Displaying publications 21 - 40 of 112 in total

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  1. Ooi JD, Jiang JH, Eggenhuizen PJ, Chua LL, van Timmeren M, Loh KL, et al.
    Nat Commun, 2019 07 29;10(1):3392.
    PMID: 31358739 DOI: 10.1038/s41467-019-11255-0
    Autoreactivity to myeloperoxidase (MPO) causes anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), with rapidly progressive glomerulonephritis. Here, we show that a Staphylococcus aureus peptide, homologous to an immunodominant MPO T-cell epitope (MPO409-428), can induce anti-MPO autoimmunity. The peptide (6PGD391-410) is part of a plasmid-encoded 6-phosphogluconate dehydrogenase found in some S. aureus strains. It induces anti-MPO T-cell autoimmunity and MPO-ANCA in mice, whereas related sequences do not. Mice immunized with 6PGD391-410, or with S. aureus containing a plasmid expressing 6PGD391-410, develop glomerulonephritis when MPO is deposited in glomeruli. The peptide induces anti-MPO autoreactivity in the context of three MHC class II allomorphs. Furthermore, we show that 6PGD391-410 is immunogenic in humans, as healthy human and AAV patient sera contain anti-6PGD and anti-6PGD391-410 antibodies. Therefore, our results support the idea that bacterial plasmids might have a function in autoimmune disease.
  2. Serrano O, Lovelock CE, B Atwood T, Macreadie PI, Canto R, Phinn S, et al.
    Nat Commun, 2019 10 02;10(1):4313.
    PMID: 31575872 DOI: 10.1038/s41467-019-12176-8
    Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservation and restoration. Australia contributes 5-11% of the C stored in VCE globally (70-185 Tg C in aboveground biomass, and 1,055-1,540 Tg C in the upper 1 m of soils). Potential CO2 emissions from current VCE losses are estimated at 2.1-3.1 Tg CO2-e yr-1, increasing annual CO2 emissions from land use change in Australia by 12-21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions.
  3. Nunes MH, Jucker T, Riutta T, Svátek M, Kvasnica J, Rejžek M, et al.
    Nat Commun, 2021 03 09;12(1):1526.
    PMID: 33750781 DOI: 10.1038/s41467-020-20811-y
    The past 40 years in Southeast Asia have seen about 50% of lowland rainforests converted to oil palm and other plantations, and much of the remaining forest heavily logged. Little is known about how fragmentation influences recovery and whether climate change will hamper restoration. Here, we use repeat airborne LiDAR surveys spanning the hot and dry 2015-16 El Niño Southern Oscillation event to measure canopy height growth across 3,300 ha of regenerating tropical forests spanning a logging intensity gradient in Malaysian Borneo. We show that the drought led to increased leaf shedding and branch fall. Short forest, regenerating after heavy logging, continued to grow despite higher evaporative demand, except when it was located close to oil palm plantations. Edge effects from the plantations extended over 300 metres into the forests. Forest growth on hilltops and slopes was particularly impacted by the combination of fragmentation and drought, but even riparian forests located within 40 m of oil palm plantations lost canopy height during the drought. Our results suggest that small patches of logged forest within plantation landscapes will be slow to recover, particularly as ENSO events are becoming more frequent.
  4. Zhang XC, Wang J, Shao GG, Wang Q, Qu X, Wang B, et al.
    Nat Commun, 2019 04 16;10(1):1772.
    PMID: 30992440 DOI: 10.1038/s41467-019-09762-1
    Deep understanding of the genomic and immunological differences between Chinese and Western lung cancer patients is of great importance for target therapy selection and development for Chinese patients. Here we report an extensive molecular and immune profiling study of 245 Chinese patients with non-small cell lung cancer. Tumor-infiltrating lymphocyte estimated using immune cell signatures is found to be significantly higher in adenocarcinoma (ADC, 72.5%) compared with squamous cell carcinoma (SQCC, 54.4%). The correlation of genomic alterations with immune signatures reveals that low immune infiltration was associated with EGFR mutations in ADC samples, PI3K and/or WNT pathway activation in SQCC. While KRAS mutations are found to be significantly associated with T cell infiltration in ADC samples. The SQCC patients with high antigen presentation machinery and cytotoxic T cell signature scores are found to have a prolonged overall survival time.
  5. Lin R, Hu E, Liu M, Wang Y, Cheng H, Wu J, et al.
    Nat Commun, 2019 04 09;10(1):1650.
    PMID: 30967531 DOI: 10.1038/s41467-019-09248-0
    Despite the importance of studying the instability of delithiated cathode materials, it remains difficult to underpin the degradation mechanism of lithium-rich cathode materials due to the complication of combined chemical and structural evolutions. Herein, we use state-of-the-art electron microscopy tools, in conjunction with synchrotron X-ray techniques and first-principle calculations to study a 4d-element-containing compound, Li2Ru0.5Mn0.5O3. We find surprisingly, after cycling, ruthenium segregates out as metallic nanoclusters on the reconstructed surface. Our calculations show that the unexpected ruthenium metal segregation is due to its thermodynamic insolubility in the oxygen deprived surface. This insolubility can disrupt the reconstructed surface, which explains the formation of a porous structure in this material. This work reveals the importance of studying the thermodynamic stability of the reconstructed film on the cathode materials and offers a theoretical guidance for choosing manganese substituting elements in lithium-rich as well as stoichiometric layer-layer compounds for stabilizing the cathode surface.
  6. Chang KY, Riley WJ, Knox SH, Jackson RB, McNicol G, Poulter B, et al.
    Nat Commun, 2021 04 15;12(1):2266.
    PMID: 33859182 DOI: 10.1038/s41467-021-22452-1
    Wetland methane (CH4) emissions ([Formula: see text]) are important in global carbon budgets and climate change assessments. Currently, [Formula: see text] projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent [Formula: see text] temperature dependence across spatial scales for use in models; however, site-level studies demonstrate that [Formula: see text] are often controlled by factors beyond temperature. Here, we evaluate the relationship between [Formula: see text] and temperature using observations from the FLUXNET-CH4 database. Measurements collected across the globe show substantial seasonal hysteresis between [Formula: see text] and temperature, suggesting larger [Formula: see text] sensitivity to temperature later in the frost-free season (about 77% of site-years). Results derived from a machine-learning model and several regression models highlight the importance of representing the large spatial and temporal variability within site-years and ecosystem types. Mechanistic advancements in biogeochemical model parameterization and detailed measurements in factors modulating CH4 production are thus needed to improve global CH4 budget assessments.
  7. Martin D, Degese MS, Vitale-Cross L, Iglesias-Bartolome R, Valera JLC, Wang Z, et al.
    Nat Commun, 2018 07 09;9(1):2372.
    PMID: 29985391 DOI: 10.1038/s41467-018-04590-1
    Dysregulation of the Hippo signaling pathway and the consequent YAP1 activation is a frequent event in human malignancies, yet the underlying molecular mechanisms are still poorly understood. A pancancer analysis of core Hippo kinases and their candidate regulating molecules revealed few alterations in the canonical Hippo pathway, but very frequent genetic alterations in the FAT family of atypical cadherins. By focusing on head and neck squamous cell carcinoma (HNSCC), which displays frequent FAT1 alterations (29.8%), we provide evidence that FAT1 functional loss results in YAP1 activation. Mechanistically, we found that FAT1 assembles a multimeric Hippo signaling complex (signalome), resulting in activation of core Hippo kinases by TAOKs and consequent YAP1 inactivation. We also show that unrestrained YAP1 acts as an oncogenic driver in HNSCC, and that targeting YAP1 may represent an attractive precision therapeutic option for cancers harboring genomic alterations in the FAT1 tumor suppressor genes.
  8. Shen X, Howard DM, Adams MJ, Hill WD, Clarke TK, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, et al.
    Nat Commun, 2020 05 08;11(1):2301.
    PMID: 32385265 DOI: 10.1038/s41467-020-16022-0
    Depression is a leading cause of worldwide disability but there remains considerable uncertainty regarding its neural and behavioural associations. Here, using non-overlapping Psychiatric Genomics Consortium (PGC) datasets as a reference, we estimate polygenic risk scores for depression (depression-PRS) in a discovery (N = 10,674) and replication (N = 11,214) imaging sample from UK Biobank. We report 77 traits that are significantly associated with depression-PRS, in both discovery and replication analyses. Mendelian Randomisation analysis supports a potential causal effect of liability to depression on brain white matter microstructure (β: 0.125 to 0.868, pFDR 
  9. Wu WY, Lo MH, Wada Y, Famiglietti JS, Reager JT, Yeh PJ, et al.
    Nat Commun, 2020 07 24;11(1):3710.
    PMID: 32709871 DOI: 10.1038/s41467-020-17581-y
    Groundwater provides critical freshwater supply, particularly in dry regions where surface water availability is limited. Climate change impacts on GWS (groundwater storage) could affect the sustainability of freshwater resources. Here, we used a fully-coupled climate model to investigate GWS changes over seven critical aquifers identified as significantly distressed by satellite observations. We assessed the potential climate-driven impacts on GWS changes throughout the 21st century under the business-as-usual scenario (RCP8.5). Results show that the climate-driven impacts on GWS changes do not necessarily reflect the long-term trend in precipitation; instead, the trend may result from enhancement of evapotranspiration, and reduction in snowmelt, which collectively lead to divergent responses of GWS changes across different aquifers. Finally, we compare the climate-driven and anthropogenic pumping impacts. The reduction in GWS is mainly due to the combined impacts of over-pumping and climate effects; however, the contribution of pumping could easily far exceed the natural replenishment.
  10. Roberts LW, Harris PNA, Forde BM, Ben Zakour NL, Catchpoole E, Stanton-Cook M, et al.
    Nat Commun, 2020 01 24;11(1):466.
    PMID: 31980604 DOI: 10.1038/s41467-019-14139-5
    Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.
  11. Cooper HV, Evers S, Aplin P, Crout N, Dahalan MPB, Sjogersten S
    Nat Commun, 2020 01 21;11(1):407.
    PMID: 31964892 DOI: 10.1038/s41467-020-14298-w
    Conversion of tropical peat swamp forest to drainage-based agriculture alters greenhouse gas (GHG) production, but the magnitude of these changes remains highly uncertain. Current emissions factors for oil palm grown on drained peat do not account for temporal variation over the plantation cycle and only consider CO2 emissions. Here, we present direct measurements of GHGs emitted during the conversion from peat swamp forest to oil palm plantation, accounting for CH4 and N2O as well as CO2. Our results demonstrate that emissions factors for converted peat swamp forest is in the range 70-117 t CO2 eq ha-1 yr-1 (95% confidence interval, CI), with CO2 and N2O responsible for ca. 60 and ca. 40% of this value, respectively. These GHG emissions suggest that conversion of Southeast Asian peat swamp forest is contributing between 16.6 and 27.9% (95% CI) of combined total national GHG emissions from Malaysia and Indonesia or 0.44 and 0.74% (95% CI) of annual global emissions.
  12. Eriksson K, Strimling P, Gelfand M, Wu J, Abernathy J, Akotia CS, et al.
    Nat Commun, 2021 Apr 26;12(1):2483.
    PMID: 33903599 DOI: 10.1038/s41467-021-22955-x
  13. Brodie Rudolph T, Ruckelshaus M, Swilling M, Allison EH, Österblom H, Gelcich S, et al.
    Nat Commun, 2020 07 17;11(1):3600.
    PMID: 32681109 DOI: 10.1038/s41467-020-17410-2
    Human wellbeing relies on the Biosphere, including natural resources provided by ocean ecosystems. As multiple demands and stressors threaten the ocean, transformative change in ocean governance is required to maintain the contributions of the ocean to people. Here we illustrate how transition theory can be applied to ocean governance. We demonstrate how current economic and social systems can adapt to existing pressures and shift towards ocean stewardship through incorporation of niche innovations within and across economic sectors and stakeholder communities. These novel approaches support an emergent but purposeful transition and suggest a clear path to a thriving and vibrant relationship between humans and the ocean. Oceans provide important natural resources, but the management and governance of the ocean is complex and the ecosystem is suffering as a result. The authors discuss current barriers to sustainable ocean governance and suggest pathways forward.
  14. Bruce JP, To KF, Lui VWY, Chung GTY, Chan YY, Tsang CM, et al.
    Nat Commun, 2021 07 07;12(1):4193.
    PMID: 34234122 DOI: 10.1038/s41467-021-24348-6
    Interplay between EBV infection and acquired genetic alterations during nasopharyngeal carcinoma (NPC) development remains vague. Here we report a comprehensive genomic analysis of 70 NPCs, combining whole-genome sequencing (WGS) of microdissected tumor cells with EBV oncogene expression to reveal multiple aspects of cellular-viral co-operation in tumorigenesis. Genomic aberrations along with EBV-encoded LMP1 expression underpin constitutive NF-κB activation in 90% of NPCs. A similar spectrum of somatic aberrations and viral gene expression undermine innate immunity in 79% of cases and adaptive immunity in 47% of cases; mechanisms by which NPC may evade immune surveillance despite its pro-inflammatory phenotype. Additionally, genomic changes impairing TGFBR2 promote oncogenesis and stabilize EBV infection in tumor cells. Fine-mapping of CDKN2A/CDKN2B deletion breakpoints reveals homozygous MTAP deletions in 32-34% of NPCs that confer marked sensitivity to MAT2A inhibition. Our work concludes that NPC is a homogeneously NF-κB-driven and immune-protected, yet potentially druggable, cancer.
  15. Ho WK, Tan MM, Mavaddat N, Tai MC, Mariapun S, Li J, et al.
    Nat Commun, 2020 07 31;11(1):3833.
    PMID: 32737321 DOI: 10.1038/s41467-020-17680-w
    Polygenic risk scores (PRS) have been shown to predict breast cancer risk in European women, but their utility in Asian women is unclear. Here we evaluate the best performing PRSs for European-ancestry women using data from 17,262 breast cancer cases and 17,695 controls of Asian ancestry from 13 case-control studies, and 10,255 Chinese women from a prospective cohort (413 incident breast cancers). Compared to women in the middle quintile of the risk distribution, women in the highest 1% of PRS distribution have a ~2.7-fold risk and women in the lowest 1% of PRS distribution has ~0.4-fold risk of developing breast cancer. There is no evidence of heterogeneity in PRS performance in Chinese, Malay and Indian women. A PRS developed for European-ancestry women is also predictive of breast cancer risk in Asian women and can help in developing risk-stratified screening programmes in Asia.
  16. Hannan MA, Ali JA, Hossain Lipu MS, Mohamed A, Ker PJ, Indra Mahlia TM, et al.
    Nat Commun, 2020 Jul 30;11(1):3792.
    PMID: 32733048 DOI: 10.1038/s41467-020-17623-5
    Three-phase induction motors (TIMs) are widely used for machines in industrial operations. As an accurate and robust controller, fuzzy logic controller (FLC) is crucial in designing TIMs control systems. The performance of FLC highly depends on the membership function (MF) variables, which are evaluated by heuristic approaches, leading to a high processing time. To address these issues, optimisation algorithms for TIMs have received increasing interest among researchers and industrialists. Here, we present an advanced and efficient quantum-inspired lightning search algorithm (QLSA) to avoid exhaustive conventional heuristic procedures when obtaining MFs. The accuracy of the QLSA based FLC (QLSAF) speed control is superior to other controllers in terms of transient response, damping capability and minimisation of statistical errors under diverse speeds and loads. The performance of the proposed QLSAF speed controller is validated through experiments. Test results under different conditions show consistent speed responses and stator currents with the simulation results.
  17. Eriksson K, Strimling P, Gelfand M, Wu J, Abernathy J, Akotia CS, et al.
    Nat Commun, 2021 03 05;12(1):1481.
    PMID: 33674587 DOI: 10.1038/s41467-021-21602-9
    Norm enforcement may be important for resolving conflicts and promoting cooperation. However, little is known about how preferred responses to norm violations vary across cultures and across domains. In a preregistered study of 57 countries (using convenience samples of 22,863 students and non-students), we measured perceptions of the appropriateness of various responses to a violation of a cooperative norm and to atypical social behaviors. Our findings highlight both cultural universals and cultural variation. We find a universal negative relation between appropriateness ratings of norm violations and appropriateness ratings of responses in the form of confrontation, social ostracism and gossip. Moreover, we find the country variation in the appropriateness of sanctions to be consistent across different norm violations but not across different sanctions. Specifically, in those countries where use of physical confrontation and social ostracism is rated as less appropriate, gossip is rated as more appropriate.
  18. Maina MB, Ahmad U, Ibrahim HA, Hamidu SK, Nasr FE, Salihu AT, et al.
    Nat Commun, 2021 06 08;12(1):3429.
    PMID: 34103514 DOI: 10.1038/s41467-021-23784-8
    Neuroscience research in Africa remains sparse. Devising new policies to boost Africa's neuroscience landscape is imperative, but these must be based on accurate data on research outputs which is largely lacking. Such data must reflect the heterogeneity of research environments across the continent's 54 countries. Here, we analyse neuroscience publications affiliated with African institutions between 1996 and 2017. Of 12,326 PubMed indexed publications, 5,219 show clear evidence that the work was performed in Africa and led by African-based researchers - on average ~5 per country and year. From here, we extract information on journals and citations, funding, international coauthorships and techniques used. For reference, we also extract the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our dataset provides insights into the current state of African neuroscience research in a global context.
  19. Dobrovolskiy OV, Vodolazov DY, Porrati F, Sachser R, Bevz VM, Mikhailov MY, et al.
    Nat Commun, 2020 Jul 03;11(1):3291.
    PMID: 32620789 DOI: 10.1038/s41467-020-16987-y
    The ultra-fast dynamics of superconducting vortices harbors rich physics generic to nonequilibrium collective systems. The phenomenon of flux-flow instability (FFI), however, prevents its exploration and sets practical limits for the use of vortices in various applications. To suppress the FFI, a superconductor should exhibit a rarely achieved combination of properties: weak volume pinning, close-to-depairing critical current, and fast heat removal from heated electrons. Here, we demonstrate experimentally ultra-fast vortex motion at velocities of 10-15 km s-1 in a directly written Nb-C superconductor with a close-to-perfect edge barrier. The spatial evolution of the FFI is described using the edge-controlled FFI model, implying a chain of FFI nucleation points along the sample edge and their development into self-organized Josephson-like junctions (vortex rivers). In addition, our results offer insights into the applicability of widely used FFI models and suggest Nb-C to be a good candidate material for fast single-photon detectors.
  20. Lawrenson K, Li Q, Kar S, Seo JH, Tyrer J, Spindler TJ, et al.
    Nat Commun, 2015 Sep 22;6:8234.
    PMID: 26391404 DOI: 10.1038/ncomms9234
    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10(-5)). For three cis-eQTL associations (P<1.4 × 10(-3), FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10(-10) for risk variants (P<10(-4)) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.
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