scholarly journals Computational methods for the ab initio identification of novel microRNA in plants: a systematic review

2019 ◽  
Vol 5 ◽  
pp. e233
Author(s):  
Buwani Manuweera ◽  
Gillian Reynolds ◽  
Indika Kahanda
Keyword(s):  
Systematic Review ◽  
Ab Initio ◽  
Computational Methods ◽  
Data Extraction ◽  
Vital Role ◽  
Biological Data ◽  
Mirna Sequence ◽  
Identification Methods ◽  
Mirna Identification ◽  
Plant Mirna

Background MicroRNAs (miRNAs) play a vital role as post-transcriptional regulators in gene expression. Experimental determination of miRNA sequence and structure is both expensive and time consuming. The next-generation sequencing revolution, which facilitated the rapid accumulation of biological data has brought biology into the “big data” domain. As such, developing computational methods to predict miRNAs has become an active area of inter-disciplinary research. Objective The objective of this systematic review is to focus on the developments of ab initio plant miRNA identification methods over the last decade. Data sources Five databases were searched for relevant articles, according to a well-defined review protocol. Study selection The search results were further filtered using the selection criteria that only included studies on novel plant miRNA identification using machine learning. Data extraction Relevant data from each study were extracted in order to carry out an analysis on their methodologies and findings. Results Results depict that in the last decade, there were 20 articles published on novel miRNA identification methods in plants of which only 11 of them were primarily focused on plant microRNA identification. Our findings suggest a need for more stringent plant-focused miRNA identification studies. Conclusion Overall, the study accuracies are of a satisfactory level, although they may generate a considerable number of false negatives. In future, attention must be paid to the biological plausibility of computationally identified miRNAs to prevent further propagation of biologically questionable miRNA sequences.

Impact of surgery timing for craniosynostosis on neurodevelopmental outcomes: a systematic review

2019 ◽  
Vol 23 (4) ◽  
pp. 442-454 ◽  
Author(s):  
Rachel Mandela ◽  
Maggie Bellew ◽  
Paul Chumas ◽  
Hannah Nash
Keyword(s):  
Systematic Review ◽  
Beneficial Effect ◽  
Data Extraction ◽  
Sociodemographic Factors ◽  
Future Research ◽  
Neurodevelopmental Outcomes ◽  
Age At Surgery ◽  
Data Extraction Form ◽  
Surgery Timing ◽  
Anesthetic Exposure

OBJECTIVEThere are currently no guidelines for the optimum age for surgical treatment of craniosynostosis. This systematic review summarizes and assesses evidence on whether there is an optimal age for surgery in terms of neurodevelopmental outcomes.METHODSThe databases MEDLINE, PsycINFO, CINAHL, Embase + Embase Classic, and Web of Science were searched between October and November 2016 and searches were repeated in July 2017. According to PICO (participants, intervention, comparison, outcome) criteria, studies were included that focused on: children diagnosed with nonsyndromic craniosynostosis, aged ≤ 5 years at time of surgery; corrective surgery for nonsyndromic craniosynostosis; comparison of age-at-surgery groups; and tests of cognitive and neurodevelopmental postoperative outcomes. Studies that did not compare age-at-surgery groups (e.g., those employing a correlational design alone) were excluded. Data were double-extracted by 2 authors using a modified version of the Cochrane data extraction form.RESULTSTen studies met the specified criteria; 5 found a beneficial effect of earlier surgery, and 5 did not. No study found a beneficial effect of later surgery. No study collected data on length of anesthetic exposure and only 1 study collected data on sociodemographic factors.CONCLUSIONSIt was difficult to draw firm conclusions from the results due to multiple confounding factors. There is some inconclusive evidence that earlier surgery is beneficial for patients with sagittal synostosis. The picture is even more mixed for other subtypes. There is no evidence that later surgery is beneficial. The authors recommend that future research use agreed-upon parameters for: age-at-surgery cut-offs, follow-up times, and outcome measures.

scholarly journals Misuse of medication in adult substance misuse services: a systematic review protocol

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e047283
Author(s):  
Rosalind Gittins ◽  
Louise Missen ◽  
Ian Maidment
Keyword(s):  
Systematic Review ◽  
Substance Misuse ◽  
Data Extraction ◽  
Meta Analysis ◽  
Grey Literature ◽  
Opioid Analgesics ◽  
Physical And Mental Health ◽  
Qualitative Synthesis ◽  
Treatment Services ◽  
The Impact

IntroductionThere is a growing concern about the misuse of over the counter (OTC) and prescription only medication (POM) because of the impact on physical and mental health, drug interactions, overdoses and drug-related deaths. These medicines include opioid analgesics, anxiolytics such as pregabalin and diazepam and antidepressants. This protocol outlines how a systematic review will be undertaken (during June 2021), which aims to examine the literature on the pattern of OTC and POM misuse among adults who are accessing substance misuse treatment services. It will include the types of medication being taken, prevalence and demographic characteristics of people who access treatment services.Methods and analysisAn electronic search will be conducted on the Cochrane, OVID Medline, Pubmed, Scopus and Web of Science databases as well as grey literature. Two independent reviewers will conduct the initial title and abstract screenings, using predetermined criteria for inclusion and exclusion. If selected for inclusion, full-text data extraction will be conducted using a pilot-tested data extraction form. A third reviewer will resolve disagreements if consensus cannot be reached. Quality and risk of bias assessment will be conducted for all included studies. A qualitative synthesis and summary of the data will be provided. If possible, a meta-analysis with heterogeneity calculation will be conducted; otherwise, Synthesis Without Meta-analysis will be undertaken for quantitative data. The reporting of this protocol follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses.Ethics and disseminationEthical approval is not required. Findings will be peer reviewed, published and shared verbally, electronically and in print, with interested clinicians and policymakers.PROSPERO registration numberCRD42020135216.

scholarly journals Laparoscopic appendectomy versus antibiotic treatment for acute appendicitis—a systematic review

2021 ◽  
Author(s):  
Franziska Köhler ◽  
Anne Hendricks ◽  
Carolin Kastner ◽  
Sophie Müller ◽  
Kevin Boerner ◽  
...  
Keyword(s):  
Systematic Review ◽  
Antibiotic Therapy ◽  
Antibiotic Treatment ◽  
Laparoscopic Appendectomy ◽  
Data Extraction ◽  
Open Appendectomy ◽  
Cochrane Library ◽  
Pubmed Database ◽  
Uncomplicated Appendicitis ◽  
Absence From Work

Abstract Background Over the last years, laparoscopic appendectomy has progressively replaced open appendectomy and become the current gold standard treatment for suspected, uncomplicated appendicitis. At the same time, though, it is an ongoing discussion that antibiotic therapy can be an equivalent treatment for patients with uncomplicated appendicitis. The aim of this systematic review was to determine the safety and efficacy of antibiotic therapy and compare it to the laparoscopic appendectomy for acute, uncomplicated appendicitis. Methods The PubMed database, Embase database, and Cochrane library were scanned for studies comparing laparoscopic appendectomy with antibiotic treatment. Two independent reviewers performed the study selection and data extraction. The primary endpoint was defined as successful treatment of appendicitis. Secondary endpoints were pain intensity, duration of hospitalization, absence from work, and incidence of complications. Results No studies were found that exclusively compared laparoscopic appendectomy with antibiotic treatment for acute, uncomplicated appendicitis. Conclusions To date, there are no studies comparing antibiotic treatment to laparoscopic appendectomy for patients with acute uncomplicated appendicitis, thus emphasizing the lack of evidence and need for further investigation.

scholarly journals What is the risk of prostate cancer mortality following negative systematic TRUS-guided biopsies? A systematic review

BMJ Open ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. e040965
Author(s):  
Sandra Miriam Kawa ◽  
Signe Benzon Larsen ◽  
John Thomas Helgstrand ◽  
Peter Iversen ◽  
Klaus Brasso ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Systematic Review ◽  
Data Extraction ◽  
Specific Antigen ◽  
Transrectal Ultrasound ◽  
Population Based ◽  
Free Text ◽  
Medical Subject Headings ◽  
Prognostic Information ◽  
Prostate Biopsies

ObjectiveTo investigate the risk of prostate cancer-specific mortality (PCSM) following initial negative systematic transrectal ultrasound-guided (TRUS) prostate biopsies.DesignSystematic review.Data sourcesPubMed and Embase were searched using a string combination with keywords/Medical Subject Headings terms and free text in the search builder. Date of search was 13 April 2020.Study selectionStudies addressing PCSM following initial negative TRUS biopsies. Randomised controlled trials and population-based studies including men with initial negative TRUS biopsies reported in English from 1990 until present were included.Data extractionData extraction was done using a predefined form by two authors independently and compared with confirm data; risk of bias was assessed using the Newcastle–Ottawa Scale for cohort studies when applicable.ResultsFour eligible studies were identified. Outcomes were reported differently in the studies as both cumulative incidence and Kaplan-Meier estimates have been used. Regardless of the study differences, all studies reported low estimated incidence of PCSM of 1.8%–5.2% in men with negative TRUS biopsies during the following 10–20 years. Main limitation in all studies was limited follow-up.ConclusionOnly a few studies have investigated the risk of PCSM following initial negative biopsies and all studies included patients before the era of MRI of the prostate. However, the studies point to the fact that the risk of PCSM is low following initial negative TRUS biopsies, and that the level of prostate-specific antigen before biopsies holds prognostic information. This may be considered when advising patients about the need for further diagnostic evaluation.PROSPERO registration numberCRD42019134548.

scholarly journals Prevalence of retinopathy in prediabetes: protocol for a systematic review and meta-analysis

BMJ Open ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. e040997
Author(s):  
Varo Kirthi ◽  
Paul Nderitu ◽  
Uazman Alam ◽  
Jennifer Evans ◽  
Sarah Nevitt ◽  
...  
Keyword(s):  
Systematic Review ◽  
Diabetic Retinopathy ◽  
Data Extraction ◽  
Meta Analysis ◽  
International Diabetes Federation ◽  
Current Data ◽  
Risk Of Bias ◽  
Fundus Photography ◽  
Primary Data ◽  
Cochrane Library

IntroductionThere is growing evidence of a higher than expected prevalence of retinopathy in prediabetes. This paper presents the protocol of a systematic review and meta-analysis of retinopathy in prediabetes. The aim of the review is to estimate the prevalence of retinopathy in prediabetes and to summarise the current data.Methods and analysisThis protocol is developed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines. A comprehensive electronic bibliographic search will be conducted in MEDLINE, EMBASE, Web of Science, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Google Scholar and the Cochrane Library. Eligible studies will report prevalence data for retinopathy on fundus photography in adults with prediabetes. No time restrictions will be placed on the date of publication. Screening for eligible studies and data extraction will be conducted by two reviewers independently, using predefined inclusion criteria and prepiloted data extraction forms. Disagreements between the reviewers will be resolved by discussion, and if required, a third (senior) reviewer will arbitrate.The primary outcome is the prevalence of any standard features of diabetic retinopathy (DR) on fundus photography, as per International Clinical Diabetic Retinopathy Severity Scale (ICDRSS) classification. Secondary outcomes are the prevalence of (1) any retinal microvascular abnormalities on fundus photography that are not standard features of DR as per ICDRSS classification and (2) any macular microvascular abnormalities on fundus photography, including but not limited to the presence of macular exudates, microaneurysms and haemorrhages. Risk of bias for included studies will be assessed using a validated risk of bias tool for prevalence studies. Pooled estimates for the prespecified outcomes of interest will be calculated using random effects meta-analytic techniques. Heterogeneity will be assessed using the I2 statistic.Ethics and disseminationEthical approval is not required as this is a protocol for a systematic review and no primary data are to be collected. Findings will be disseminated through peer-reviewed publications and presentations at national and international meetings including Diabetes UK, European Association for the Study of Diabetes, American Diabetes Association and International Diabetes Federation conferences.PROSPERO registration numberCRD42020184820.

scholarly journals Health insurance awareness and its uptake in India: a systematic review protocol

BMJ Open ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. e043122
Author(s):  
Bhageerathy Reshmi ◽  
Bhaskaran Unnikrishnan ◽  
Shradha S Parsekar ◽  
Eti Rajwar ◽  
Ratheebhai Vijayamma ◽  
...  
Keyword(s):  
Systematic Review ◽  
Health Insurance ◽  
Data Extraction ◽  
Adult Population ◽  
Social Science Research ◽  
Healthcare Utilisation ◽  
Science Research ◽  
Research Network ◽  
Universal Healthcare ◽  
Government Websites

IntroductionHealth insurance is one of the important approaches that can help in boosting universal healthcare coverage through improved healthcare utilisation and financial protection. This objectives of this review are to identify various interventions implemented in India to promote awareness of health insurance, and to provide evidence for the effectiveness of such interventions on the awareness and uptake of health insurance by the resident Indian population.Methods and analysisA systematic review will be carried out based on the Cochrane handbook for systematic reviews of interventions. The review will include experimental and analytical observational studies that have included adult population (>18 years) in India. We will include any intervention, policy or programme that directly or indirectly affects awareness or uptake of health insurance. The following outcomes will be eligible to be included: awareness or health insurance literacy, attitude such as readiness to buy health insurance or decision making, uptake of health insurance, demand-side and supply-side factors for awareness of health insurance, and awareness as a factor for uptake and re-enrolment in health insurance. Databases such as MEDLINE (PubMed), Web of Science, Scopus, 3ie impact evaluation repository and Social Science Research Network will be searched from January 2010 to 15 July 2020. Additionally, important government websites and references of the included studies will be scanned to identify potential records. Three authors, independently, will carry out screening and data extraction. Studies will be categorised into quantitative and qualitative, and mixed-methods synthesis will be employed to analyse the findings.Ethics and disseminationThis review will be based on published studies and will not recruit human participants directly, therefore, ethical clearance is not applicable. We will disseminate the final review findings in a national or international conference and publish in a peer-reviewed journal.

scholarly journals Effectiveness of Antalgic Therapies in Patients with Vertebral Bone Metastasis: A Protocol for a Systematic Review and Meta-Analysis

2021 ◽  
Vol 18 (8) ◽  
pp. 3991
Author(s):  
Antonio Jose Martin-Perez ◽  
María Fernández-González ◽  
Paula Postigo-Martin ◽  
Marc Sampedro Pilegaard ◽  
Carolina Fernández-Lao ◽  
...  
Keyword(s):  
Systematic Review ◽  
Bone Metastasis ◽  
Data Extraction ◽  
Meta Analysis ◽  
Risk Of Bias ◽  
Cochrane Library ◽  
Pharmacological Intervention ◽  
Vertebral Metastasis ◽  
Randomized Controlled Clinical Trials

There is no systematic review that has identified existing studies evaluating the pharmacological and non-pharmacological intervention for pain management in patients with bone metastasis. To fill this gap in the literature, this systematic review with meta-analysis aims to evaluate the effectiveness of different antalgic therapies (pharmacological and non-pharmacological) in the improvement of pain of these patients. To this end, this protocol has been written according to the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P) and registered in PROSPERO (CRD42020135762). A systematic search will be carried out in four international databases: Medline (Via PubMed), Web of Science, Cochrane Library and SCOPUS, to select the randomized controlled clinical trials. The Risk of Bias Tool developed by Cochrane will be used to assess the risk of bias and the quality of the identified studies. A narrative synthesis will be used to describe and compare the studies, and after the data extraction, random effects model and a subgroup analyses will be performed according to the type of intervention, if possible. This protocol aims to generate a systematic review that compiles and synthesizes the best and most recent evidence on the treatment of pain derived from vertebral metastasis.

scholarly journals Effectiveness of trauma care systems at different stages of development in reducing mortality: a systematic review and meta-analysis protocol

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e047439
Author(s):  
Rayan Jafnan Alharbi ◽  
Virginia Lewis ◽  
Sumina Shrestha ◽  
Charne Miller
Keyword(s):  
Systematic Review ◽  
Trauma Care ◽  
Data Extraction ◽  
Meta Analysis ◽  
Trauma System ◽  
Secondary Data ◽  
Trauma Centre ◽  
Trauma Patients ◽  
Trauma Systems ◽  
Stages Of Development

IntroductionThe introduction of trauma systems that began in the 1970s resulted in improved trauma care and a decreased rate of morbidity and mortality of trauma patients. Worldwide, little is known about the effectiveness of trauma care system at different stages of development, from establishing a trauma centre, to implementing a trauma system and as trauma systems mature. The objective of this study is to extract and analyse data from research that evaluates mortality rates according to different stages of trauma system development globally.Methods and analysisThe proposed review will comply with the checklist of the ‘Preferred reporting items for systematic review and meta-analysis’. In this review, only peer-reviewed articles written in English, human-related studies and published between January 2000 and December 2020 will be included. Articles will be retrieved from MEDLINE, EMBASE and CINAHL. Additional articles will be identified from other sources such as references of included articles and author lists. Two independent authors will assess the eligibility of studies as well as critically appraise and assess the methodological quality of all included studies using the Cochrane Risk of Bias for Non-randomised Studies of Interventions tool. Two independent authors will extract the data to minimise errors and bias during the process of data extraction using an extraction tool developed by the authors. For analysis calculation, effect sizes will be expressed as risk ratios or ORs for dichotomous data or weighted (or standardised) mean differences and 95% CIs for continuous data in this systematic review.Ethics and disseminationThis systematic review will use secondary data only, therefore, research ethics approval is not required. The results from this study will be submitted to a peer-review journal for publication and we will present our findings at national and international conferences.PROSPERO registration numberCRD42019142842.

scholarly journals Epidemiology of hepatitis E virus infection in animals in Africa: a systematic review and meta-analysis

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Abdou Fatawou Modiyinji ◽  
Jean Joel Bigna ◽  
Sebastien Kenmoe ◽  
Fredy Brice N. Simo ◽  
Marie A. Amougou ◽  
...  
Keyword(s):  
Systematic Review ◽  
Hepatitis E Virus ◽  
Data Extraction ◽  
Meta Analysis ◽  
Hepatitis E ◽  
Epidemiological Studies ◽  
Cross Sectional ◽  
Resource Limited ◽  
Study Selection ◽  
Language Restriction

Abstract Background Hepatitis E virus (HEV) is a major cause of acute hepatitis in humans worldwide and have high burden in the resource-limited countries. Better knowledge of the epidemiology of hepatitis in animals in Africa can help to understand the epidemiology among humans. The objective of this study was to summarize the prevalence of HEV infection and distribution of HEV genotypes among animals in Africa. Methods In this systematic review and meta-analysis, we comprehensively searched PubMed, EMBASE, African Journals Online, and Africa Index Medicus from January 1st, 2000 to March 22th, 2020 without any language restriction. We considered cross-sectional studies of HEV infection in animals in Africa. Study selection, data extraction, and methodological quality of included studies were done independently by two investigators. Prevalence data were pooled using the random-effects meta-analysis. This review was registered in PROSPERO, CRD42018087684. Results Twenty-five studies (13 species and 6983 animals) were included. The prevalence (antibodies or ribonucleic acid [RNA]) of HEV infection in animals varied widely depending on biological markers of HEV infection measured: 23.4% (95% confidence interval; 12.0–37.2) for anti-HEV immunoglobulins G, 13.1% (3.1–28.3) for anti-HEV immunoglobulins M, and 1.8% (0.2–4.3) for RNA; with substantial heterogeneity. In subgroup analysis, the immunoglobulins G seroprevalence was higher among pigs 37.8% (13.9–65.4). The following HEV genotypes were reported in animals: Rat-HEV genotype 1 (rats and horses), HEV-3 (pigs), HEV-7 (dromedaries), and Bat hepeviruses (bats). Conclusions We found a high prevalence of HEV infection in animals in Africa and HEV genotypes close to that of humans. Some animals in Africa could be the reservoir of HEV, highlighting the need of molecular epidemiological studies for investigating zoonotic transmission.

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