Earthquake detection capacity of Dense Oceanfloor Network system for Earthquakes and Tsunamis (DONET)

We adopted the Probability-based Magnitude of Completeness (PMC) method and performed a case analysis of the Nankai Trough, a target region monitored for future megathrust earthquakes. JAMSTEC (Japan Agency for Marine-Earth Science and Technology) has created a seismicity catalog that includes events in this region observed by DONET. Using seismicity data for 2015-2019, we found spatiotemporal variability of completeness magnitude Mp. Mp was lower than 1 in one of the areas where stations are densely deployed, whereas Mp was larger than 2 at the periphery and outside of the DONET area. We then evaluated the temporal evolution of Mp, highlighting how the failure of sets of observing stations influenced Mp if not repaired. Stations are aggregated around the 12 science nodes (hubs that connect the stations) and connected through the two oceanfloor backbone cables to JAMSTEC. We explored the possible use of PMC as a tool with simulation computation of node malfunction. A simulation showed that completeness estimates in the area near failure nodes were about 1 magnitude larger. If such failure occurred for nodes near the region which straddles the rupture zones of the previous Tonankai and Nankai earthquakes in 1940's, it would most pronouncedly affect earthquake monitoring among nodes' failures. It is desirable to repair these nodes or replace with new ones when their malfunction occurs. We then demonstrated an example of how to use Mp information as prior knowledge to seismicity-related studies. We used the b value of the Gutenberg-Richter distribution, and computed it taking Mp into consideration. We found that the spatial and temporal changes in b were strongly correlated to the magnitude-6 class slow slip that grew over two years on the Nankai Trough plate boundary, indicating the b value as a proxy that can help to image stress heterogeneity when there is a slow slip event.Comment: 6 figure

Risk Factors for Scrub Typhus, Murine Typhus, and Spotted Fever Seropositivity in Urban Areas, Rural Plains, and Peri-Forest Hill Villages in South India: A Cross-Sectional Study.

Scrub typhus and spotted fever group rickettsioses are thought to be common causes of febrile illness in India, whereas they rarely test for murine typhus. This cross-sectional study explored the risk factors associated with scrub typhus, tick-borne spotted fever, and murine typhus seropositivity in three different geographical settings, urban, rural, and hill villages in Tamil Nadu, South India. We enrolled 1,353 participants living in 48 clusters. The study included a questionnaire survey and blood sampling. Blood was tested for Orientia tsutsugamushi (scrub typhus), Rickettsia typhi (murine typhus), and spotted fever group Rickettsia IgG using ELISA. The seroprevalence of scrub typhus, spotted fever, and murine typhus were 20.4%, 10.4%, and 5.4%, respectively. Scrub typhus had the highest prevalence in rural areas (28.1%), and spotted fever was most common in peri-forested areas (14.9%). Murine typhus was more common in rural (8.7%) than urban areas (5.4%) and absent in peri-forested hill areas. Agricultural workers had a higher relative risk for scrub typhus, especially in urban areas. For murine typhus, proximity to a waterbody and owning a dog were found to be major risk factors. The main risk factors for spotted fever were agricultural work and living in proximity to a forest. Urban, rural plains, and hill settings display distinct epidemiological pattern of Orientia and rickettsial infections. Although scrub typhus and spotted fever were associated with known risk factors in this study, the findings suggest a different ecology of murine typhus transmission compared with other studies conducted in Asia

Population density, water supply, and the risk of dengue fever in Vietnam: cohort study and spatial analysis.

BACKGROUND: Aedes aegypti, the major vector of dengue viruses, often breeds in water storage containers used by households without tap water supply, and occurs in high numbers even in dense urban areas. We analysed the interaction between human population density and lack of tap water as a cause of dengue fever outbreaks with the aim of identifying geographic areas at highest risk. METHODS AND FINDINGS: We conducted an individual-level cohort study in a population of 75,000 geo-referenced households in Vietnam over the course of two epidemics, on the basis of dengue hospital admissions (n = 3,013). We applied space-time scan statistics and mathematical models to confirm the findings. We identified a surprisingly narrow range of critical human population densities between around 3,000 to 7,000 people/km² prone to dengue outbreaks. In the study area, this population density was typical of villages and some peri-urban areas. Scan statistics showed that areas with a high population density or adequate water supply did not experience severe outbreaks. The risk of dengue was higher in rural than in urban areas, largely explained by lack of piped water supply, and in human population densities more often falling within the critical range. Mathematical modeling suggests that simple assumptions regarding area-level vector/host ratios may explain the occurrence of outbreaks. CONCLUSIONS: Rural areas may contribute at least as much to the dissemination of dengue fever as cities. Improving water supply and vector control in areas with a human population density critical for dengue transmission could increase the efficiency of control efforts. Please see later in the article for the Editors' Summary

Challenges in diagnosing scrub typhus among hospitalized patients with undifferentiated fever at a national tertiary hospital in northern Vietnam

BACKGROUND: Scrub typhus (ST) is a leading cause of non-malarial febrile illness in Southeast Asia, but evidence of its true disease burden is limited because of difficulties of making the clinical diagnosis and lack of adequate diagnostic tests. To describe the epidemiology and clinical characteristics of ST, we conducted an observational study using multiple diagnostic assays at a national tertiary hospital in Hanoi, Vietnam. METHODOLOGY/PRINCIPAL FINDINGS: We enrolled 1,127 patients hospitalized with documented fever between June 2012 and May 2013. Overall, 33 (2.9%) patients were diagnosed with ST by PCR and/or screening of ELISA for immunoglobulin M (IgM) with confirmatory tests: 14 (42.4%) were confirmed by indirect immunoperoxidase assay (IIP), and 19 (57.6%) were by IIP and PCR. Living by farming, conjunctival injection, eschar, aspartate aminotransferase elevation, and alanine aminotransferase elevation were significantly associated with ST cases (adjusted odds ratios (aORs): 2.8, 3.07, 48.8, 3.51, and 4.13, respectively), and having a comorbidity and neutrophilia were significantly less common in ST cases (aORs: 0.29 and 0.27, respectively). The majority of the ST cases were not clinically diagnosed with rickettsiosis (72.7%). Dominant IIP reactions against a single antigen were identified in 15 ST cases, whereas indistinguishably high reactions against multiple antigens were seen in 11 ST cases. The most frequently observed dominant IIP reaction was against Karp antigen (eight cases) followed by Gilliam (four cases). The highest diagnostic accuracy of IgM ELISA in acute samples was 78%. In a phylogenetic analysis of the 56-kDa type-specific antigen gene, the majority (14 cases) were located in the Karp-related branch followed by the Gilliam-related (two cases), Kato-related (two cases), and TA763-related clades (one case). CONCLUSIONS/SIGNIFICANCE: Both the clinical and laboratory diagnoses of ST remain challenging at a tertiary hospital. Implementation of both serological and nucleic acid amplification assays covering endemic O. tsutsugamushi strains is essential

Variabilidade no domínio LRR de peptídeos codificados em "clusters" homólogos ao SH3 em diferentes genomas de Coffea.

O locus SH3 é relacionado com as reações de defesa contra Hemileia vastatrix, o agente causador da ferrugem alaranjada. Há um ?cluster? de genes CC-NBS-LRR no locus SH3 da variedade IAPAR59 de Coffea arabica. Esse ?cluster? reúne oito cópias de CC-NBS-LRRs, que variam na sua estrutura primária, especialmente na região carboxi-terminal onde são localizados motivos ricos em leucina. Esses motivos LRR são característicos de proteínas que participam do reconhecimento de patógenos pelas plantas. Os ?clusters? homólogos na variedade Caturra e em um cafeeiro de origem etíope da espécie C. arabica, em C. canephora DH200-94 e em C. eugenioides CCC68 foram identificados. A variabilidade das regiões codificadoras incluídas no ?cluster? SH3 foi avaliada alinhando com o aplicativo CLUSTAW e agrupando pelo método de Fitsh-Margoliash as sequências da região carboxi-terminal dos peptídeos deduzidos de todas as cópias de NBS-LRRs codificadas em ?clusters? homólogos naqueles quatro genótipos e também previamente analisadas em IAPAR59 e em C. canephora IF200. Concluiu-se que há divergência entre as sequências dos domínios LRR de diferentes membros dos ?clusters? em diferentes genótipos, o que pode ser parcialmente resultante dos processos de sequenciamento e montagem, mas que também resulta de evolução e seleção. Também há diferença no número de cópias do gene em diferentes genótipos. Consideramos a hipótese de que o número, a organização, a integridade e a estrutura primária dos genes nos ?clusters? SH3 podem estar relacionados com o mecanismo de reconhecimento das raças fisiológicas de H. vastatrix por diferentes variedades de cafeeiros.Título em inglês: LRR domain variability for peptides encoded in gene clusters homologous to the SH3 in different Coffea genomes

Vaccinia Scars Associated with Improved Survival among Adults in Rural Guinea-Bissau

BACKGROUND: In urban Guinea-Bissau, adults with a vaccinia scar had better survival but also a higher prevalence of HIV-2 infection. We therefore investigated the association between vaccinia scar and survival and HIV infection in a rural area of Guinea-Bissau. METHODOLOGY/PRINCIPAL FINDINGS: In connection with a study of HIV in rural Guinea-Bissau, we assessed vaccinia and BCG scars in 193 HIV-1 or HIV-2 infected and 174 uninfected participants. Mortality was assessed after 2½–3 years of follow-up. The analyses were adjusted for age, sex, village, and HIV status. The prevalence of vaccinia scar was associated with age, village, and HIV-2 status but not with sex and schooling. Compared with individuals without any scar, individuals with a vaccinia scar had better survival (mortality rate ratio (MR) = 0.22 (95% CI 0.08–0.61)), the MR being 0.19 (95% CI 0.06–0.57) for women and 0.40 (95% CI 0.04–3.74) for men. Estimates were similar for HIV-2 infected and HIV-1 and HIV-2 uninfected individuals. The HIV-2 prevalence was higher among individuals with a vaccinia scar compared to individuals without a vaccinia scar (RR = 1.57 (95% CI 1.02–2.36)). CONCLUSION: The present study supports the hypothesis that vaccinia vaccination may have a non-specific beneficial effect on adult survival

Progress towards antibiotic use targets in eight high-income countries.

Objective: To compare antibiotic sales in eight high-income countries using the 2019 World Health Organization (WHO) Access, Watch and Reserve (AWaRe) classification and the target of 60% consumption of Access category antibiotics. Methods: We analysed data from a commercial database of sales of systemic antibiotics in France, Germany, Italy, Japan, Spain, Switzerland, United Kingdom of Great Britain and Northern Ireland, and United States of America over the years 2013-2018. We classified antibiotics according to the 2019 AWaRe categories: Access, Watch, Reserve and Not Recommended. We measured antibiotic sales per capita in standard units (SU) per capita and calculated Access group sales as a percentage of total antibiotic sales. Findings: In 2018, per capita antibiotic sales ranged from 7.4 SU (Switzerland) to 20.0 SU (France); median sales of Access group antibiotics were 10.9 SU per capita (range: 3.5-15.0). Per capita sales declined moderately over 2013-2018. The median percentage of Access group antibiotics was 68% (range: 22-77 %); the Access group proportion increased in most countries between 2013 and 2018. Five countries exceeded the 60% target; two countries narrowly missed it (> 55% in Germany and Italy). Sales of Access antibiotics in Japan were low (22%), driven by relatively high sales of oral cephalosporins and macrolides. Conclusion: We have identified changes to prescribing that could allow countries to achieve the WHO target. The 60% Access group target provides a framework to inform national antibiotic policies and could be complemented by absolute measures and more ambitious values in specific settings

Development and validation of an allele-specific marker for resistance to bacterial halo blight in coffea arabica.

Bacterial halo blight (BHB) is a bacterial disease, caused by Pseudomonas syringae pv. garcae, which has been gaining prominence in the main coffee-producing regions. Chemical control of this disease increases production costs and is environmentally undesirable. In this scenario, the development of new cultivars resistant to BHB is the most economical and sustainable alternative. Marker-Assisted Selection (MAS) is an appropriate strategy to assist breeding programs for resistant genotype selection. In a previous Genome-Wide Association Study (GWAS) for C. arabica and P. syringae pv. garcae interaction, we identified a locus, probably linked to qualitative resistance to the pathogen. In this work, we developed and validated a pair of Allele-Specific-Polymerase Chain Reaction (AS-PCR) primers for this locus in C. arabica breeding populations. This pair of AS-PCR primers, called Psg_QL1, was tested both in a backcross (BC) (n = 38) and in an F2 population (n = 138) segregating for resistance to BHB. The linkage between the Psg_QL1 marker and qualitative resistance showed an accuracy of 93.75%. Our results demonstrated that the Psg_QL1 marker can be applied in MAS in a robust, simple, fast, and low-cost way