Bayesian variable selection for high dimensional predictors and self-reported outcomes

BACKGROUND: The onset of silent diseases such as type 2 diabetes is often registered through self-report in large prospective cohorts. Self-reported outcomes are cost-effective; however, they are subject to error. Diagnosis of silent events may also occur through the use of imperfect laboratory-based diagnostic tests. In this paper, we describe an approach for variable selection in high dimensional datasets for settings in which the outcome is observed with error. METHODS: We adapt the spike and slab Bayesian Variable Selection approach in the context of error-prone, self-reported outcomes. The performance of the proposed approach is studied through simulation studies. An illustrative application is included using data from the Women\u27s Health Initiative SNP Health Association Resource, which includes extensive genotypic ( \u3e 900,000 SNPs) and phenotypic data on 9,873 African American and Hispanic American women. RESULTS: Simulation studies show improved sensitivity of our proposed method when compared to a naive approach that ignores error in the self-reported outcomes. Application of the proposed method resulted in discovery of several single nucleotide polymorphisms (SNPs) that are associated with risk of type 2 diabetes in a dataset of 9,873 African American and Hispanic participants in the Women\u27s Health Initiative. There was little overlap among the top ranking SNPs associated with type 2 diabetes risk between the racial groups, adding support to previous observations in the literature of disease associated genetic loci that are often not generalizable across race/ethnicity populations. The adapted Bayesian variable selection algorithm is implemented in R. The source code for the simulations are available in the Supplement. CONCLUSIONS: Variable selection accuracy is reduced when the outcome is ascertained by error-prone self-reports. For this setting, our proposed algorithm has improved variable selection performance when compared to approaches that neglect to account for the error-prone nature of self-reports

The challenges of extending climate risk insurance to fisheries

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordNatural Environment Research Council (NERC)Centre for Environment, Fisheries and Aquaculture Science (Cefas)Willis Research NetworkCommonwealth Marine Economies Programme, UK Foreign and Commonwealth Offic

Highly Active Nanostructured CoS2/CoS Heterojunction Electrocatalysts for Aqueous Polysulfide/Iodide Redox Flow Batteries

Aqueous polysulfide/iodide redox flow batteries are attractive for scalable energy storage due to their high energy density and low cost. However, their energy efficiency and power density are usually limited by poor electrochemical kinetics of the redox reactions of polysulfide/iodide ions on graphite electrodes, which has become the main obstacle for their practical applications. Here, CoS2/CoS heterojunction nanoparticles with uneven charge distribution, which are synthesized in situ on graphite felt by a one-step solvothermal process, can significantly boost electrocatalytic activities of I−/I3− and S2−/Sx2−redox reactions by improving absorptivity of charged ions and promoting charge transfer. The polysulfide/iodide flow battery with the graphene felt-CoS2/CoS heterojunction can deliver a high energy efficiency of 84.5% at a current density of 10 mA cm−2, a power density of 86.2 mW cm−2 and a stable energy efficiency retention of 96% after approximately 1000 h of continuous operation

Contamination of Fresh Produce with Antibiotic-Resistant Bacteria and Associated Risks to Human Health: A Scoping Review.

Fresh produce, when consumed raw, can be a source of exposure to antimicrobial residues, antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) of clinical importance. This review aims to determine: (1) the presence and abundance of antimicrobial residues, ARB and ARGs in fresh agricultural products sold in retail markets and consumed raw; (2) associated health risks in humans; and (3) pathways through which fresh produce becomes contaminated with ARB/ARGs. We searched the Ovid Medline, Web of Science and Hinari databases as well as grey literature, and identified 40 articles for inclusion. All studies investigated the occurrence of multidrug-resistant bacteria, and ten studies focused on ARGs in fresh produce, while none investigated antimicrobial residues. The most commonly observed ARB were E. coli (42.5%) followed by Klebsiella spp. (22.5%), and Salmonella spp. (20%), mainly detected on lettuce. Twenty-five articles mentioned health risks from consuming fresh produce but none quantified the risk. About half of the articles stated produce contamination occurred during pre- and post-harvest processes. Our review indicates that good agricultural and manufacturing practices, behavioural change communication and awareness-raising programs are required for all stakeholders along the food production and consumption supply chain to prevent ARB/ARG exposure through produce

Effective Treatment Strategies for the Removal of Antibiotic-Resistant Bacteria, Antibiotic-Resistance Genes, and Antibiotic Residues in the Effluent From Wastewater Treatment Plants Receiving Municipal, Hospital, and Domestic Wastewater: Protocol for a Systematic Review.

BACKGROUND: The widespread and unrestricted use of antibiotics has led to the emergence and spread of antibiotic-resistant bacteria (ARB), antibiotic-resistance genes (ARGs), and antibiotic residues in the environment. Conventional wastewater treatment plants (WWTPs) are not designed for effective and adequate removal of ARB, ARGs, and antibiotic residues, and therefore, they play an important role in the dissemination of antimicrobial resistance (AMR) in the natural environment. OBJECTIVE: We will conduct a systematic review to determine the most effective treatment strategies for the removal of ARB, ARGs, and antibiotic residues from the treated effluent disposed into the environment from WWTPs that receive municipal, hospital, and domestic discharge. METHODS: We will search the MEDLINE, EMBASE, Web of Science, World Health Organization Global Index Medicus, and ProQuest Environmental Science Collection databases for full-text peer-reviewed journal articles published between January 2001 and December 2020. We will select only articles published in the English language. We will include studies that measured (1) the presence, concentration, and removal rate of ARB/ARGs going from WWTP influent to effluent, (2) the presence, concentration, and types of antibiotics in the effluent, and (3) the possible selection of ARB in the effluent after undergoing treatment processes in WWTPs. At least two independent reviewers will extract data and perform risk of bias assessment. An acceptable or narrative synthesis method will be followed to synthesize the data and present descriptive characteristics of the included studies in a tabular form. The study has been approved by the Ethics Review Board at the International Centre for Diarrhoeal Disease Research, Bangladesh (protocol number: PR-20113). RESULTS: This protocol outlines our proposed methodology for conducting a systematic review. Our results will provide an update to the existing literature by searching additional databases. CONCLUSIONS: Findings from our systematic review will inform the planning of proper treatment methods that can effectively reduce the levels of ARB, ARGs, and residual antibiotics in effluent, thus lowering the risk of the environmental spread of AMR and its further transmission to humans and animals. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/33365

Luminol/Sulfamic Acid Electrochemiluminescence and Its Application for Dopamine Detection

在本文中,我们首次观察到氨基磺酸可以显著增强鲁米诺电化学发光,而且鲁米诺电化学发光的强度随着氨基磺酸浓度在0.1 μmol·L-1至500 μmol·L-1范围增加而线性增加。同时,我们观察到多巴胺可以显著猝灭鲁米诺-氨基磺酸电化学发光。基于该猝灭现象,我们建立了多巴胺的电化学发光分析方法,该方法的线性范围为0.5至20 μmol·L-1,检出限为30 nmol·L-1。该方法具有较好的选择性,尿酸、抗坏血酸、糖和一些氨基酸对电化学发光影响较小。采用标准加入法,成功地将鲁米诺-氨基磺酸体系用于尿液中多巴胺的电化学发光测定,回收率为103% ~ 105%。另外,我们还考察了多巴胺的猝灭机理,并用Stern-Volmer方程计算了的动态猝灭常数。Herein, sulfamic acid (SA) was utilized, for the first time, to enhance significantly the luminol electrochemiluminescence (ECL). With the SA concentration increased from 0.1 μmol·L-1 to 500 μmol·L-1 the ECL intensity increased proportionally. The developed luminol/SA ECL system was employed to detect dopamine (DA) based on its prominent quenching effect. The Stern-Volmer equation of Io/I= 1+Ksv[DA] could be applied to express well the quenching mechanism of DA in the luminol/SA ECL system. The calibration plot showed that the increase in the DA concentration from 0.5 to 20 μmol·L-1 decreased linearly the ECL intensity with a detection limit of 30 nmol·L-1. The luminol/SA ECL system was successfully carried out for DA detection in urine real sample by employing the standard addition method with the excellent recoveries of 103% ~ 105%. Selectivity of the as-developed ECL system was also investigated by using uric acid, ascorbic acid, sugars and amino acids. The results indicated that the ECL intensities changed negligibly in the presence of other substances.通讯作者:徐国宝E-mail:[email protected]:Guo-BaoXuE-mail:[email protected].中国科学院长春应用化学研究所电分析化学国家重点实验室,吉林 长春 1300222.中国科学技术大学应用化学与工程学院,安徽 合肥 2300263.Wolkite university, College of natural & computational science, Department of chemistry,P.O Box 07, Wolkite, Ethiopia4.Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, 35516, Mansoura, Egypt5.深圳大学化学与环境工程学院及物理与光电工程学院,深圳 广东 5180006.Ambo University, College of Medicine and Health Sciences, Department of Pharmacy, P. O. Box 19, Ambo, Ethiopia7.Jimma University, College of Natural Sciences, Department of Chemistry, P. O. Box 378, Jimma, Ethiopia1. State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, Jilin,China2. School of Applied chemistry and Engineering, University of Science and Technology of China, Hefei 230026, Anhui, China3. Wolkite university, College of Natural & Computational Science, Department of Chemistry, P.O Box 07, Wolkite, Ethiopia4. Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, 35516, Mansoura, Egypt5. College of Chemistry and Environmental Engineering and College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, Guangdong, China6. Ambo University, College of Medicine and Health Sciences, Department of Pharmacy, P. O. Box 19, Ambo, Ethiopia7. Jimma University, College of Natural Sciences, Department of Chemistry, P. O. Box 378, Jimma, Ethiopi

Association between footwear use and neglected tropical diseases: a systematic review and meta-analysis

BACKGROUND The control of neglected tropical diseases (NTDs) has primarily focused on preventive chemotherapy and case management. Less attention has been placed on the role of ensuring access to adequate water, sanitation, and hygiene and personal preventive measures in reducing exposure to infection. Our aim was to assess whether footwear use was associated with a lower risk of selected NTDs. METHODOLOGY We conducted a systematic review and meta-analysis to assess the association between footwear use and infection or disease for those NTDs for which the route of transmission or occurrence may be through the feet. We included Buruli ulcer, cutaneous larva migrans (CLM), leptospirosis, mycetoma, myiasis, podoconiosis, snakebite, tungiasis, and soil-transmitted helminth (STH) infections, particularly hookworm infection and strongyloidiasis. We searched Medline, Embase, Cochrane, Web of Science, CINAHL Plus, and Popline databases, contacted experts, and hand-searched reference lists for eligible studies. The search was conducted in English without language, publication status, or date restrictions up to January 2014. Studies were eligible for inclusion if they reported a measure of the association between footwear use and the risk of each NTD. Publication bias was assessed using funnel plots. Descriptive study characteristics and methodological quality of the included studies were summarized. For each study outcome, both outcome and exposure data were abstracted and crude and adjusted effect estimates presented. Individual and summary odds ratio (OR) estimates and corresponding 95% confidence intervals (CIs) were calculated as a measure of intervention effect, using random effects meta-analyses. PRINCIPAL FINDINGS Among the 427 studies screened, 53 met our inclusion criteria. Footwear use was significantly associated with a lower odds of infection of Buruli ulcer (OR=0.15; 95% CI: 0.08-0.29), CLM (OR=0.24; 95% CI: 0.06-0.96), tungiasis (OR=0.42; 95% CI: 0.26-0.70), hookworm infection (OR=0.48; 95% CI: 0.37-0.61), any STH infection (OR=0.57; 95% CI: 0.39-0.84), strongyloidiasis (OR=0.56; 95% CI: 0.38-0.83), and leptospirosis (OR=0.59; 95% CI: 0.37-0.94). No significant association between footwear use and podoconiosis (OR=0.63; 95% CI: 0.38-1.05) was found and no data were available for mycetoma, myiasis, and snakebite. The main limitations were evidence of heterogeneity and poor study quality inherent to the observational studies included. CONCLUSIONS/SIGNIFICANCE Our results show that footwear use was associated with a lower odds of several different NTDs. Access to footwear should be prioritized alongside existing NTD interventions to ensure a lasting reduction of multiple NTDs and to accelerate their control and elimination. PROTOCOL REGISTRATION PROSPERO International prospective register of systematic reviews CRD42012003338

The burden of neglected tropical diseases in Ethiopia, and opportunities for integrated control and elimination

Background: Neglected tropical diseases (NTDs) are a group of chronic parasitic diseases and related conditions that are the most common diseases among the 2·7 billion people globally living on less than US$2 per day. In response to the growing challenge of NTDs, Ethiopia is preparing to launch a NTD Master Plan. The purpose of this review is to underscore the burden of NTDs in Ethiopia, highlight the state of current interventions, and suggest ways forward. Results: This review indicates that NTDs are significant public health problems in Ethiopia. From the analysis reported here, Ethiopia stands out for having the largest number of NTD cases following Nigeria and the Democratic Republic of Congo. Ethiopia is estimated to have the highest burden of trachoma, podoconiosis and cutaneous leishmaniasis in sub-Saharan Africa (SSA), the second highest burden in terms of ascariasis, leprosy and visceral leishmaniasis, and the third highest burden of hookworm. Infections such as schistosomiasis, trichuriasis, lymphatic filariasis and rabies are also common. A third of Ethiopians are infected with ascariasis, one quarter is infected with trichuriasis and one in eight Ethiopians lives with hookworm or is infected with trachoma. However, despite these high burdens of infection, the control of most NTDs in Ethiopia is in its infancy. In terms of NTD control achievements, Ethiopia reached the leprosy elimination target of 1 case/10,000 population in 1999. No cases of human African trypanosomiasis have been reported since 1984. Guinea worm eradication is in its final phase. The Onchocerciasis Control Program has been making steady progress since 2001. A national blindness survey was conducted in 2006 and the trachoma program has kicked off in some regions. Lymphatic Filariasis, podoconiosis and rabies mapping are underway. Conclusion: Ethiopia bears a significant burden of NTDs compared to other SSA countries. To achieve success in integrated control of NTDs, integrated mapping, rapid scale up of interventions and operational research into co implementation of intervention packages will be crucial

Pathogenesis of progressive scarring trachoma in Ethiopia and Tanzania and its implications for disease control: two cohort studies.

BACKGROUND: Trachoma causes blindness through a conjunctival scarring process initiated by ocular Chlamydia trachomatis infection; however, the rates, drivers and pathophysiological determinants are poorly understood. We investigated progressive scarring and its relationship to conjunctival infection, inflammation and transcript levels of cytokines and fibrogenic factors. METHODOLOGY/PRINCIPAL FINDINGS: We recruited two cohorts, one each in Ethiopia and Tanzania, of individuals with established trachomatous conjunctival scarring. They were followed six-monthly for two years, with clinical examinations and conjunctival swab sample collection. Progressive scarring cases were identified by comparing baseline and two-year photographs, and compared to individuals without progression. Samples were tested for C. trachomatis by PCR and transcript levels of S100A7, IL1B, IL13, IL17A, CXCL5, CTGF, SPARCL1, CEACAM5, MMP7, MMP9 and CD83 were estimated by quantitative RT-PCR. Progressive scarring was found in 135/585 (23.1%) of Ethiopian participants and 173/577 (30.0%) of Tanzanian participants. There was a strong relationship between progressive scarring and increasing inflammatory episodes (Ethiopia: OR 5.93, 95%CI 3.31-10.6, p<0.0001. Tanzania: OR 5.76, 95%CI 2.60-12.7, p<0.0001). No episodes of C. trachomatis infection were detected in the Ethiopian cohort and only 5 episodes in the Tanzanian cohort. Clinical inflammation, but not scarring progression, was associated with increased expression of S100A7, IL1B, IL17A, CXCL5, CTGF, CEACAM5, MMP7, CD83 and reduced SPARCL1. CONCLUSIONS/SIGNIFICANCE: Scarring progressed in the absence of detectable C. trachomatis, which raises uncertainty about the primary drivers of late-stage trachoma. Chronic conjunctival inflammation appears to be central and is associated with enriched expression of pro-inflammatory factors and altered expression of extracellular matrix regulators. Host determinants of scarring progression appear more complex and subtle than the features of inflammation. Overall this indicates a potential role for anti-inflammatory interventions to interrupt progression and the need for trichiasis disease surveillance and surgery long after chlamydial infection has been controlled at community level

Incidence, prevalence and mortality rates of malaria in Ethiopia from 1990 to 2015: analysis of the global burden of diseases 2015

Background: In Ethiopia there is no complete registration system to measure disease burden and risk factors accurately. In this study, the 2015 Global Burden of Diseases, Injuries and Risk factors (GBD) data were used to analyse the incidence, prevalence and mortality rates of malaria in Ethiopia over the last 25 years. Methods: GBD 2015 used verbal autopsy (VA) surveys, reports, and published scientific articles to estimate the burden of malaria in Ethiopia. Age and gender-specific causes of death for malaria were estimated using Cause of Death Ensemble Modelling (CODEm). Results: The number of new cases of malaria declined from 2.8 million (95% uncertainty interval (UI): 1.4-4.5million) in 1990 to 621,345 (95% UI: 462,230-797,442) in 2015. Malaria caused an estimated 30,323.9 deaths (95% UI: 11,533.3-61,215.3) in 1990 and 1,561.7 deaths (95% UI: 752.8-2,660.5) in 2015, a 94.8% reduction over the 25 years. Age-standardized mortality rate of malaria has declined by 96.5% between 1990 and 2015 with an annual rate of change (ARC) of 13.4%. Age-standardized malaria incidence rate among all ages and gender declined by 88.7% between 1990 and 2015. The number of disability-adjusted life years lost (DALY) due to malaria decreased from 2.2 million (95% UI: 0.76-4.7 million) in 1990 to 0.18 million (95% UI: 0.12-0.26 million) in 2015, with a total reduction 91.7%. Similarly, age-standardized DALY rate declined by 94.8% during the same period. Conclusions: Ethiopia has achieved a 50% reduction target of malaria of the Millennium Development Goals (MDGs). The country should strengthen its malaria control and treatment strategies to achieve the Sustainable Development Goals (SDG)