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  1. Fulltext LMDI Decomposition Analysis of E-Waste Generation in the ASEAN
    Choi G, Kim T, Kim M
    Int J Environ Res Public Health, 2021 12 06;18(23).
    PMID: 34886589 DOI: 10.3390/ijerph182312863
    The economies of ASEAN member states are growing rapidly, and electrical and electronic waste (E-waste) generated from them are also showing a rapid increase. In this context, this study conducted an LMDI decomposition analysis on the amount of E-waste generated in ASEAN member countries from 2015 to 2019 and decomposed it into E-waste intensity, economic growth, and population effects. Then, based on analysis results, policy implications are suggested to improve their E-waste management. According to the analysis results, ASEAN countries can be classified into three groups. The first group includes Indonesia, the Philippines, Singapore, Thailand; economic growth was the main driving factor of E-waste increase in these countries. However, E-waste had also decreased due to the effect of E-waste intensity. The second group includes countries where economic growth was not the only driving factor for E-waste increase, but also where E-waste had increased due to the effect of E-waste intensity. These countries include Cambodia, Malaysia, and Viet Nam. Finally, the third group consists of countries where the effect of E-waste intensity is the main driving factor, including Brunei Darussalam, Lao PDR, and Myanmar. This research shows that ASEAN countries need policies that can effectively deal with the threat of E-waste as a result of high economic growth and policies that can improve intensity by reducing the generation of E-waste.
  2. Current surgical treatment of obstructed defecation among selected European opinion leaders in pelvic floor surgery
    Kim M, Meurette G, Ragu R, Lehur PA
    Tech Coloproctol, 2016 Jun;20(6):395-399.
    PMID: 27170284 DOI: 10.1007/s10151-016-1473-z
    BACKGROUND: The aim of this study was to perform a survey on the surgical management of obstructed defecation (OD) across advocated selected coloproctological experts across Europe.

    METHODS: Surgeons from 42 centers of coloproctology in Europe were asked to complete a questionnaire, including seven questions about their past and present operative treatment strategy for patients with OD.

    RESULTS: The questionnaire was completed by 32 experts of pelvic floor surgery in 13 European countries. All but one indicated that they consider surgical treatment for OD. Seventy-four percent of these have been using transanal stapled rectal resection (STARR) and 96 % transabdominal rectopexy. While only 65 %, who have begun performing STARR are still using transanal resection, the technique is still being used by all surgeons performing abdominal procedures. Rectopexy only, STARR only, or both approaches are offered by 52, 3, and 45 % of surgeons, respectively.

    CONCLUSIONS: The use of STARR in the treatment of OD is decreasing among European opinion leaders in the field of pelvic floor surgery, while the application of transabdominal procedures continues.

  3. Carcinoma arising in enteric diversion or rectal neobladder for bladder exstrophy
    Ragu R, Meurette G, Kim M, Le Normand L, Lehur PA
    Tech Coloproctol, 2016 Nov;20(11):745-752.
    PMID: 27592221
    Bladder exstrophy is a rare malformation. Ureteral diversion, such as ureterosigmoidostomy or a neorectal bladder, has been described. When the patients reach adulthood, cancer may arise in these reconstructions. Our aim was to perform a systematic review (all languages) of the published literature on neoplasia after urinary diversion and suggested management in cases of cancer. PubMed and Cochrane library were searched for relevant articles published within the last 20 years. All identified articles were reviewed for inclusion. Carcinoma occurring in the bladder and unreconstructed exstrophy were excluded. Out of 47 articles found, 12 matched our search criteria. The outcomes of 23 patients (including 2 from the authors' institution) were reported. Twenty-two patients with adenocarcinoma and 1 with carcinoid tumour were identified. Median age at urinary diversion was 3 (range 1-13) years. There were 20 ureterosigmoidostomies and 2 neorectal bladders. Cancer was diagnosed subsequently at a median of 31 (range 5-55) years after urinary diversion still in place (n = 18) or 21 years (range 1-30) after incomplete excision of ureteric stump when re-diverted (n = 5). The long-term outcomes of 15 patients were available. Ten died due to colorectal adenocarcinoma, and 5 were disease-free at 3 years. Patients with enteric diversion for bladder exstrophy, including those with subsequent reconstruction, are at risk of adenocarcinoma during adulthood. It is important to provide adequate surveillance. If lesions suggestive of carcinoma are seen, complete excision of the receptive bowel and urinary diversion are mandatory.
  4. Distinct bacterial communities dominate tropical and temperate zone leaf litter
    Kim M, Kim WS, Tripathi BM, Adams J
    Microb Ecol, 2014 May;67(4):837-48.
    PMID: 24549745 DOI: 10.1007/s00248-014-0380-y
    Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
  5. Functional Results and Quality of Life Following Magnetic Anal Sphincter Augmentation in Severely Incontinent Patients
    Kim M, Meurette G, Ragu R, Wyart V, Lehur PA
    Ann Surg, 2019 02;269(2):310-314.
    PMID: 28902668 DOI: 10.1097/SLA.0000000000002512
    OBJECTIVE: Magnetic anal sphincter augmentation is a novel surgical option in the treatment of severe fecal incontinence. This study aimed to analyze functional results, quality of life, and satisfaction after implantation in the mid-term, and to identify factors associated with success of this new treatment.

    METHODS: All patients, who underwent magnetic anal sphincter augmentation procedure at a single center between December 2008 and January 2016, were consecutively included. Symptom severity [Cleveland Clinic Incontinence Score (CCIS)], quality of life [Fecal-Incontinence Quality of Life Questionnaire (FIQL)], bowel diary data, and patients' satisfaction were assessed before and after implantation.

    RESULTS: Forty-five patients (43 female), mean (s.d.) age 66.82 (±10.07), were followed for a median of 36 months (range 6-84). Two patients were explanted and 1 lost to follow-up. On a 3-week diary, major leakage rate significantly improved as did CCIS and FIQL. No significant difference was seen for flatus and minor leaks. Postoperative decrease of CCIS by ≥5.5 points correlated best with satisfaction, expressed by 22 patients (48% in intention-to-treat analysis). An independent predictive factor for success after implantation was no previous fecal incontinence surgical treatment.

    CONCLUSIONS: Satisfaction, functional, and quality of life outcomes improve significantly following magnetic anal sphincter augmentation.

  6. Characteristics and outcome of autoimmune liver disease in Asian children
    Lee WS, Lum SH, Lim CB, Chong SY, Khoh KM, Ng RT, et al.
    Hepatol Int, 2015 Apr;9(2):292-302.
    PMID: 25788179 DOI: 10.1007/s12072-014-9558-0
    BACKGROUND: Little is known about autoimmune liver disease (AILD) in Asian children. We studied the clinical features and predictors of outcome in childhood AILD in an Asian population.

    METHODS: Retrospective review of AILD [autoimmune hepatitis type 1 and 2 (AIH1, AIH2), primary sclerosing cholangitis (PSC) and autoimmune sclerosing cholangitis (ASC)] seen at two pediatric liver units in Malaysia.

    RESULTS: At presentation, 17 (56%) of the 32 children [19 females, 59%; median (range) age 7.7 (1.8-15.5) years] with AILD (AIH1 = 18, AIH2 = 5, PSC = 0, ASC = 9) had liver cirrhosis. At final review [median (range) duration of follow-up 4.8 (0.4-12) years], 24 patients (75%) survived with a native liver. Twenty-one (66%) were in remission; 19 (AIH1 = 11; AIH2 = 4, ASC = 4) were on prednisolone and/or azathioprine, one on cyclosporine and another on mycophenolate mofetil. Three (AIH1 = 3) were in partial remission. Of the two who underwent liver transplantation (LT; 6.5%; both ASC), one died of primary graft failure after LT. Six patients (19%) died without LT (acute liver failure, n = 1; end-stage liver disease, n = 5). The overall survival rate (native liver and survival post-LT) was 78%. A delay in seeking treatment adversely affected the final outcome [survival with native liver vs. LT or death (duration between onset of disease and treatment; median ± standard error) = 2.5 ± 2.9 months vs. 24.0 ± 13.3 months; p = 0.012].

    CONCLUSIONS: Although remission was achieved in the majority of patients with prednisolone and/or azathioprine therapy, delay in seeking diagnosis and treatment adversely affects the outcome of childhood AILD in Malaysia.
  7. Seroprevalence of Pteropine orthoreovirus in humans remain similar after nearly two decades (2001-2002 vs. 2017) in Tioman Island, Malaysia
    Leong WJ, Quek XF, Tan HY, Wong KM, Muhammad HS, Mohamed NA, et al.
    J Med Virol, 2022 02;94(2):771-775.
    PMID: 34708881 DOI: 10.1002/jmv.27422
    Pteropine orthoreovirus (PRV) is an emerging zoonotic respiratory virus that can be transmitted from bats to humans. In Malaysia, aside from PRV2P (Pulau virus) being isolated from Pteropus hypomelanus sampled in Tioman Island, PRV3M (Melaka virus), PRV4K (Kampar virus), and PRV7S (Sikamat virus) were all isolated from samples of patients who reported having a disease spectrum from acute respiratory distress to influenza-like illness and sometimes even with enteric symptoms such as diarrhea and abdominal pain. Screening of sera collected from human volunteers on Tioman Island in 2001-2002 demonstrated that 12.8% (14/109) were positive for PRV2P and PRV3M. Taking all these together, we aim to investigate the serological prevalence of PRV (including PRV4K and PRV7S) among Tioman Island inhabitants again with the assumption that the seroprevalence rate will remain nearly similar to the above reported if human exposure to bats is still happening in the island. Using sera collected from human volunteers on the same island in 2017, we demonstrated seroprevalence of 17.8% (28/157) against PRV2P and PRV3M, respectively. Seropositivity of 11.4% among Tioman Island inhabitants against PRV4K and PRV7S, respectively, was described in this study. In addition, the seroprevalence of 89.5% (17/19), 73.6% (14/19), 63.0% (12/19), and 73.6% (14/19) against PRV2P, PRV3M, PRV4K, and PRV7S, respectively, were observed among pteropid bats in the island. We revealed that the seroprevalence of PRV among island inhabitants remains nearly similar after nearly two decades, suggesting that potential spill-over events in bat-human interface areas in the Tioman Island. We are unclear whether such spillover was directly from bats to humans, as suspected for the PRV3M human cases, or from an intermediate host(s) yet to be identified. There is a high possibility of the viruses circulating among the bats as demonstrated by high seroprevalence against PRV in the bats.
  8. The impact of tropical forest logging and oil palm agriculture on the soil microbiome
    Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H, et al.
    Mol Ecol, 2016 May;25(10):2244-57.
    PMID: 26994316 DOI: 10.1111/mec.13620
    Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.
  9. Fulltext pH dominates variation in tropical soil archaeal diversity and community structure
    Tripathi BM, Kim M, Lai-Hoe A, Shukor NA, Rahim RA, Go R, et al.
    FEMS Microbiol Ecol, 2013 Nov;86(2):303-11.
    PMID: 23773164 DOI: 10.1111/1574-6941.12163
    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.
  10. From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?
    Kerfahi D, Tripathi BM, Dong K, Kim M, Kim H, Ferry Slik JW, et al.
    Microb Ecol, 2019 Jan;77(1):168-185.
    PMID: 29882154 DOI: 10.1007/s00248-018-1215-z
    Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon "classical" views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.
  11. Origins of suspended particulate matter based on sterol distribution in low salinity water mass observed in the offshore East China Sea
    Kim M, Jung JH, Jin Y, Han GM, Lee T, Hong SH, et al.
    Mar Pollut Bull, 2016 Jul 15;108(1-2):281-8.
    PMID: 27167134 DOI: 10.1016/j.marpolbul.2016.04.049
    The molecular composition and distribution of sterols were investigated in the East China Sea to identify the origins of suspended particulate matter (SPM) in offshore waters influenced by Changjiang River Diluted Water (CRDW). Total sterol concentrations ranged from 3200 to 31,900pgL(-1) and 663 to 5690pgL(-1) in the particulate and dissolved phases, respectively. Marine sterols dominated representing 71% and 66% in the particulate and dissolved phases, respectively. Typical sewage markers, such as coprostanol, were usually absent at ~250km offshore. However, sterols from allochthonous terrestrial plants were still detected at these sites. A negative relationship was observed between salinity and concentrations of terrestrial sterols in SPM, suggesting that significant amounts of terrestrial particulate matter traveled long distance offshore in the East China Sea, and the Changjiang River Diluted Water (CRDW) was an effective carrier of land-derived particulate organic matter to the offshore East China Sea.
  12. The anti-inflammatory and anti-nociceptive effects of Korean black ginseng
    Lee YY, Saba E, Irfan M, Kim M, Chan JY, Jeon BS, et al.
    Phytomedicine, 2019 Feb 15;54:169-181.
    PMID: 30668366 DOI: 10.1016/j.phymed.2018.09.186
    BACKGROUND: Different processing conditions alter the ginseng bioactive compounds, promoting or reducing its anti-inflammatory effects. We compared black ginseng (BG) - that have been steamed 5 times - with red ginseng (RG).

    HYPOTHESIS/ PURPOSE: To compare the anti-inflammatory activities and the anti-nociceptive properties of RG and BG.

    METHODS: Nitric Oxide (NO) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay, quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR), western blot, xylene-induced ear edema, carrageenan-induced paw edema RESULTS: The ginsenoside contents were confirmed using high-performance liquid chromatography (HPLC) and has been altered through increased processing. The highest concentration of these extracts inhibited NO production to near-basal levels in lipopolysaccharide (LPS)-stimulated RAW 264.7 without exhibiting cytotoxicity. Pro-inflammatory cytokine expression at the mRNA level was investigated using qRT-PCR. Comparatively, BG exhibited better inhibition of pro-inflammatory mediators, iNOS and COX-2 and pro-inflammatory cytokines, IL-1β, IL-6 and TNF-α. Protein expression was determined using western blot analysis and BG exhibited stronger inhibition. Xylene-induced ear edema model in mice and carrageenan-induced paw edema in rats were carried out and tested with the effects of ginseng as well as dexamethasone and indomethacin - commonly used drugs. BG is a more potent anti-inflammatory agent, possesses anti-nociceptive properties, and has a strong potency comparable to the NSAIDs.

    CONCLUSION: BG has more potent anti-inflammatory and anti-nociceptive effects due to the change in ginsenoside component with increased processing.

  13. Distinctive phyllosphere bacterial communities in tropical trees
    Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, Ainuddin AN, et al.
    Microb Ecol, 2012 Apr;63(3):674-81.
    PMID: 21990015 DOI: 10.1007/s00248-011-9953-1
    Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.
  14. Distinctive bacterial communities in the rhizoplane of four tropical tree species
    Oh YM, Kim M, Lee-Cruz L, Lai-Hoe A, Go R, Ainuddin N, et al.
    Microb Ecol, 2012 Nov;64(4):1018-27.
    PMID: 22767122 DOI: 10.1007/s00248-012-0082-2
    It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.
  15. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests
    Tripathi BM, Lee-Cruz L, Kim M, Singh D, Go R, Shukor NA, et al.
    Microb Ecol, 2014 Aug;68(2):247-58.
    PMID: 24658414
    Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.
  16. Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too
    Tripathi BM, Kim M, Singh D, Lee-Cruz L, Lai-Hoe A, Ainuddin AN, et al.
    Microb Ecol, 2012 Aug;64(2):474-84.
    PMID: 22395784 DOI: 10.1007/s00248-012-0028-8
    The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.
  17. Fulltext A plasmid-encoded peptide from Staphylococcus aureus induces anti-myeloperoxidase nephritogenic autoimmunity
    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.
  18. Fulltext Data Descriptor: Daily observations of stable isotope ratios of rainfall in the tropics
    Munksgaard NC, Kurita N, Sánchez-Murillo R, Ahmed N, Araguas L, Balachew DL, et al.
    Sci Rep, 2019 10 08;9(1):14419.
    PMID: 31595004 DOI: 10.1038/s41598-019-50973-9
    We present precipitation isotope data (δ2H and δ18O values) from 19 stations across the tropics collected from 2012 to 2017 under the Coordinated Research Project F31004 sponsored by the International Atomic Energy Agency. Rainfall samples were collected daily and analysed for stable isotopic ratios of oxygen and hydrogen by participating laboratories following a common analytical framework. We also calculated daily mean stratiform rainfall area fractions around each station over an area of 5° x 5° longitude/latitude based on TRMM/GPM satellite data. Isotope time series, along with information on rainfall amount and stratiform/convective proportions provide a valuable tool for rainfall characterisation and to improve the ability of isotope-enabled Global Circulation Models to predict variability and availability of inputs to fresh water resources across the tropics.
  19. Horizon Scan of the Belt and Road Initiative
    Hughes AC, Lechner AM, Chitov A, Horstmann A, Hinsley A, Tritto A, et al.
    Trends Ecol Evol, 2020 Jul;35(7):583-593.
    PMID: 32521242 DOI: 10.1016/j.tree.2020.02.005
    The Belt and Road Initiative (BRI) represents the largest infrastructure and development project in human history, and presents risks and opportunities for ecosystems, economies, and communities. Some risks (habitat fragmentation, roadkill) are obvious, however, many of the BRI's largest challenges for development and conservation are not obvious and require extensive consideration to identify. In this first BRI Horizon Scan, we identify 11 frontier issues that may have large environmental and social impacts but are not yet recognised. More generally, the BRI will increase China's participation in international environmental governance. Thus, new cooperative modes of governance are needed to balance geopolitical, societal, and environmental interests. Upgrading and standardising global environmental standards is essential to safeguard ecological systems and human societies.
  20. Development of the clinical assessment scale in autoimmune encephalitis
    Lim JA, Lee ST, Moon J, Jun JS, Kim TJ, Shin YW, et al.
    Ann Neurol, 2019 03;85(3):352-358.
    PMID: 30675918 DOI: 10.1002/ana.25421
    OBJECTIVE: There is no scale for rating the severity of autoimmune encephalitis (AE). In this study, we aimed to develop a novel scale for rating severity in patients with diverse AE syndromes and to verify the reliability and validity of the developed scale.

    METHODS: The key items were generated by a panel of experts and selected according to content validity ratios. The developed scale was initially applied to 50 patients with AE (development cohort) to evaluate its acceptability, reproducibility, internal consistency, and construct validity. Then, the scale was applied to another independent cohort (validation cohort, n = 38).

    RESULTS: A new scale consisting of 9 items (seizure, memory dysfunction, psychiatric symptoms, consciousness, language problems, dyskinesia/dystonia, gait instability and ataxia, brainstem dysfunction, and weakness) was developed. Each item was assigned a value of up to 3 points. The total score could therefore range from 0 to 27. We named the scale the Clinical Assessment Scale in Autoimmune Encephalitis (CASE). The new scale showed excellent interobserver (intraclass correlation coefficient [ICC] = 0.97) and intraobserver (ICC = 0.96) reliability for total scores, was highly correlated with modified Rankin scale (r = 0.86, p

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