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Biochimica Et Biophysica Acta.... Mar 2021Structure determination of membrane proteins is critical to the molecular understanding of many life processes, yet it has historically been a technically challenging... (Meta-Analysis)
Meta-Analysis
Structure determination of membrane proteins is critical to the molecular understanding of many life processes, yet it has historically been a technically challenging endeavor. This past decade has given rise to a number of technological advancements, techniques, and reagents, which have facilitated membrane protein structural biology, resulting in an ever-growing number of membrane protein structures determined. To collate these advances, we have mined available literature to analyze the purification and structure determination specifics for all uniquely solved membrane protein structures from 2010 to 2019. Our analyses demonstrate the strong impact of single-particle cryo-electron microscopy on the field and illustrate how this technique has affected detergent and membrane mimetic usage. Furthermore, we detail how different structure determination methods, taxonomic domains and protein classes have unique detergent/membrane mimetic profiles, highlighting the importance of tailoring their selection. Our analyses provide a quantitative overview of where the field of membrane protein structural biology stands and how it has developed over time. We anticipate that these will serve as a useful tool to streamline future membrane protein structure determination by guiding the choice of detergent/membrane mimetic.
Topics: Biomimetic Materials; Cryoelectron Microscopy; Detergents; Lipid Bilayers; Membrane Proteins
PubMed: 33340490
DOI: 10.1016/j.bbamem.2020.183533 -
Epidemiology and Health 2018John Cunningham virus (JCV) is a polyoma virus that infects humans, mainly in childhood or adolescence, and presents no symptomatic manifestations. JCV can cause... (Review)
Review
OBJECTIVES
John Cunningham virus (JCV) is a polyoma virus that infects humans, mainly in childhood or adolescence, and presents no symptomatic manifestations. JCV can cause progressive multifocal leukoencephalopathy (PML) in immunosuppressed individuals, including those undergoing treatment for multiple sclerosis (MS) and neuromyelitis optica (NMO). PML is a severe and potentially fatal disease of the brain. The prevalence of JCV antibodies in human serum has been reported to be between 50.0 and 90.0%. The aim of the present study was to review worldwide data on populations of patients with MS and NMO in order to establish the rates of JCV seropositivity in these individuals.
METHODS
The present review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and used the following search terms: "JCV" OR "JC virus" AND "multiple sclerosis" OR "MS" OR "NMO" OR "neuromyelitis optica" AND "prevalence." These terms were searched for both in smaller and in larger clusters of words. The databases searched included PubMed, MEDLINE, SciELO, LILACS, Google Scholar, and Embase.
RESULTS
After the initial selection, 18 papers were included in the review. These articles reported the prevalence of JCV antibodies in the serum of patients with MS or NMO living in 26 countries. The systematic review identified data on 29,319 patients with MS/NMO and found that 57.1% of them (16,730 individuals) were seropositive for the anti-JCV antibody (range, 40.0 to 69.0%).
CONCLUSIONS
The median worldwide prevalence of JCV among adults with MS or NMO was found to be 57.1%.
Topics: Antibodies, Viral; Global Health; Humans; JC Virus; Multiple Sclerosis; Neuromyelitis Optica; Prevalence
PubMed: 29370683
DOI: 10.4178/epih.e2018001 -
Journal of Clinical Microbiology Dec 2015Respiratory syncytial virus (RSV) rapid antigen detection tests (RADT) are extensively used in clinical laboratories. We performed a systematic review and meta-analysis... (Meta-Analysis)
Meta-Analysis Review
Respiratory syncytial virus (RSV) rapid antigen detection tests (RADT) are extensively used in clinical laboratories. We performed a systematic review and meta-analysis to evaluate the accuracy of RADTs for diagnosis of RSV infection and to determine factors associated with accuracy estimates. We searched EMBASE and PubMed for diagnostic-accuracy studies of commercialized RSV RADTs. Studies reporting sensitivity and specificity data compared to a reference standard (reverse transcriptase PCR [RT-PCR], immunofluorescence, or viral culture) were considered. Two reviewers independently extracted data on study characteristics, diagnostic-accuracy estimates, and study quality. Accuracy estimates were pooled using bivariate random-effects regression models. Heterogeneity was investigated with prespecified subgroup analyses. Seventy-one articles met inclusion criteria. Overall, RSV RADT pooled sensitivity and specificity were 80% (95% confidence interval [CI], 76% to 83%) and 97% (95% CI, 96% to 98%), respectively. Positive- and negative-likelihood ratios were 25.5 (95% CI, 18.3 to 35.5) and 0.21 (95% CI, 0.18 to 0.24), respectively. Sensitivity was higher in children (81% [95% CI, 78%, 84%]) than in adults (29% [95% CI, 11% to 48%]). Because of this disparity, further subgroup analyses were restricted to pediatric data (63 studies). Test sensitivity was poorest using RT-PCR as a reference standard and highest using immunofluorescence (74% versus 88%; P < 0.001). Industry-sponsored studies reported significantly higher sensitivity (87% versus 78%; P = 0.01). Our results suggest that the poor sensitivity of RSV RADTs in adults may preclude their use in this population. Furthermore, industry-sponsored studies and those that did not use RT-PCR as a reference standard likely overestimated test sensitivity.
Topics: Adult; Antigens, Viral; Child; Child, Preschool; Humans; Immunoassay; Respiratory Syncytial Virus Infections; Respiratory Syncytial Viruses; Sensitivity and Specificity; Time Factors
PubMed: 26354816
DOI: 10.1128/JCM.01816-15 -
The Science of the Total Environment Oct 2021Indoor air purifiers are increasingly marketed for their health benefits, but their cardiovascular effects remain unclear. We systematically reviewed and meta-analysed... (Meta-Analysis)
Meta-Analysis
Indoor air purifiers are increasingly marketed for their health benefits, but their cardiovascular effects remain unclear. We systematically reviewed and meta-analysed randomized controlled trials (RCTs) on the cardiovascular effects of indoor air purification interventions in humans of all ages. We searched Embase, Medline, PubMed, and Web of Science from inception to 22 August 2020. Fourteen cross-over RCTs (18 publications) were included. Systolic blood pressure (SBP) was significantly reduced after intervention (-2.28 (95% CI: -3.92, -0.64) mmHg). There were tendencies of reductions in diastolic blood pressure (-0.35 [-1.52, 0.83] mmHg), pulse pressure (PP) (-0.86 [-2.07, 0.34] mmHg), C-reactive protein (-0.23 [-0.63, 0.18] mg/L), and improvement in reactive hyperaemia index (RHI) (0.10 [-0.04, 0.24]) after indoor air purification, although the effects were not statistically significant. However, when restricting the analyses to RCTs using physical-type purifiers only, significant improvements in PP (-1.56 [-2.98, -0.15] mmHg) and RHI (0.13 [0.01, 0.25]) were observed. This study found potential evidence on the short-term cardiovascular benefits of using indoor air purifiers, especially for SBP, PP and RHI. However, under the Grading of Recommendations Assessment, Development and Evaluation framework, the overall certainty of evidence was very low, which discourage unsubstantiated claims on the cardiovascular benefits of air purifiers. We have also identified several key methodological limitations, including small sample size, short duration of intervention, and the lack of wash-out period. Further RCTs with larger sample size and longer follow-up duration are needed to clarify the cardiovascular benefits of air purification interventions.
Topics: Air Filters; Air Pollution, Indoor; Blood Pressure; Cardiovascular Diseases; Humans; Randomized Controlled Trials as Topic
PubMed: 34058577
DOI: 10.1016/j.scitotenv.2021.147882 -
Scientific Reports Oct 2021Kidney transplantation recipients (KTR) with coronavirus disease 2019 (COVID-19) are at higher risk of death than general population. However, mortality risk factors in... (Meta-Analysis)
Meta-Analysis
Kidney transplantation recipients (KTR) with coronavirus disease 2019 (COVID-19) are at higher risk of death than general population. However, mortality risk factors in KTR are still not clearly identified. Our objective was to systematically analyze published evidence for risk factors associated with mortality in COVID-19 KTR. Electronic databases were searched for eligible studies on 1 August 2021. All prospective and retrospective studies of COVID-19 in KTR were considered eligible without language restriction. Since data in case reports and series could potentially be subsets of larger studies, only studies with ≥ 50 patients were included. Random-effects model meta-analysis was used to calculate weighted mean difference (WMD) and pooled odds ratio (OR) of factors associated with mortality. From a total 1,137 articles retrieved, 13 were included in the systematic review and meta-analysis comprising 4,440 KTR. Compared with survivors, non-survivors were significantly older (WMD 10.5 years, 95% CI 9.3-11.8). KTR of deceased donor were at higher risk of death (OR 1.73, 95% CI 1.10-2.74). Comorbidities including diabetes mellitus, cardiovascular disease, and active cancer significantly increased mortality risk. KTR with dyspnea (OR 5.68, 95% CI 2.11-15.33) and pneumonia (OR 10.64, 95% CI 3.37-33.55) at presentation were at higher mortality risk, while diarrhea decreased the risk (OR 0.61, 95% CI 0.47-0.78). Acute kidney injury was associated with mortality (OR 3.24, 95% CI 1.36-7.70). Inflammatory markers were significantly higher in the non-survivors, including C-reactive protein, procalcitonin, and interleukine-6. A number of COVID-19 mortality risk factors were identified from KTR patient characteristics, presenting symptoms, and laboratory investigations. KTR with these risk factors should receive more intensive monitoring and early therapeutic interventions to optimize health outcomes.
Topics: Acute Kidney Injury; COVID-19; Cardiovascular Diseases; Comorbidity; Diabetes Mellitus; Humans; Kidney Transplantation; Neoplasms; Risk Factors; SARS-CoV-2; Transplant Recipients
PubMed: 34625642
DOI: 10.1038/s41598-021-99713-y -
Cancer Mar 2021Despite the significant societal burden of human papillomavirus (HPV)-associated cancers, clinical screening interventions for HPV-associated noncervical cancers are not... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Despite the significant societal burden of human papillomavirus (HPV)-associated cancers, clinical screening interventions for HPV-associated noncervical cancers are not available. Blood-based biomarkers may help close this gap in care.
METHODS
Five databases were searched, 5687 articles were identified, and 3631 unique candidate titles and abstracts were independently reviewed by 2 authors; 702 articles underwent a full-text review. Eligibility criteria included the assessment of a blood-based biomarker within a cohort or case-control study.
RESULTS
One hundred thirty-seven studies were included. Among all biomarkers assessed, HPV-16 E seropositivity and circulating HPV DNA were most significantly correlated with HPV-associated cancers in comparison with cancer-free controls. In most scenarios, HPV-16 E6 seropositivity varied nonsignificantly according to tumor type, specimen collection timing, and anatomic site (crude odds ratio [cOR] for p16+ or HPV+ oropharyngeal cancer [OPC], 133.10; 95% confidence interval [CI], 59.40-298.21; cOR for HPV-unspecified OPC, 25.41; 95% CI, 8.71-74.06; cOR for prediagnostic HPV-unspecified OPC, 59.00; 95% CI, 15.39-226.25; cOR for HPV-unspecified cervical cancer, 12.05; 95% CI, 3.23-44.97; cOR for HPV-unspecified anal cancer, 73.60; 95% CI, 19.68-275.33; cOR for HPV-unspecified penile cancer, 16.25; 95% CI, 2.83-93.48). Circulating HPV-16 DNA was a valid biomarker for cervical cancer (cOR, 15.72; 95% CI, 3.41-72.57). In 3 cervical cancer case-control studies, cases exhibited unique microRNA expression profiles in comparison with controls. Other assessed biomarker candidates were not valid.
CONCLUSIONS
HPV-16 E6 antibodies and circulating HPV-16 DNA are the most robustly analyzed and most promising blood-based biomarkers for HPV-associated cancers to date. Comparative validity analyses are warranted. Variations in tumor type-specific, high-risk HPV DNA prevalence according to anatomic site and world region highlight the need for biomarkers targeting more high-risk HPV types. Further investigation of blood-based microRNA expression profiling appears indicated.
Topics: Antibodies, Viral; Anus Neoplasms; Biomarkers; DNA, Viral; Female; Human papillomavirus 16; Humans; Oropharyngeal Neoplasms; Papillomavirus Infections; Uterine Cervical Neoplasms
PubMed: 33270909
DOI: 10.1002/cncr.33221 -
Le Infezioni in Medicina Sep 2017Panton-Valentine Leukocidin (PVL) producing Staphylococcus aureus has been associated with severity of skin infections and pathology that suggest a major role in... (Meta-Analysis)
Meta-Analysis Review
Panton-Valentine Leukocidin (PVL) producing Staphylococcus aureus has been associated with severity of skin infections and pathology that suggest a major role in pathogenicity. The present study aimed to determine the overall prevalence of PVL harbouring S. aureus isolates from cutaneous infections in Iran. A systematic search was performed by using Medline electronic databases (PubMed) from the papers published by Iranian authors to the end of March 2017. Ten publications which met our inclusion criteria were then selected for data extraction and analysis by Comprehensive Meta-Analysis Software. The pooled prevalence of PVL in cutaneous infections was estimated at 27.9% (95% CI: 17.9-40.6). The range of PVL positivity among S. aureus isolates obtained from cutaneous infections was from 7.4% to 55.6%. In summary, despite the emergence of multiple-drug resistant strains, it seems that the overall prevalence of PVL carrying S. aureus in Iran remains steady regardless of methicillin resistance. However, further research is required to elucidate the interplay between the risk of invasive disease and PVL, especially in Iran.
Topics: Bacterial Toxins; Burns; Exotoxins; Humans; Incidence; Iran; Leukocidins; Methicillin-Resistant Staphylococcus aureus; Staphylococcal Skin Infections; Staphylococcus aureus; Wound Infection
PubMed: 28956538
DOI: No ID Found -
Journal of Medical Virology Jul 2021Rapid and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential to prevent the spread of the virus. We investigated... (Meta-Analysis)
Meta-Analysis
Rapid and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential to prevent the spread of the virus. We investigated the diagnostic accuracy of the Xpert Xpress and the ID NOW assays for rapid detection of SARS-CoV-2 using a systemic review and meta-analysis approach. A systematic literature search was performed using PubMed, Embase, and the Cochrane COVID-19 Study Register. The sensitivity and specificity of these tests for detecting viruses in patients with suspected SARS-CoV-2 infection were pooled. We used commercial and laboratory-developed reverse transcription-polymerase chain reactions as reference standards. The Quality Assessment of Diagnostic Accuracy Studies-2 tool was used to assess the risk of bias. We identified 11 studies involving 1734 subjects for the Xpert Xpress assay and 10 studies involving 1778 subjects for the ID NOW assay. The pooled sensitivity and specificity of the Xpert Xpress assay for detection of SARS-CoV-2 were 0.99 (95% confidence interval [CI], 0.97 to 0.99) and 0.97 (95% CI, 0.95 to 0.98), respectively. The pooled sensitivity and specificity of the ID NOW assay were 0.79 (95% CI, 0.69 to 0.86) and 1.00 (95% CI, 0.98 to 1.00), respectively. The studies included in our analysis seemed to have low methodological quality. The Xpert Xpress assay showed excellent diagnostic accuracy for rapid detection of SARS-CoV-2. However, as the ID NOW assay showed relatively low sensitivity, this test might miss several positive samples.
Topics: COVID-19; COVID-19 Testing; Coronavirus Envelope Proteins; Coronavirus Nucleocapsid Proteins; Humans; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques; Phosphoproteins; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2; Sensitivity and Specificity
PubMed: 33913533
DOI: 10.1002/jmv.26994 -
Indian Journal of Pharmacology 2020Knowledge of structural details is very much essential from the drug-design perspective. In the systematic review, we systematically reviewed the structural basis of...
Knowledge of structural details is very much essential from the drug-design perspective. In the systematic review, we systematically reviewed the structural basis of different target proteins of SARS-corona virus (CoV2) from a viral life cycle and from drug design perspective. We searched four literature (PubMed, EMBASE, NATURE, and Willey online library) databases and one structural database (RCSB.org) with appropriate keywords till April 18, and finally, 26 articles were included in the systematic review. The published literature mainly centered upon the structural details of "spike protein," "main protease/M Pro/3CL pro," "RNA-dependent RNA polymerase," and "nonstructural protein 15 Endoribonuclease" of SARS-CoV-2. However, inhibitor bound structures were very less. We need better structures elucidating the interactions between different targets and their inhibitors which will help us in understanding the atomic level importance of different amino acid residues in the functionality of the target structures. To summarize, we need structures with fine resolution, co-crystallized structures with biologically validated inhibitors, and functional characterization of different target proteins. Some other routes of entry of SARS-CoV-2 are also mentioned (e.g., CD147); however, these findings are not structurally validated. This review may pave way for better understanding of SARS-CoV-2 life cycle from structural biology perspective.
Topics: Antiviral Agents; Betacoronavirus; COVID-19; Coronavirus Infections; Drug Design; Humans; Pandemics; Pneumonia, Viral; SARS-CoV-2; COVID-19 Drug Treatment
PubMed: 32565603
DOI: 10.4103/ijp.IJP_338_20 -
PloS One 2016There has been an increasing incidence of Lyme disease (LD) in Canada and the United States corresponding to the expanding range of the Ixodes tick vector and Lyme... (Meta-Analysis)
Meta-Analysis Review
There has been an increasing incidence of Lyme disease (LD) in Canada and the United States corresponding to the expanding range of the Ixodes tick vector and Lyme disease agent (Borrelia burgdorferi sensu stricto). There are many diagnostic tests for LD available in North America, all of which have some performance issues, and physicians are concerned about the appropriate use and interpretation of these tests. The objective of this systematic review is to summarize the North American evidence on the accuracy of diagnostic tests and test regimes at various stages of LD. Included in the review are 48 studies on diagnostic tests used in North America published since 1995. Thirteen studies examined a two-tier serological test protocol vs. clinical diagnosis, 24 studies examined single assays vs. clinical diagnosis, 9 studies examined single immunoblot vs. clinical diagnosis, 7 studies compared culture or PCR direct detection methods vs. clinical diagnosis, 22 studies compared two or more tests with each other and 8 studies compared a two-tiered serological test protocol to another test. Recent studies examining the sensitivity and specificity of various test protocols noted that the Immunetics® C6 B. burgdorferi ELISA™ and the two tier approach have superior specificity compared to proposed replacements, and the CDC recommended western blot algorithm has equivalent or superior specificity over other proposed test algorithms. There is a dramatic increase in test sensitivity with progression of B. burgdorferi infection from early to late LD. Direct detection methods, culture and PCR of tissue or blood samples were not as sensitive or timely compared to serological testing. It was also noted that there are a large number of both commercial (n = 42) and in-house developed tests used by private laboratories which have not been evaluated in the primary literature.
Topics: Antibodies, Bacterial; Borrelia burgdorferi; DNA, Bacterial; Databases, Factual; Diagnostic Tests, Routine; Enzyme-Linked Immunosorbent Assay; Humans; Lyme Disease; Polymerase Chain Reaction; Reproducibility of Results; Sensitivity and Specificity; Serologic Tests
PubMed: 28002488
DOI: 10.1371/journal.pone.0168613