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A revision of the InfiniumPurify R package for genome-wide correction of tumor purity in Infinium DNA methylation array data

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Genes & Diseases 2023年第3期10卷 698-700页

作者： Phuc H.Hoang Division of Cancer epidemiology and Genetics National Cancer InstituteBethesdaMD 20892USA

Understanding DNA methylation(DNAm)alterations in tumors is important to develop novel therapeutic targets and powerful biomarkers,and to gain insights into tumorigenesis processes.As many studies have highlighted the confounding effects of tumor purity in DNAm analyses,1,2,3 various tools have also been developed to tackle the issue.2,3,4 Among them,InfiniumPurify R package is a popular and widely cited tool,2,3,5 consisting of a set of statistical methods to estimate and account for tumor purity in cancer DNAm analyses.

关键词： alterations purity correction

Mechanism of Japanese encephalitis virus genotypes replacement based on human,porcine and mosquito-originated cell lines model

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Asian Pacific Journal of Tropical Medicine 2016年第4期9卷 325-328页

作者： Loan Phuong Do Trang Minh Bui Nga Thi Phan National institute of Hygiene and epidemiology

Objective:To examine the multiplication efficiency Japanese encephalitis virus(JEV)genotype Ⅰ(G Ⅰ) and genotype Ⅲ(GⅢ) of different cell lines which originated from human,porcine,mosquitoes in order to prove mechanism of JEV G Ⅰ replacement JEV GⅢ since it emerging in nature recent decades.Methods:The mixture of Gi and GⅢ JEV isolates was inoculated on human rhabdomyosarcoma(RD).pig kidney epithelial(PS) and Aedes albopictus C6/36 clone(C6/36) which originated from human,porcine and mosquitoes,respectively.Plaque assays were performed to calculate virus titer and real-time RT-PCR with GⅠand GⅢspecific primer sets to quantify the number of GⅠ and GUI RNA copies.Results:The highest virus titer reached at the 3rd day of post infection when G Ⅰand GⅢ mixture was inoculated on RD and PS and that of C636 was at the 4^(th)day.JEVs were amplified and maintained by C6/36 cells after 10 passages whereas that by RD and PS only limited within 8 and 6 passages,respectively.GⅠ strain amplified and maintained more efficiently on C6/36 and PS but not RD.whereas GⅢ strain amplified and maintained more efficiently on RD.Conclusions:There is a correlation between the multiplication efficiency of GⅠ and GⅢ JEV strains when these two genotype strains co-infected on different cell lines with the predominance of GⅠstrains in C6/36 and PS and the limited detection of G 1 strains in RD cells proving a possible mechanism of shift JEV genotypes in nature recent decades since GⅠ emerging.

关键词： Japanese encephalitis virus Genotype I Genotype Ⅲ Multiplication Shift genotype

Could a phase model help to improve translational animal research?

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Animal Models and Experimental Medicine 2022年第6期5卷 550-556页

作者： Benjamin Mayer Jan Tuckermann Rainer Muche Institute of Epidemiology and Medical Biometry Ulm UniversityUlmGermany institute of Comparative Molecular Endocrinology Ulm UniversityUlmGermany

Background:Animal models are widely applied in medical research for different purposes.In particular,results from translational experiments may be used for subsequent clinical development.However,transferability of these findings to the human organism is controversial.Among other factors,this may be traced back to a lack of clear differentiation of the evidence(explorative vs.confirmatory)provided by such experimental results.In general,inferential statistics(i.e.p values)should not be interpreted in as confirmatory unless crucial methodological requirements are met.Methods:Therefore,we propose a phase model which reflects the well-established process of clinical research,and we discuss its potential to improve decision making in translational research.The model aims to clarify the reliability of results derived from animal models.Results:The phase model proposes subdividing translational,pre-clinical research into pilot,exploration,and confirmation phases.Experiments for which there is no valid estimation of the expected effect size are designated as pilot studies.Based on these data,experiments in subsequent phases may be planned using both appropriate design and statistical methods.Conclusion:Separating the entire process of translational animal research into three phases could contribute to improved transparency of the evidence derived from such experiments.

关键词： confirmatory trials hypothesis testing results interpretation transferability

Introduction of Zika virus in Bangladesh:An impending public health threat

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Asian Pacific Journal of Tropical Medicine 2017年第9期10卷 925-928页

作者： A.K.M.Muraduzzaman Sharmin Sultana Tahmina Shirin Selina Khatun MdTarikul Islam Mahmudur Rahman Department of Virology Institute of EpidemiologyDisease Control&Research(IEDCR)DhakaBangladesh Department of epidemiology Institute of EpidemiologyDisease Control&Research(IEDCR)DhakaBangladesh Laboratory of Genetics and Genomics Institute for Developing Science and Health InitiativesDhakaBangladesh Institute of Epidemiology Disease Control&Research(IEDCR)DhakaBangladesh

Objective: To explore the presence of Zika virus(ZIKV) in Bangladesh and to understand the associated risk factors.Methods: A retrospective sero-surveillance was performed on stored serum samples of dengue surveillance conducted from 2013 to 2016. Real time RT-PCR was performed on randomly selected acute serum samples to detect the Zika virus nucleic acid.Results: Of 200 samples screened, one was found positive for ZIKV by real time RTPCR and further confirmed by genome sequencing. The case was a 65 years old male from a metropolitan city of Bangladesh who had no history of travel outside Bangladesh.Phylogenetic analysis of partial E gene sequences from Bangladeshi isolates demonstrated a close relationship with ZIKV from Brazil and current South American strains clustering within a monophyletic clade distinct from African lineage.Conclusions: Presence of ZIKV raises serious public health concerns in Bangladesh owing to its association with congenital anomalies/neurological-manifestations. We,therefore, recommend every suspected viral fever patient, particularly pregnant women be screened for ZIKV infection to rule out yet another emerging infection in Bangladesh.

关键词： Zika 病毒孟加拉国公共健康影响

The impact of weather on summer and winter exercise behaviors

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Journal of Sport and Health Science 2019年第1期8卷 39-45页

作者： Abram L.Wagner Florian Keusch Ting Yan Philippa J.Clarke Department of epidemiology University of Michigan institute for Social Research University of Michigan

Background: Outdoor exercise is an enjoyable way for individuals to improve fitness, but it is dependent on weather conditions. This study examines the association between weather conditions and outdoor exercise after adjustment for age, sex, race, and socioeconomic status.Methods: We used data representative of American adults from the University of Michigan/Thomson Reuters June 2013 surveys of consumers(core and supplement) to investigate self-reported exercise behavior in summer and winter. Multivariate multinomial logistic regression models estimated the odds of delayed or indoor exercise compared with outdoor exercise.Results: Of the 502 respondents, 16.3% did not regularly exercise outdoors(i.e., at least once a week), and many would delay exercise both in summer(51.8%) and winter(43.9%). Individuals listing rain as the predominant adverse weather condition had 3.33 times higher odds of exercising indoors(95% confidence interval(CI): 1.34-8.28) and 3.49 times higher odds of delaying exercise(95%CI: 1.69-7.21) compared with those mentioning heat as the predominant adverse condition. Individuals for whom ice or snow was an adverse winter weather condition were more likely to delay exercise(odds ratio(OR) = 3.34; 95%CI: 1.19-9.36), compared with those concerned with cold.Conclusion: This study found that race, age, and education exacerbate the negative effects of adverse weather conditions on the decision to exercise outdoors. Accordingly, any recommendation for an individual to exercise outdoors should be combined with an evaluation of the individual's outdoor environment along with strategies for the individual to continue exercising, indoors or outdoors, when adverse weather is present.

关键词： Outdoor exercise Physical activity Rain Seasons Snow Survey

Pharmaceutical effluent evokes superbugs in the environment:A call to action

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Biosafety and Health 2023年第6期5卷 363-371页

作者： Rehab A.Rayan Department of epidemiology High Institute of Public HealthAlexandria UniversityAlexandria 21526Egypt

Antimicrobial resistance(AMR)is a growing global threat,especially in low-and middle-income countries(LMICs),causing prolonged illnesses,heightened antimicrobial use,increased healthcare expenses,and avoidable deaths.If not tackled,AMR could force 24 million people into severe poverty by 2030 and hinder progress on Sustainable Development Goals(SDGs).AMR spreads through interconnected ecosystems,with humans,animals,and the environment serving as reservoirs.Pharmaceutical wastewater,loaded with antibiotics and resistance genes,poses a significant environmental risk,mainly due to inadequate treatment and irresponsible disposal.The pharmaceutical industry is a notable contributor to environmental antibiotic pollution,with varying effluent management practices.Contaminated pharmaceutical wastewater discharge harms water sources and ecosystems.Urgent collaborative efforts are needed across policymakers,regulators,manufacturers,researchers,civil society,and communities,adopting a One Health approach to curb AMR's spread.Developing global standards for pharmaceutical effluent antibiotic residues,effective treatment methods,and improved diagnostics are vital in addressing AMR's environmental impact while safeguarding public health and the environment.National action plans should encompass comprehensive strategies to combat AMR.Preserving antibiotic efficacy and ensuring sustainable production require a united front from all stakeholders.

关键词： One Health Environmental Health Public Health Antibiotics Antimicrobial resistance Superbugs Antimicrobial stewardship Pharmaceutical industry Pharmaceutical effluent

A small,polyphyletic group of Firmicutes synthesizes trimethylamine from L-carnitine

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mLife 2023年第3期2卷 267-271页

作者： Marius Vital Ylenia Heinrich-Sanchez Hannover Medical School Institute for Medical Microbiology and Hospital EpidemiologyHannoverGermany

Impact statement Gut microbiota-derived trimethylamine(TMA)is associated with cardiometabolic disorders and exemplifies a microbial involvement in the etiology of emerging,noncommunicable diseases,the leading causes of death worldwide.Three bio-chemical pathways taking dietary compounds as intake have been described with distinct taxa involved that are all present at low relative abundances.A recently discovered pathway is now considered to be the main route for TMA synthesis from L-carnitine involvingγ-butyrobetaine as an intermediate product.By comprehensive(meta)genomic screening of publicly available data,namely,genomes of the UHGG catalog(n>200,000)and 10 metagenomic(transcriptomic)data sets,we revealed bacteria synthesizing TMA via this pathway and specified their ecophysiology.Results will contribute to stratification of individuals based on their gut microbiota's potential to synthesize TMA and might aid in the development of strategies restricting TMA formation.

关键词： product. synthesize statement

Reverse spillover of SARS-CoV-2 from human to wild animals

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Science China(Life Sciences) 2022年第9期65卷 1902-1904页

作者： Mingyuan Li Xiaohe Cheng Chengfeng Qin State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyAMMSBeijing 100071China

The heavily transmitted and mutated SARS-CoV-2 has constitutes a sustained threat to global health.A recent article published in Nature,firstly provided solid evidence confirming the cross-species transmission of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)from human to free-ranging white-tailed deer(Hale et al.,2022).More importantly,circulation of SARS-CoV-2 among deer rapidly resulted into new phylogenetic clades of deer-only viruses which were believed linking to the high infection rate of SARS-CoV-2 within white-tailed deer in northeast Ohio,USA(Hale et al.,2022).

关键词： sustained acute

Pandora of Ebola virus: are we ready?

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Chinese Science Bulletin 2014年第32期59卷 4235-4236页

作者： Ruifu Yang Beijing institute of Microbiology and epidemiology

在 2014 年 3 月 23 日，畿尼的健康的部通知了在东南的 forested 区域的 Ebola 病毒疾病(EVD ) 的很快传播的爆发，并且 4 ? 天以后，疾病被证实被传给 Conakry，畿尼的首都。疾病很快也传播了到利比里亚，尼日利亚和塞拉利昂。2014 年... 详细信息

在 2014 年 3 月 23 日，畿尼的健康的部通知了在东南的 forested 区域的 Ebola 病毒疾病(EVD ) 的很快传播的爆发，并且 4 ? 天以后，疾病被证实被传给 Conakry，畿尼的首都。疾病很快也传播了到利比里亚，尼日利亚和塞拉利昂。2014 年 7 月 27 日，累积数字证实(909 ) ，可能(276 ) 并且在上述四个国家的嫌疑犯(138 ) EVD 盒子到达了 1,323，包括 729 死亡(与 55.1 的死亡率 ?%)(http://www.***.int/csr/don/2014_07_31_ebola/en/) 。这是 EVD 的最大的爆发直到现在并且第一次疾病在韦斯特检测了非洲。

关键词：埃博拉病毒 EVD 森林地区利比里亚塞拉利昂尼日利亚 HTTP 几内亚