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  1. Fulltext Rates and drivers of mangrove deforestation in Southeast Asia, 2000-2012
    Richards DR, Friess DA
    Proc Natl Acad Sci U S A, 2016 Jan 12;113(2):344-9.
    PMID: 26712025 DOI: 10.1073/pnas.1510272113
    The mangrove forests of Southeast Asia are highly biodiverse and provide multiple ecosystem services upon which millions of people depend. Mangroves enhance fisheries and coastal protection, and store among the highest densities of carbon of any ecosystem globally. Mangrove forests have experienced extensive deforestation owing to global demand for commodities, and previous studies have identified the expansion of aquaculture as largely responsible. The proportional conversion of mangroves to different land use types has not been systematically quantified across Southeast Asia, however, particularly in recent years. In this study we apply a combined geographic information system and remote sensing method to quantify the key proximate drivers (i.e., replacement land uses) of mangrove deforestation in Southeast Asia between 2000 and 2012. Mangrove forests were lost at an average rate of 0.18% per year, which is lower than previously published estimates. In total, more than 100,000 ha of mangroves were removed during the study period, with aquaculture accounting for 30% of this total forest change. The rapid expansion of rice agriculture in Myanmar, and the sustained conversion of mangroves to oil palm plantations in Malaysia and Indonesia, are identified as additional increasing and under-recognized threats to mangrove ecosystems. Our study highlights frontiers of mangrove deforestation in the border states of Myanmar, on Borneo, and in Indonesian Papua. To implement policies that conserve mangrove forests across Southeast Asia, it is essential to consider the national and subnational variation in the land uses that follow deforestation.
  2. Difficulty levels of extracted human teeth used for pre-clinical training in endodontics in an Australian dental school
    Decurcio DA, Lim E, Nagendrababu V, Estrela C, Rossi-Fedele G
    Aust Endod J, 2020 Apr;46(1):47-51.
    PMID: 31267618 DOI: 10.1111/aej.12355
    This study aimed to determine the difficulty level of extracted teeth treated by undergraduate students for pre-clinical endodontic training. Two independent observers assessed a consecutive sample of 1000 periapical radiographs of extracted teeth used in endodontic pre-clinical training. Chi-square test was used to evaluate the adjustment of the distribution, and inter- and intra-examiner agreement were calculated. Minimal, moderate and high difficulty teeth represented 23.1%, 52.1% and 24.8%, respectively. The presence of curvature was the most common grading factor, with 'moderate curvature' reported in 28.7%, and 'extreme curvature' reported in 15.6% of the sample. A difference in the distribution of frequencies was found, favouring the moderate category (P 
  3. Machine-assisted Agitation Reduces Postoperative Pain during Root Canal Treatment: A Systematic Review and Meta-analysis from Randomized Clinical Trials
    Decurcio DA, Rossi-Fedele G, Estrela C, Pulikkotil SJ, Nagendrababu V
    J Endod, 2019 Apr;45(4):387-393.e2.
    PMID: 30833095 DOI: 10.1016/j.joen.2019.01.013
    INTRODUCTION: This systematic review and meta-analysis aimed to assess whether machine-assisted agitation resulted in less postoperative pain (PP) compared with syringe irrigation with needle alone in adult patients undergoing root canal treatment.

    METHODS: A literature search was performed in 3 electronic databases for articles published before August 2018. Randomized clinical trials published in English that compared PP between machine-assisted agitation and syringe irrigation with needles as part of nonsurgical root canal treatment were included. Two authors were independently involved in the article selection process, data extraction, and assessment of the quality of included studies using the revised Cochrane risk of bias tool. The pooled effect estimates of the standardized mean difference (SMD) between machine-assisted agitation and syringe irrigation with needle was calculated by a random effects-modeled meta-analysis. A subgroup meta-analysis was performed. The quality of evidence was evaluated by the Grading of Recommendations, Assessment, Development and Evaluations approach.

    RESULTS: Six studies were included for systematic review. Meta-analysis was performed using 3 studies and showed that machine-assisted agitation resulted in less PP compared with syringe irrigation with needle at 24 hours (SMD = -0.73; 95% confidence interval, -1.04 to -0.42; I2 = 30.6%) and 48 hours (SMD = -0.60; 95% CI, -0.85 to -0.35; I2 = 0%). The quality of evidence by Grading of Recommendations, Assessment, Development and Evaluations for the PP outcomes (24 hours and 48 hours) was graded as "moderate" quality.

    CONCLUSIONS: Machine-assisted agitation reduced PP compared with syringe irrigation with needles in nonsurgical root canal treatment. Future clinical trials are needed to support the result of this review.

  4. Policy challenges and approaches for the conservation of mangrove forests in Southeast Asia
    Friess DA, Thompson BS, Brown B, Amir AA, Cameron C, Koldewey HJ, et al.
    Conserv Biol, 2016 10;30(5):933-49.
    PMID: 27341487 DOI: 10.1111/cobi.12784
    Many drivers of mangrove forest loss operate over large scales and are most effectively addressed by policy interventions. However, conflicting or unclear policy objectives exist at multiple tiers of government, resulting in contradictory management decisions. To address this, we considered four approaches that are being used increasingly or could be deployed in Southeast Asia to ensure sustainable livelihoods and biodiversity conservation. First, a stronger incorporation of mangroves into marine protected areas (that currently focus largely on reefs and fisheries) could resolve some policy conflicts and ensure that mangroves do not fall through a policy gap. Second, examples of community and government comanagement exist, but achieving comanagement at scale will be important in reconciling stakeholders and addressing conflicting policy objectives. Third, private-sector initiatives could protect mangroves through existing and novel mechanisms in degraded areas and areas under future threat. Finally, payments for ecosystem services (PES) hold great promise for mangrove conservation, with carbon PES schemes (known as blue carbon) attracting attention. Although barriers remain to the implementation of PES, the potential to implement them at multiple scales exists. Closing the gap between mangrove conservation policies and action is crucial to the improved protection and management of this imperiled coastal ecosystem and to the livelihoods that depend on them.
  5. Lipopolysaccharide reduces gonadotrophin-releasing hormone (GnRH) gene expression: role of RFamide-related peptide-3 and kisspeptin
    Lee CY, Li S, Li XF, Stalker DAE, Cooke C, Shao B, et al.
    Reprod Fertil Dev, 2019 May;31(6):1134-1143.
    PMID: 30922440 DOI: 10.1071/RD18277
    RFamide-related peptide (RFRP)-3 reduces luteinising hormone (LH) secretion in rodents. Stress has been shown to upregulate the expression of the RFRP gene (Rfrp) with a concomitant reduction in LH secretion, but an effect on expression of the gonadotrophin-releasing hormone (GnRH) gene (Gnrh1) has not been shown. We hypothesised that lipopolysaccharide (LPS)-induced stress affects expression of Rfrp, the gene for kisspeptin (Kiss1) and/or Gnrh1, leading to suppression of LH levels in rats. Intracerebroventricular injections of RFRP-3 (0.1, 1, 5 nmol) or i.v. LPS (15μgkg-1) reduced LH levels. Doses of 1 and 5 nmol RFRP-3 were then administered to analyse gene expression by in situ hybridisation. RFRP-3 (5 nmol) had no effect on Gnrh1 or Kiss1 expression. LPS stress reduced GnRH and Kiss1 expression, without affecting Rfrp1 expression. These data indicate that LPS stress directly or indirectly reduces Gnrh1 expression, but this is unlikely to be due to a change in Rfrp1 expression.
  6. The value of small mangrove patches
    Curnick DJ, Pettorelli N, Amir AA, Balke T, Barbier EB, Crooks S, et al.
    Science, 2019 01 18;363(6424):239.
    PMID: 30655434 DOI: 10.1126/science.aaw0809
  7. Fulltext A Novel International Partnership for Actionable Evidence on Urban Health in Latin America: LAC-Urban Health and SALURBAL
    Diez Roux AV, Slesinski SC, Alazraqui M, Caiaffa WT, Frenz P, Jordán Fuchs R, et al.
    Glob Chall, 2019 Apr;3(4):1800013.
    PMID: 31565372 DOI: 10.1002/gch2.201800013
    This article describes the origins and characteristics of an interdisciplinary multinational collaboration aimed at promoting and disseminating actionable evidence on the drivers of health in cities in Latin America and the Caribbean: The Network for Urban Health in Latin America and the Caribbean and the Wellcome Trust funded SALURBAL (Salud Urbana en América Latina, or Urban Health in Latin America) Project. Both initiatives have the goals of supporting urban policies that promote health and health equity in cities of the region while at the same time generating generalizable knowledge for urban areas across the globe. The processes, challenges, as well as the lessons learned to date in launching and implementing these collaborations, are described. By leveraging the unique features of the Latin American region (one of the most urbanized areas of the world with some of the most innovative urban policies), the aim is to produce generalizable knowledge about the links between urbanization, health, and environments and to identify effective ways to organize, design, and govern cities to improve health, reduce health inequalities, and maximize environmental sustainability in cities all over the world.
  8. Fulltext Silver nanoparticles reduce brain inflammation and related neurotoxicity through induction of H2S-synthesizing enzymes
    Gonzalez-Carter DA, Leo BF, Ruenraroengsak P, Chen S, Goode AE, Theodorou IG, et al.
    Sci Rep, 2017 03 02;7:42871.
    PMID: 28251989 DOI: 10.1038/srep42871
    Silver nanoparticles (AgNP) are known to penetrate into the brain and cause neuronal death. However, there is a paucity in studies examining the effect of AgNP on the resident immune cells of the brain, microglia. Given microglia are implicated in neurodegenerative disorders such as Parkinson's disease (PD), it is important to examine how AgNPs affect microglial inflammation to fully assess AgNP neurotoxicity. In addition, understanding AgNP processing by microglia will allow better prediction of their long term bioreactivity. In the present study, the in vitro uptake and intracellular transformation of citrate-capped AgNPs by microglia, as well as their effects on microglial inflammation and related neurotoxicity were examined. Analytical microscopy demonstrated internalization and dissolution of AgNPs within microglia and formation of non-reactive silver sulphide (Ag2S) on the surface of AgNPs. Furthermore, AgNP-treatment up-regulated microglial expression of the hydrogen sulphide (H2S)-synthesizing enzyme cystathionine-γ-lyase (CSE). In addition, AgNPs showed significant anti-inflammatory effects, reducing lipopolysaccharide (LPS)-stimulated ROS, nitric oxide and TNFα production, which translated into reduced microglial toxicity towards dopaminergic neurons. Hence, the present results indicate that intracellular Ag2S formation, resulting from CSE-mediated H2S production in microglia, sequesters Ag+ ions released from AgNPs, significantly limiting their toxicity, concomitantly reducing microglial inflammation and related neurotoxicity.
  9. Fulltext Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins
    Vale FF, Nunes A, Oleastro M, Gomes JP, Sampaio DA, Rocha R, et al.
    Sci Rep, 2017 02 16;7:42471.
    PMID: 28205536 DOI: 10.1038/srep42471
    Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3' end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.
  10. Phytochemical analysis and antioxidant activity of the seed of Telfairia occidentalis Hook (Cucurbitaceae)
    Eseyin OA, Daniel A, Paul TS, Attih E, Emmanuel E, Ekarika J, et al.
    Nat Prod Res, 2018 Feb;32(4):444-447.
    PMID: 28361553 DOI: 10.1080/14786419.2017.1308366
    The 2,2-diphenyl-1-picryl hydrazyl (DPPH) radical, nitric oxide, reducing power, hydrogen peroxide scavenging, and total antioxidant activities of the methanol extract, n-hexane, dichloromethane, ethyl acetate, butanol and aqueous fractions of the seed of Telfairia occidentalis were evaluated. Total phenolic content was determined using the Folin-Ciocalteu method. The dichloromethane fraction exhibited the highest DPPH radical scavenging, reducing power and total antioxidant activities. Two pure compounds which were identified by FTIR, H-and 2D NMR and Mass spectroscopy as 9-octadecenoic acid (TOS B) and 10-hydroxyoctadecanoic acid (TOS C) and four oily isolates, TOS A, TOS D, TOS E and TOS F were obtained from the dichloromethane fraction. TOS E had the highest DPPH radical scavening activity comparable to that of ascorbic acid. GC-MS analysis revealed the major compounds in TOS E as 4-(2,2-Dimethyl-6-methylene cyclohexylidene)-2-butanol; 3-(3-hydroxybutyl)-2,4,4-trimethyl-2-cyclohexene-1-one and 1,2-Benzenedicarboxylic acid disooctyl ester. Thus, the seed of T. occidentalis can be consumed for its antioxidant property.
  11. Fulltext Mangroves give cause for conservation optimism, for now
    Friess DA, Yando ES, Abuchahla GMO, Adams JB, Cannicci S, Canty SWJ, et al.
    Curr Biol, 2020 02 24;30(4):R153-R154.
    PMID: 32097637 DOI: 10.1016/j.cub.2019.12.054
    Friess et al. discuss the results of conservation efforts for mangrove forests in recent years.
  12. Fulltext Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants
    Zhao H, Zhao S, International Network for Bamboo and Rattan, Fei B, Liu H, Yang H, et al.
    Gigascience, 2017 07 01;6(7):1-7.
    PMID: 28637269 DOI: 10.1093/gigascience/gix046
    Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of bamboo and rattan genetics through genome analysis. GABR includes 2 core subprojects: Bamboo-T1K (Transcriptomes of 1000 Bamboos) and Rattan-G5 (Genomes of 5 Rattans), and several other subprojects. Here we describe the organization, directions, and status of GABR.
  13. Fulltext Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia
    Heery EC, Hoeksema BW, Browne NK, Reimer JD, Ang PO, Huang D, et al.
    Mar Pollut Bull, 2018 Oct;135:654-681.
    PMID: 30301085 DOI: 10.1016/j.marpolbul.2018.07.041
    Given predicted increases in urbanization in tropical and subtropical regions, understanding the processes shaping urban coral reefs may be essential for anticipating future conservation challenges. We used a case study approach to identify unifying patterns of urban coral reefs and clarify the effects of urbanization on hard coral assemblages. Data were compiled from 11 cities throughout East and Southeast Asia, with particular focus on Singapore, Jakarta, Hong Kong, and Naha (Okinawa). Our review highlights several key characteristics of urban coral reefs, including "reef compression" (a decline in bathymetric range with increasing turbidity and decreasing water clarity over time and relative to shore), dominance by domed coral growth forms and low reef complexity, variable city-specific inshore-offshore gradients, early declines in coral cover with recent fluctuating periods of acute impacts and rapid recovery, and colonization of urban infrastructure by hard corals. We present hypotheses for urban reef community dynamics and discuss potential of ecological engineering for corals in urban areas.
  14. Fulltext Prostate-specific antigen velocity in a prospective prostate cancer screening study of men with genetic predisposition
    Mikropoulos C, Selkirk CGH, Saya S, Bancroft E, Vertosick E, Dadaev T, et al.
    Br J Cancer, 2018 Jan;118(2):266-276.
    PMID: 29301143 DOI: 10.1038/bjc.2017.429
    BACKGROUND: Prostate-specific antigen (PSA) and PSA-velocity (PSAV) have been used to identify men at risk of prostate cancer (PrCa). The IMPACT study is evaluating PSA screening in men with a known genetic predisposition to PrCa due to BRCA1/2 mutations. This analysis evaluates the utility of PSA and PSAV for identifying PrCa and high-grade disease in this cohort.

    METHODS: PSAV was calculated using logistic regression to determine if PSA or PSAV predicted the result of prostate biopsy (PB) in men with elevated PSA values. Cox regression was used to determine whether PSA or PSAV predicted PSA elevation in men with low PSAs. Interaction terms were included in the models to determine whether BRCA status influenced the predictiveness of PSA or PSAV.

    RESULTS: 1634 participants had ⩾3 PSA readings of whom 174 underwent PB and 45 PrCas diagnosed. In men with PSA >3.0 ng ml-l, PSAV was not significantly associated with presence of cancer or high-grade disease. PSAV did not add to PSA for predicting time to an elevated PSA. When comparing BRCA1/2 carriers to non-carriers, we found a significant interaction between BRCA status and last PSA before biopsy (P=0.031) and BRCA2 status and PSAV (P=0.024). However, PSAV was not predictive of biopsy outcome in BRCA2 carriers.

    CONCLUSIONS: PSA is more strongly predictive of PrCa in BRCA carriers than non-carriers. We did not find evidence that PSAV aids decision-making for BRCA carriers over absolute PSA value alone.

  15. Fulltext Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants
    Dadaev T, Saunders EJ, Newcombe PJ, Anokian E, Leongamornlert DA, Brook MN, et al.
    Nat Commun, 2018 06 11;9(1):2256.
    PMID: 29892050 DOI: 10.1038/s41467-018-04109-8
    Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.
  16. Mammal responses to global changes in human activity vary by trophic group and landscape
    Burton AC, Beirne C, Gaynor KM, Sun C, Granados A, Allen ML, et al.
    Nat Ecol Evol, 2024 Mar 18.
    PMID: 38499871 DOI: 10.1038/s41559-024-02363-2
    Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human-wildlife interactions along gradients of human influence.
  17. 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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