50 mg, emtricitabine 200 mg, and tenofovir disoproxil fumarate 300 mg, each with corresponding matching placebo. Randomisation was stratified by hepatitis B e antigen (HBeAg) status (positive vs negative), HBV DNA (<8 vs ≥8 log10 IU/mL), and CD4 count (<50 vs ≥50 cells per μL) at screening. All investigators, participants, and staff providing treatment, assessing outcomes, and collecting data were masked to study treatment for 96 weeks. Coprimary endpoints were the proportion of participants with plasma HIV-1 RNA less than 50 copies per mL (defined by the US Food and Drug Administration snapshot algorithm) and plasma HBV DNA less than 29 IU/mL (using the missing-equals-failure approach) at week 48, with a prespecified non-inferiority margin of -12%. Coprimary endpoints were assessed in the full analysis set, which included all randomly assigned participants who received at least one dose of study drug and had at least one post-baseline HIV-1 RNA or HBV DNA result while on study drug. Safety endpoints were assessed in all randomly assigned participants who received at least one dose of study drug. This trial is registered with ClinicalTrials.gov, NCT03547908.

    FINDINGS: Between May 30, 2018 and March 16, 2021, 381 participants were screened, of whom 243 initiated treatment (121 in the receive bictegravir, emtricitabine, and tenofovir alafenamide group; 122 in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group). At week 48, both endpoints met the criteria for non-inferiority: 113 (95%) of 119 participants in the bictegravir, emtricitabine, and tenofovir alafenamide group and 111 (91%) of 122 participants in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group had HIV-1 RNA less than 50 copies per mL (difference 4·1, 95% CI -2·5 to 10·8; p=0·21), and 75 (63%) of 119 participants in the bictegravir, emtricitabine, and tenofovir alafenamide group versus 53 (43%) of 122 participants in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group had HBV DNA suppression (difference 16·6, 5·9 to 27·3; nominal p=0·0023). Drug-related adverse events up to week 96 occurred in 35 (29%) of 121 participants in the bictegravir, emtricitabine, and tenofovir alafenamide group and 34 (28%) of 122 participants in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group. One (1%) of 121 participants in the bictegravir, emtricitabine, and tenofovir alafenamide group reported a serious adverse event (cryptococcal meningitis attributed to immune reconstitution inflammatory syndrome) that was deemed to be treatment-related.

    INTERPRETATION: Coformulated bictegravir, emtricitabine, and tenofovir alafenamide is an effective therapy for adults with HIV-1 and HBV coinfection starting antiviral therapy.

    FUNDING: Gilead Sciences.

  9. Divergent accumulation of amino sugars and lignins mediated by soil functional carbon pools under tropical forest conversion
    Li T, Cheng H, Li Y, Mou Z, Zhu X, Wu W, et al.
    Sci Total Environ, 2023 Jul 10;881:163204.
    PMID: 37044342 DOI: 10.1016/j.scitotenv.2023.163204
    Tropical primary forests are being destroyed at an alarming rate and converted for other land uses which is expected to greatly influence soil carbon (C) cycling. However, our understanding of how tropical forest conversions affect the accumulation of compounds in soil functional C pools remains unclear. Here, we collected soils from primary forests (PF), secondary forests (SF), oil-palm (OP), and rubber plantations (RP), and assessed the accumulation of plant- and microbial-derived compounds within soil organic carbon (SOC), particulate (POC) and mineral-associated (MAOC) organic C. PF conversion to RP greatly decreased SOC, POC, and MAOC concentrations, whereas conversion to SF increased POC concentrations and decreased MAOC concentrations, and conversion to OP only increased POC concentrations. PF conversion to RP decreased lignin concentrations and increased amino sugar concentrations in SOC pools which increased the stability of SOC, whereas conversion to SF only increased the lignin concentrations in POC, and conversion to OP just increased lignin concentrations in POC and decreased it in MAOC. We observed divergent dynamics of amino sugars (decrease) and lignin (increase) in SOC with increasing SOC. Only lignin concentrations increased in POC with increasing POC and amino sugars concentrations decreased in MAOC with increasing MAOC. Conversion to RP significantly decreased soil enzyme activities and microbial biomasses. Lignin accumulation was associated with microbial properties, whereas amino sugar accumulation was mainly associated with soil nutrients and stoichiometries. These results suggest that the divergent accumulation of plant- and microbial-derived C in SOC was delivered by the distribution and original composition of functional C pools under forest conversions. Forest conversions changed the formation and stabilization processes of SOC in the long run which was associated with converted plantations and management. The important roles of soil nutrients and stoichiometry also provide a natural-based solution to enhance SOC sequestration via nutrient management in tropical forests.
  10. Fulltext Bioinspired soft robots for deep-sea exploration
    Li G, Wong TW, Shih B, Guo C, Wang L, Liu J, et al.
    Nat Commun, 2023 Nov 04;14(1):7097.
    PMID: 37925504 DOI: 10.1038/s41467-023-42882-3
    The deep ocean, Earth's untouched expanse, presents immense challenges for exploration due to its extreme pressure, temperature, and darkness. Unlike traditional marine robots that require specialized metallic vessels for protection, deep-sea species thrive without such cumbersome pressure-resistant designs. Their pressure-adaptive forms, unique propulsion methods, and advanced senses have inspired innovation in designing lightweight, compact soft machines. This perspective addresses challenges, recent strides, and design strategies for bioinspired deep-sea soft robots. Drawing from abyssal life, it explores the actuation, sensing, power, and pressure resilience of multifunctional deep-sea soft robots, offering game-changing solutions for profound exploration and operation in harsh conditions.
  11. Fulltext The Tsinghua-Lancet Commission on Healthy Cities in China: unlocking the power of cities for a healthy China
    Yang J, Siri JG, Remais JV, Cheng Q, Zhang H, Chan KKY, et al.
    Lancet, 2018 05 26;391(10135):2140-2184.
    PMID: 29678340 DOI: 10.1016/S0140-6736(18)30486-0
  12. Fulltext Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis
    Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, et al.
    Nat Genet, 2022 Nov;54(11):1640-1651.
    PMID: 36333501 DOI: 10.1038/s41588-022-01213-w
    Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P 
  13. Integrated image-based deep learning and language models for primary diabetes care
    Li J, Guan Z, Wang J, Cheung CY, Zheng Y, Lim LL, et al.
    Nat Med, 2024 Jul 19.
    PMID: 39030266 DOI: 10.1038/s41591-024-03139-8
    Primary diabetes care and diabetic retinopathy (DR) screening persist as major public health challenges due to a shortage of trained primary care physicians (PCPs), particularly in low-resource settings. Here, to bridge the gaps, we developed an integrated image-language system (DeepDR-LLM), combining a large language model (LLM module) and image-based deep learning (DeepDR-Transformer), to provide individualized diabetes management recommendations to PCPs. In a retrospective evaluation, the LLM module demonstrated comparable performance to PCPs and endocrinology residents when tested in English and outperformed PCPs and had comparable performance to endocrinology residents in Chinese. For identifying referable DR, the average PCP's accuracy was 81.0% unassisted and 92.3% assisted by DeepDR-Transformer. Furthermore, we performed a single-center real-world prospective study, deploying DeepDR-LLM. We compared diabetes management adherence of patients under the unassisted PCP arm (n = 397) with those under the PCP+DeepDR-LLM arm (n = 372). Patients with newly diagnosed diabetes in the PCP+DeepDR-LLM arm showed better self-management behaviors throughout follow-up (P 
  14. Evidence for the Higgs Boson Decay to a Z Boson and a Photon at the LHC
    Aad G, Abbott B, Abeling K, Abicht NJ, Abidi SH, Aboulhorma A, et al.
    Phys Rev Lett, 2024 Jan 12;132(2):021803.
    PMID: 38277607 DOI: 10.1103/PhysRevLett.132.021803
    The first evidence for the Higgs boson decay to a Z boson and a photon is presented, with a statistical significance of 3.4 standard deviations. The result is derived from a combined analysis of the searches performed by the ATLAS and CMS Collaborations with proton-proton collision datasets collected at the CERN Large Hadron Collider (LHC) from 2015 to 2018. These correspond to integrated luminosities of around 140  fb^{-1} for each experiment, at a center-of-mass energy of 13 TeV. The measured signal yield is 2.2±0.7 times the standard model prediction, and agrees with the theoretical expectation within 1.9 standard deviations.
  15. Combination of Measurements of the Top Quark Mass from Data Collected by the ATLAS and CMS Experiments at sqrt[s]=7 and 8 TeV
    Hayrapetyan A, Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, et al.
    Phys Rev Lett, 2024 Jun 28;132(26):261902.
    PMID: 38996325 DOI: 10.1103/PhysRevLett.132.261902
    A combination of fifteen top quark mass measurements performed by the ATLAS and CMS experiments at the LHC is presented. The datasets used correspond to an integrated luminosity of up to 5 and 20  fb^{-1} of proton-proton collisions at center-of-mass energies of 7 and 8 TeV, respectively. The combination includes measurements in top quark pair events that exploit both the semileptonic and hadronic decays of the top quark, and a measurement using events enriched in single top quark production via the electroweak t channel. The combination accounts for the correlations between measurements and achieves an improvement in the total uncertainty of 31% relative to the most precise input measurement. The result is m_{t}=172.52±0.14(stat)±0.30(syst)  GeV, with a total uncertainty of 0.33 GeV.
  16. Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1
    Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
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