scholarly journals Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 655 ◽  
Author(s):  
Junier ◽  
Huber ◽  
Schmutz ◽  
Kufner ◽  
Zagordi ◽  
...  
Keyword(s):  
Quality Control ◽  
Viral Infections ◽  
Lessons Learned ◽  
Viral Metagenomics ◽  
Reference Database ◽  
Shotgun Metagenomics ◽  
Dna And Rna ◽  
Definition Of ◽  
Next Generation Sequencing Ngs ◽  
The Impact

Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5–10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.

scholarly journals Demystification of RNAseq Quality Control

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Dragana Dudić ◽  
Bojana Banović Đeri ◽  
Vesna Pajić ◽  
Gordana Pavlović-Lažetić
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Rna Sequencing ◽  
Next Generation ◽  
Comprehensive Guidance ◽  
Dna And Rna ◽  
Control Evaluation ◽  
Downstream Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next Generation Sequencing (NGS) analysis has become a widely used method for studying the structure of DNA and RNA, but complexity of the procedure leads to obtaining error-prone datasets which need to be cleansed in order to avoid misinterpretation of data. We address the usage and proper interpretations of characteristic metrics for RNA sequencing (RNAseq) quality control, implemented in and reported by FastQC, and provide a comprehensive guidance for their assessment in the context of total RNAseq quality control of Illumina raw reads. Additionally, we give recommendations how to adequately perform the quality control preprocessing step of raw total RNAseq Illumina reads according to the obtained results of the quality control evaluation step; the aim is to provide the best dataset to downstream analysis, rather than to get better FastQC results. We also tested effects of different preprocessing approaches to the downstream analysis and recommended the most suitable approach.

scholarly journals Immunopathologic Effects of Prednisolone and Cyclosporine A on Feline Immunodeficiency Virus Replication and Persistence

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 805
Author(s):  
Craig Miller ◽  
Jordan Powers ◽  
Esther Musselman ◽  
Ryan Mackie ◽  
John Elder ◽  
...  
Keyword(s):  
Cyclosporine A ◽  
Feline Immunodeficiency Virus ◽  
Viral Infections ◽  
Th2 Response ◽  
Drug Induced ◽  
Opportunistic Disease ◽  
Dna And Rna ◽  
Immunodeficiency Virus ◽  
Pre Treatment ◽  
The Impact

Feline immunodeficiency virus (FIV) induces opportunistic disease in chronically infected cats, and both prednisolone and cyclosporine A (CsA) are clinically used to treat complications such as lymphoma and stomatitis. However, the impact of these compounds on FIV infection are still unknown and understanding immunomodulatory effects on FIV replication and persistence is critical to guide safe and effective therapies. To determine the immunologic and virologic effects of prednisolone and CsA during FIV infection, FIV-positive cats were administered immunosuppressive doses of prednisolone (2 mg/kg) or CsA (5 mg/kg). Both prednisolone and CsA induced acute and transient increases in FIV DNA and RNA loads as detected by quantitative PCR. Changes in the proportion of lymphocyte immunophenotypes were also observed between FIV-infected and naïve cats treated with CsA and prednisolone, and both treatments caused acute increases in CD4+ lymphocytes that correlated with increased FIV RNA. CsA and prednisolone also produced alterations in cytokine expression that favored a shift toward a Th2 response. Pre-treatment with CsA slightly enhanced the efficacy of antiretroviral therapy but did not enhance clearance of FIV. Results highlight the potential for drug-induced perturbation of FIV infection and underscore the need for more information regarding immunopathologic consequences of therapeutic agents on concurrent viral infections.

scholarly journals Search for Viral Infections in Cerebrospinal Fluid From Patients With Autoimmune Encephalitis

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Karol Perlejewski ◽  
Agnieszka Pawełczyk ◽  
Iwona Bukowska-Ośko ◽  
Małgorzata Rydzanicz ◽  
Tomasz Dzieciątkowski ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Viral Infections ◽  
Autoimmune Encephalitis ◽  
Rt Pcr ◽  
Shotgun Metagenomics ◽  
Specific Pcr ◽  
Dna And Rna ◽  
Brain Tissue Damage ◽  
Dipeptidyl Aminopeptidase

Abstract Background It has been reported that virus-mediated brain tissue damage can lead to autoimmune encephalitis (AE) characterized by the presence of antibodies against neuronal surface antigens. In the study, we investigate the presence of viruses in cerebrospinal fluid (CSF) from patients with AE using reverse transcription polymerase chain reaction (RT-PCR)/PCR and shotgun metagenomics. Methods CSF samples collected from 200 patients with encephalitis were tested for the presence of antibodies against antiglutamate receptor (NMDAR), contactin-associated protein 2 (CASPR2), glutamate receptors (type AMPA1/2), leucine-rich glioma-inactivated protein 1 (LGI1), dipeptidyl aminopeptidase-like protein 6 (DPPX), and GABA B receptor, and those found positive were further analyzed with real-time RT-PCR/PCR for common viral neuroinfections and shotgun DNA- and RNA-based metagenomics. Results Autoantibodies against neuronal cells were detected in CSF from 8 individuals (4% of all encephalitis patients): 7 (3.5%) had anti-NMDAR and 1 (0.5%) had anti-GABA B. RT-PCR/PCR identified human herpes virus type 1 (HSV-1; 300 copies/mL) and the representative of Enterovirus genus (550 copies/mL) in 1 patient each. Torque teno virus (TTV) was found in another patient using metagenomic analysis, and its presence was confirmed by specific PCR. Conclusions We detected the presence of HSV, TTV, and Enterovirus genus in CSF samples from 3 out of 8 AE patients. These findings support the concept of viral involvement in the pathogenesis of this disease.

scholarly journals Psychological Reactions of Hospital Workers to a Pandemic: A Comparison of SARS-CoV-2 in 2020 and SARS in 2003

2022 ◽  
Vol 19 (2) ◽  
pp. 833
Author(s):  
Yu Lee ◽  
Liang-Jen Wang ◽  
Wen-Jiun Chou ◽  
Ming-Chu Chiang ◽  
Shan Huang ◽  
...  
Keyword(s):  
Viral Infections ◽  
Medical Center ◽  
Psychiatric Morbidity ◽  
Psychological Impact ◽  
Current Data ◽  
Lessons Learned ◽  
Hospital Workers ◽  
Impact Of Event Scale ◽  
Event Scale ◽  
The Impact

Epidemic viral infections, including the outbreak of severe acute respiratory syndrome (SARS) in 2003 and SARS-CoV-2 in 2019, have brought tremendous loss to people across the nations. The aim of this study was to compare the psychological impact of the SARS-CoV-2 pandemic in 2020 and the SARS pandemic in 2003 on hospital workers. Hospital workers at a medical center in Southern Taiwan (n = 1816) were invited to complete questionnaires (SARS-CoV-2 Exposure Experience, the Impact of Event Scale, the Chinese Health Questionnaire, and the Distress Thermometer). The current data were compared to the data collected from hospital workers (n = 1257) at the same medical center during the SARS pandemic in 2003. We found the psychological impact on hospital workers during the SARS-CoV-2 pandemic was significantly lower than that during the previous SARS period. During the SARS-CoV-2 pandemic period, hospital workers with SARS experience were more accepting of the risk, felt a greater responsibility to take care of the SARS-CoV-2 patients, and were more likely to perceive the danger of becoming infected. The associated factors of psychiatric morbidity in hospital workers with SARS experience were being female, the degree of intrusion severity, and severity of psychological distress. Proper management strategies and lessons learned from the SARS experience might have led to low psychiatric morbidity during the SARS-CoV-2 pandemic.

Characterization of Interventional Studies of the Cholera Epidemic in Haiti

2018 ◽  
Vol 33 (2) ◽  
pp. 176-181
Author(s):  
Jessica Miller ◽  
Marvin L. Birnbaum
Keyword(s):  
International Development ◽  
Lessons Learned ◽  
World Health ◽  
Publication Type ◽  
Cholera Epidemic ◽  
Pubmed Search ◽  
Definition Of ◽  
Health Organization ◽  
The Impact

AbstractIn October 2010, the Haitian Ministry of Public Health and Population (MSPP; Port au Prince, Haiti) reported a cholera epidemic caused by contamination of the Artibonite River by a United Nation Stabilization Mission camp. Interventional studies of the subsequent responses, including a descriptive Methods section and systematic approach, may be useful in facilitating comparisons and applying lessons learned to future outbreaks. The purpose of this study was to examine publicly available documents relating to the 2010 cholera outbreak to answer: (1) What information is publicly available on interventional studies conducted during the epidemic, and what was/were the impact(s)? and (2) Can the interventions be compared, and what lessons can be learned from their comparison?A PubMed (National Center for Biotechnology Information, National Institutes of Health; Bethesda, Maryland USA) search was conducted using the parameters “Haiti” and “cholera.” Studies were categorized as “interventional research,” “epidemiological research,” or “other.” A distinction was made between studies and narrative reports. The PubMed search yielded 171 papers, 59 (34.0%) of which were epidemiological and 12 (7.0%) were interventional studies. The remaining 100 papers (59.0%) comprised largely of narrative, anecdotal descriptions. An expanded examination of publications by the World Health Organization (WHO; Geneva, Switzerland), the Center for Research in the Epidemiology of Disasters (CRED; Brussels, Belgium), United States Agency for International Development (USAID; Washington, DC USA)-Development Experience Clearinghouse (DEC), and US National Library of Medicine’s (NLM; Bethesda, Maryland USA) Disaster Literature databases yielded no additional interventional studies. The unstructured formats and differing levels of detail prohibited comparisons between interventions, even between those with a similar approach. Only two (17.0%) interventional studies included any impact data, although neither commented whether the intervention improved health or reduced incidence or mortality related to cholera. Agreed frameworks for guiding responses and subsequent reporting are needed to ensure reports contain sufficient detail to draw conclusions for the definition of best practices and for the design of future interventions.MillerJ, BirnbaumML. Characterization of interventional studies of the cholera epidemic in Haiti. Prehosp Disaster Med. 2018;33(2):176–181.

PERTANGGUNGJAWABAN KERUGIAN NEGARA DALAM PENGELOLAAN KEUANGAN DAERAH

EDUKASI ◽  
2018 ◽  
Vol 16 (1) ◽  
Author(s):  
Hendra Karianga
Keyword(s):  
Financial Management ◽  
Criminal Liability ◽  
The State ◽  
Legal Proceedings ◽  
Regional Finance ◽  
Regional Budget ◽  
State Finance ◽  
Budget Policy ◽  
Definition Of ◽  
The Impact

Sources of revenue and expenditure of APBD (regional budget) can be allocated to finance the compulsory affairs and optional affairs in the form of programs and activities related to the improvement of public services, job creation, poverty alleviation, improvement of environmental quality, and regional economic growth. The implications of these policies is the need for funds to finance the implementation of the functions, that have become regional authority, is also increasing. In practice, regional financial management still poses a complicated issue because the regional head are reluctant to release pro-people regional budget policy, even implication of regional autonomy is likely to give birth to little kings in region causing losses to state finance and most end up in legal proceedings. This paper discusses the loss of state finance and forms of liability for losses to the state finance. The result of the study can be concluded firstly,  there are still many differences in giving meaning and definition of the loss of state finace and no standard definition of state losses, can cause difficulties. The difficulty there is in an effort to determine the amount of the state finance losses. The calculation of state/regions losses that occur today is simply assessing the suitability of the size of the budget and expenditure without considering profits earned by the community and the impact of the use of budget to the community. Secondly, the liability for losses to the state finance is the fulfillment of the consequences for a person to give or to do something in the regional financial management by giving birth to three forms of liability, namely the Criminal liability, Civil liability, and Administrative liability.Keywords: state finance losses, liability, regional finance.

cMOOCs and Global Learning: An Authentic Alternative

2013 ◽  
Vol 17 (2) ◽  
Author(s):  
Carol Yeager ◽  
Betty Hurley-Dasgupta ◽  
Catherine A. Bliss
Keyword(s):  
Online Courses ◽  
Lessons Learned ◽  
Massive Open Online Courses ◽  
Research Review ◽  
Press Coverage ◽  
Open Educational Resource ◽  
Educational Resource ◽  
Global Learning ◽  
Massive Open Online ◽  
Definition Of

Massive Open Online Courses (MOOCs) continue to attract press coverage as they change almost daily in their format, number of registrations and potential for credentialing. An enticing aspect of the MOOC is its global reach. In this paper, we will focus on a type of MOOC called a cMOOC, because it is based on the theory of connectivism and fits the definition of an Open Educational Resource (OER) identified for this special edition of JALN. We begin with a definition of the cMOOC and a discussion of the connectivism on which it is based. Definitions and a research review are followed with a description of two MOOCs offered by two of the authors. Research on one of these MOOCs completed by a third author is presented as well. Student comments that demonstrate the intercultural connections are shared. We end with reflections, lessons learned and recommendations.

Empowering Women Entrepreneurs Through Microfinance - A Case of Rural Bangladesh

2017 ◽  
Vol 3 (2) ◽  
pp. 7
Author(s):  
Saida Parvin
Keyword(s):  
Women's Empowerment ◽  
Assessment Tools ◽  
Women’S Empowerment ◽  
Case Study Method ◽  
Policy Makers ◽  
Theoretical Contribution ◽  
Donor Agencies ◽  
Definition Of ◽  
The Impact

Women’s empowerment has been at the centre of research focus for many decades. Extant literature examined the process, outcome and various challenges. Some claimed substantial success, while others contradicted with evidence of failure. But the success remains a matter of debate due to lack of empirical evidence of actual empowerment of women around the world. The current study aimed to address this gap by taking a case study method. The study critically evaluates 20 cases carefully sampled to include representatives from the entire country of Bangladesh. The study demonstrates popular beliefs about microfinance often misguide even the borrowers and they start living in a fabricated feeling of empowerment, facing real challenges to achieve true empowerment in their lives. The impact of this finding is twofold; firstly there is a theoretical contribution, where the definition of women’s empowerment is proposed to be revisited considering findings from these cases. And lastly, the policy makers at governmental and non-governmental organisations, and multinational donor agencies need to revise their assessment tools for funding.

Characteristics of Physician Relocation Following Hurricane Katrina

2009 ◽  
Vol 95 (1) ◽  
pp. 6-12
Author(s):  
Kusuma Madamala ◽  
Claudia R. Campbell ◽  
Edbert B. Hsu ◽  
Yu-Hsiang Hsieh ◽  
James James
Keyword(s):  
Hurricane Katrina ◽  
Gulf Coast ◽  
General Medicine ◽  
The United States ◽  
Lessons Learned ◽  
Bivariate Analysis ◽  
Fisher Exact Test ◽  
Exact Test ◽  
Factors Associated ◽  
The Impact

ABSTRACT Introduction: On Aug. 29, 2005, Hurricane Katrina made landfall along the Gulf Coast of the United States, resulting in the evacuation of more than 1.5 million people, including nearly 6000 physicians. This article examines the relocation patterns of physicians following the storm, determines the impact that the disaster had on their lives and practices, and identifies lessons learned. Methods: An Internet-based survey was conducted among licensed physicians reporting addresses within Federal Emergency Management Agency-designated disaster zones in Louisiana and Mississippi. Descriptive data analysis was used to describe respondent characteristics. Multivariate logistic regression was performed to identify the factors associated with physician nonreturn to original practice. For those remaining relocated out of state, bivariate analysis with x2 or Fisher exact test was used to determine factors associated with plans to return to original practice. Results: A total of 312 eligible responses were collected. Among disaster zone respondents, 85.6 percent lived in Louisiana and 14.4 percent resided in Mississippi before the hurricane struck. By spring 2006, 75.6 percent (n = 236) of the respondents had returned to their original homes, whereas 24.4 percent (n = 76) remained displaced. Factors associated with nonreturn to original employment included family or general medicine practice (OR 0.42, 95 percent CI 0.17–1.04; P = .059) and severe or complete damage to the workplace (OR 0.24, 95 percent CI 0.13–0.42; P < .001). Conclusions: A sizeable proportion of physicians remain displaced after Hurricane Katrina, along with a lasting decrease in the number of physicians serving in the areas affected by the disaster. Programs designed to address identified physician needs in the aftermath of the storm may give confidence to displaced physicians to return.

Sign in / Sign up

Export Citation Format

Share Document