scholarly journals RADAR: Differential analysis of MeRIP-seq data with a random effect model

2019 ◽  
Author(s):  
Zijie Zhang ◽  
Qi Zhan ◽  
Mark Eckert ◽  
Allen Zhu ◽  
Agnieszka Chryplewicz ◽  
...  
Keyword(s):  
Random Effect ◽  
Random Effect Model ◽  
Differential Analysis ◽  
Rna Modifications ◽  
Methylation Analysis ◽  
Accurate Identification ◽  
Functional Studies ◽  
Effect Model ◽  
Differential Methylation Analysis

AbstractEpitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real datasets analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.

scholarly journals RADAR: differential analysis of MeRIP-seq data with a random effect model

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zijie Zhang ◽  
Qi Zhan ◽  
Mark Eckert ◽  
Allen Zhu ◽  
Agnieszka Chryplewicz ◽  
...  
Keyword(s):  
Random Effect ◽  
Random Effect Model ◽  
Differential Analysis ◽  
Rna Modifications ◽  
Methylation Analysis ◽  
Accurate Identification ◽  
Functional Studies ◽  
Effect Model ◽  
Differential Methylation Analysis

AbstractEpitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real dataset analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.

scholarly journals Therapeutic potential of ivermectin as add on treatment in COVID 19: A systematic review and meta-analysis

2020 ◽  
Vol 23 ◽  
pp. 462-469
Author(s):  
Biswa Mohan Padhy ◽  
Rashmi Ranjan Mohanty ◽  
Smita Das ◽  
Bikash Ranjan Meher
Keyword(s):  
Systematic Review ◽  
Therapeutic Potential ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Symptomatic Treatment ◽  
Effect Model ◽  
Usual Therapy

The current management of COVID-19 is mostly limited to general supportive care and symptomatic treatment. Ivermectin is a broad-spectrum anti-parasitic drug used widely for the treatment of onchocerciasis and lymphatic filariasis. Apart from its anti-parasitic effect it also exhibits antiviral activity against a number of viruses both in vitro and in vivo. Hence, we conducted this systematic review and meta-analysis to assess the currently available data on the therapeutic potential of ivermectin for the treatment of COVID‐19 as add on therapy. A total of 629 patients were included in the 4 studies and all were COVID-19 RT-PCR positive. Among them, 397 patients received ivermectin along with usual therapy. The random effect model showed the overall pooled OR to be 0.53 (95%CI: 0.29 to0.96) for the primary outcome (all-cause mortality) which was statistically significant (P=0.04). Similarly, the random effect model revealed that adding ivermectin led to significant clinical improvement compared to usual therapy (OR=1.98, 95% CI: 1.11 to 3.53, P=0.02).  However, this should be inferred cautiously as the quality of evidence is very low. Currently, many clinical trials are on-going, and definitive evidence for repurposing this drug for COVID-19 patients will emerge only in the future.

Analisis Pengaruh Kepemilikan Blockholder, Kepemilikan Manajerial, Kepemilikan Institusional, dan Komite Audit terhadap Nilai Perusahaan

2018 ◽  
Vol 2 (1) ◽  
pp. 96-121
Author(s):  
Iwan Wirawardhana ◽  
Meco Sitardja
Keyword(s):  
Firm Value ◽  
Audit Committee ◽  
Stock Exchange ◽  
Random Effect ◽  
Random Effect Model ◽  
Institutional Ownership ◽  
Managerial Ownership ◽  
Estimation Model ◽  
Effect Model ◽  
Positive Effect

The aim of this study is to analyse the effect of Blockholder Ownership, Managerial Ownership,Institutional Ownership, and Audit Committee towards Firm Value. The background of this research isthe agency theory and ownership theory. The population in this study are 46 property companies listedon the Indonesia Stock Exchange (IDX) for the period 2012-2016. By using purposive samplingtechnique, 35 companies are qualified as data samples. This research uses the random effect model asthe estimation model and multiple regression as the method of analysis. The results of this study showsthat Institutional Ownership has a positive effect on Firm Value. Meanwhile, Blockholder Ownership,Managerial Ownership, and Audit Committee have no effect on Firm Value. Moreover, the F-testimplies that the variables, blockholder ownership, managerial ownership, institutional ownership, andaudit committee, simultaneously influence firm value.

scholarly journals Alteration of Postural Balance in Patients with Fibromyalgia Syndrome—A Systematic Review and Meta-Analysis

Diagnostics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 127
Author(s):  
David Núñez-Fuentes ◽  
Esteban Obrero-Gaitán ◽  
Noelia Zagalaz-Anula ◽  
Alfonso Javier Ibáñez-Vera ◽  
Alexander Achalandabaso-Ochoa ◽  
...  
Keyword(s):  
Systematic Review ◽  
Postural Balance ◽  
Fibromyalgia Syndrome ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Healthy Controls ◽  
Functional Balance ◽  
Sensory Organization ◽  
Effect Model

Balance problems are one of the most frequent symptoms in patients with Fibromyalgia Syndrome (FMS). However, the extent and nature of this balance disorder are not known. The objective of this work was to determine the best evidence for the alteration of postural balance in patients with FMS and analyze differences with healthy controls. To meet this objective, a systematic review with meta-analysis was performed. A bibliographical search was carried out in PubMed Medline, Scopus, Web of Science, CINAHL and SciELO. Observational studies that assessed postural balance in patients with FMS compared to healthy subjects in baseline conditions, were selected. In a random-effect model, the pooled effect was calculated with the Standardized Mean Difference (SMD) and its 95% confidence interval (CI). Nineteen studies reporting data of 2347 participants (95% female) were included. FMS patients showed poor balance with a large effect on static (SMD = 1.578; 95% CI = 1.164, 1.992), dynamic (SMD = 0.946; 95% CI = 0.598, 1.294), functional balance (SMD = 1.138; 95% CI = 0.689, 1.588) and on balance confidence (SMD = 1.194; 95% CI = 0.914, 1.473). Analysis of the Sensory Organization Test showed large alteration of vestibular (SMD = 1.631; 95% CI = 0.467, 2.795) and visual scores (SMD = 1.317; 95% CI = 0.153, 2.481) compared to healthy controls. Patients with FMS showed worse scores for different measures of postural balance compared to healthy controls. Concretely, FMS patients appear to have poor vestibular and visual scores with a possible somatosensory dependence.

scholarly journals Designing a Bonus-Malus system reflecting the claim size under the dependent frequency–severity model

2021 ◽  
pp. 1-25
Author(s):  
Rosy Oh ◽  
Joseph H.T. Kim ◽  
Jae Youn Ahn
Keyword(s):  
Recent Literature ◽  
Insurance Industry ◽  
Random Effect ◽  
Random Effect Model ◽  
Partial Solution ◽  
Risk Classification ◽  
Transition Rule ◽  
Auto Insurance ◽  
Dependent Frequency ◽  
Effect Model

In the auto insurance industry, a Bonus-Malus System (BMS) is commonly used as a posteriori risk classification mechanism to set the premium for the next contract period based on a policyholder's claim history. Even though the recent literature reports evidence of a significant dependence between frequency and severity, the current BMS practice is to use a frequency-based transition rule while ignoring severity information. Although Oh et al. [(2020). Bonus-Malus premiums under the dependent frequency-severity modeling. Scandinavian Actuarial Journal 2020(3): 172–195] claimed that the frequency-driven BMS transition rule can accommodate the dependence between frequency and severity, their proposal is only a partial solution, as the transition rule still completely ignores the claim severity and is unable to penalize large claims. In this study, we propose to use the BMS with a transition rule based on both frequency and size of claim, based on the bivariate random effect model, which conveniently allows dependence between frequency and severity. We analytically derive the optimal relativities under the proposed BMS framework and show that the proposed BMS outperforms the existing frequency-driven BMS. Later, numerical experiments are also provided using both hypothetical and actual datasets in order to assess the effect of various dependencies on the BMS risk classification and confirm our theoretical findings.

scholarly journals Magnitude and determinants of neural tube defect in Africa: a systematic review and meta-analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Daniel Atlaw ◽  
Yohannes Tekalegn ◽  
Biniyam Sahiledengle ◽  
Kenbon Seyoum ◽  
Damtew Solomon ◽  
...  
Keyword(s):  
Systematic Review ◽  
Neural Tube ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Folic Acid Supplementation ◽  
Maternal Exposure ◽  
X Ray ◽  
Effect Model ◽  
Pooled Prevalence

Abstract Background Neural tube defects (NTDs) are a group of disorders that arise from the failure of the neural tube close between 21 and 28 days after conception. About 90% of neural tube defects and 95% of death due to these defects occurs in low-income countries. Since these NTDs cause considerable morbidity and mortality, this study aimed to determine the prevalence and associated factors of NTDs in Africa. Methods The protocol of this study was registered in the International Prospective Register of Systematic Reviews (PROSPERO number: CRD42020149356). All major databases such as PubMed/MEDLINE, EMBASE, CINAHL, Web of Science, African Journals Online (AJOL), and Google Scholar search engine were systematically searched. A random-effect model was used to estimate the pooled prevalence of NTDs in Africa, and Cochran’s Q-statistics and I2 tests were used to assess heterogeneity between included studies. Publication bias was assessed using Begg ’s tests, and the association between determinant factors and NTDs was estimated using a random-effect model. Results Of the total 2679 articles, 37 articles fulfilled the inclusion criteria and were included in this systematic review and meta-analysis. The pooled prevalence of NTDs in Africa was 50.71 per 10,000 births (95% CI: 48.03, 53.44). Folic acid supplementation (AOR: 0.40; 95% CI: 0.19–0.85), maternal exposure to pesticide (AOR: 3.29; 95% CI: 1.04–10.39), mothers with a previous history of stillbirth (AOR: 3.35, 95% CI: 1.99–5.65) and maternal exposure to x-ray radiation (AOR 2.34; 95% CI: 1.27–4.31) were found to be determinants of NTDs. Conclusions The pooled prevalence of NTDs in Africa was found to be high. Maternal exposure to pesticides and x-ray radiation were significantly associated with NTDs. Folic acid supplementation before and within the first month of pregnancy was found to be a protective factor for NTDs.

scholarly journals Efficacy of interventions to increase physical activity for people with heart failure: a meta-analysis

Open Heart ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. e001687
Author(s):  
Aliya Amirova ◽  
Theodora Fteropoulli ◽  
Paul Williams ◽  
Mark Haddad
Keyword(s):  
Physical Activity ◽  
Heart Failure ◽  
Meta Analysis ◽  
Behavioural Change ◽  
Mode Of Delivery ◽  
Random Effect ◽  
Random Effect Model ◽  
Action Planning ◽  
Exercise Programme ◽  
Effect Model

ObjectivesThis meta-analysis aims to (1) evaluate the efficacy of physical activity interventions in heart failure and (2) to identify intervention characteristics significantly associated with the interventions’ efficacy.MethodsRandomised controlled trials reporting intervention effects on physical activity in heart failure were combined in a meta-analysis using a random-effect model. Exploratory meta-analysis was performed by specifying the general approach (eg, cardiac rehabilitation), strategies used (eg, action planning), setting (eg, centre based), mode of delivery (eg, face to face or online), facilitator (eg, nurse), contact time and behavioural change theory use as predictors in the random-effect model.ResultsInterventions (n=21) had a significant overall effect (SMD=0.54, 95% CI (0.13 to 0.95), p<0.0005). Combining an exercise programme with behavioural change intervention was found efficacious (SMD=1.26, 95% CI (0.26 to 2.26), p<0.05). Centre-based (SMD=0.98, 95% CI (0.35 to 1.62), and group-based (SMD=0.89, 95% CI (0.29 to 1.50),) delivery by a physiotherapist (SMD=0.84, 95% CI (0.03 to 1.65),) were significantly associated with efficacy. The following strategies were identified efficacious: prompts/cues (SMD=3.29, 95% CI (1.97 to 4.62)), credible source (standardised mean difference, SMD=2.08, 95% CI (0.95;3.22)), adding objects to the environment (SMD=1.47, 95% CI (0.41 to 2.53)), generalisation of the target behaviour SMD=1.32, 95% CI (0.22 to 2.41)), monitoring of behaviour by others without feedback (SMD=1.02, 95% CI (0.05 to 1.98)), self-monitoring of outcome(s) of behaviour (SMD=0.79, 95% CI (0.06 to 1.52), graded tasks (SMD=0.73, 95% CI (0.22 to 1.24)), behavioural practice/rehearsal (SMD=0.72, 95% CI (0.26 to 1.18)), action planning (SMD=0.62, 95% CI (0.03 to 1.21)) and goal setting (behaviour) (SMD=0.56, 95% CI (0.03 to 1.08)).ConclusionThe meta-analysis suggests intervention characteristics that may be suitable for promoting physical activity in heart failure. There is moderate evidence in support of an exercise programme combined with a behavioural change intervention delivered by a physiotherapist in a group-based and centre-based settings.PROSPERO registerationCRD42015015280.

Association between circulating leptin levels and multiple sclerosis: a systematic review and meta-analysis

2018 ◽  
Vol 94 (1111) ◽  
pp. 278-283 ◽  
Author(s):  
Xue-Feng Xie ◽  
Xiao-Hui Huang ◽  
Ai-Zong Shen ◽  
Jun Li ◽  
Ye-Huan Sun
Keyword(s):  
Multiple Sclerosis ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Control Group ◽  
Sample Type ◽  
Healthy Controls ◽  
Eligibility Criteria ◽  
Effect Model ◽  
Healthy Control

AimLeptin, synthesised by adipocytes, has been identified as a hormone that can influence inflammatory activity. Several studies have investigated leptin levels in patients with multiple sclerosis (MS), but the results are not consistent. This study aims to derive a more precise evaluation on the relationship between circulating leptin levels and MS.DesignA comprehensive literature searched up to July 2017 was conducted to evaluate the association of circulating leptin levels and MS. The random-effect model was applied to calculate pooled standardised mean difference (SMD) and its 95% CI.Main outcome measuresCirculating leptin levels of patients with MS and healthy controls.ResultsOf 2155 studies identified, 33 met eligibility criteria and 9 studies with 645 patients with MS and 586 controls were finally included in the meta-analysis. Meta-analysis revealed that, compared with the healthy control group, the MS group had significantly higher plasma/serum leptin levels, with the SMD of 0.70% and 95% CI (0.24 to 1.15). Subgroup analyses suggested that the leptin levels of patients with MS were associated with region, age, study sample size, measurement type, gender and blood sample type.ConclusionOverall, our study suggests that patients with MS have a significantly higher leptin level than in healthy controls. Further mechanism studies and longitudinal large cohort studies are still needed to further reveal the role of leptin in the pathogenesis of MS.

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