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Nevin Manimala Statistics

Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates

Gene Rep. 2021 Feb 19:101044. doi: 10.1016/j.genrep.2021.101044. Online ahead of print.

ABSTRACT

SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.

PMID:33623833 | PMC:PMC7893251 | DOI:10.1016/j.genrep.2021.101044

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The Relative Effects of Prazosin on Individual PTSD Symptoms: Evidence for Pathophysiologically-Related Clustering

Chronic Stress (Thousand Oaks). 2021 Feb 9;5:2470547020979780. doi: 10.1177/2470547020979780. eCollection 2021 Jan-Dec.

ABSTRACT

BACKGROUND: The α1-adrenoreceptor antagonist prazosin has in many but not all studies been found to be effective for PTSD associated nightmares, hyperarousal symptoms, and total symptom severity. The particular efficacy of prazosin for nightmares and hyperarousal symptoms suggests there may be a subset of PTSD symptoms that are more tightly associated with an α1-adrenoreceptor mediated noradrenergic mechanism, but cross traditional diagnostic symptom clusters. However, the efficacy of prazosin for individual symptoms other than nightmares and sleep disruption has not previously been examined.

METHODS: In a post hoc reanalysis of a previously published, randomized controlled trial of twice daily prazosin for PTSD, we examined the relative effect of prazosin on individual items of the CAPS for DSM-IV, and tested whether prazosin responsiveness predicted the partial correlation of the changes in symptom intensity at the level of individual subjects. Results were not adjusted for multiple comparisons.

RESULTS: Prazosin showed the largest effect for distressing dreams, anhedonia, difficulty falling or staying asleep, difficulty concentrating, and hypervigilance. These items were also (a) of higher baseline severity in the underlying population, and (b) more related in how they fluctuated at the level of individual subjects. Covariance analysis did not support a clear cutoff between highly prazosin responsive items and those showing a smaller, not statistically significant response.

CONCLUSIONS: In this data set, twice daily prazosin substantially reduced not only nightmares and sleep disruption, but the majority of hyperarousal symptoms, with some evidence of efficacy for avoidance symptoms. The relationship of baseline symptom distribution to which symptoms showed significant response to prazosin reinforces the possibility that differences in a clinical trial’s participant populations may significantly influence trial outcome. The pattern of symptom endorsement at the level of individual subjects was consistent with prazosin-responsive items sharing a common pathophysiologic mechanism.

PMID:33623856 | PMC:PMC7876758 | DOI:10.1177/2470547020979780

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Nevin Manimala Statistics

Is There an Association Between Authors’ Conflicts of Interest and Outcomes in Clinical Studies Involving Autologous Chondrocyte Implantation?

Orthop J Sports Med. 2021 Feb 9;9(2):2325967120979988. doi: 10.1177/2325967120979988. eCollection 2021 Feb.

ABSTRACT

BACKGROUND: Autologous chondrocyte implantation (ACI) is an increasingly popular technique for the treatment of articular cartilage defects. Because several companies have financial interests in ACI, it is important to consider possible conflicts of interest when evaluating studies reporting outcomes of ACI.

PURPOSE: To determine whether there is an association between authors’ financial conflicts of interest and the outcomes of ACI studies.

STUDY DESIGN: Cross-sectional study.

METHODS: A search of PubMed and MEDLINE databases for “autologous chondrocyte implantation” was performed. Clinical studies published after 2012 through May 15, 2019, and in English were included. Studies were determined to have financial conflicts of interest if any contributing author had relevant conflicts, either self-reported in the published study’s disclosures section or reported online in the American Academy of Orthopaedic Surgeons Disclosure database or the Centers for Medicare & Medicaid Services Open Payments database. The outcomes of each study were rated as favorable, equivocal, or unfavorable based on predefined criteria and then tested for association with conflicts of interest through use of the Fisher exact test.

RESULTS: A total of 79 studies met the inclusion criteria. Nearly all studies were of level 3 or 4 evidence. Conflicts of interest were established in 51.90% of studies (n = 41). Conflicts that were not self-reported by the authors were discovered in 18% of studies. The level of evidence was not associated with conflict of interest. No statistically significant difference was found in the rate of favorable outcomes between studies with conflicts (92.68%) and those with no conflicts (81.58%) (P = .126). Publications by US authors were more likely to have financial conflicts of interest (P = .003).

CONCLUSION: Favorable results were reported in a majority of studies involving ACI. No statistical association was found between the frequency of favorable outcomes and the presence of financial conflicts of interest, country of authorship, or level of evidence. There was a trend toward more favorable outcomes in studies with conflicts of interest. Additionally, nearly 20% of publications had possible conflicts found online that were not self-reported. It is critical for orthopaedic surgeons to judiciously evaluate published studies and consider financial conflicts of interest before performing ACI techniques on patients.

PMID:33623797 | PMC:PMC7876765 | DOI:10.1177/2325967120979988

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Nevin Manimala Statistics

Characteristics of the First 102 Severe COVID-19 Cases Treated With Convalescent Plasma or Tocilizumab or Both in Al-Nahdha Hospital, Oman

Health Serv Res Manag Epidemiol. 2021 Feb 10;8:2333392820986639. doi: 10.1177/2333392820986639. eCollection 2021 Jan-Dec.

ABSTRACT

BACKGROUND: In the absence of an effective vaccine, the coronavirus disease (COVID-19) continues to cause more deaths. Evidence on the effectiveness of various COVID-19 management plans is inconclusive. This paper describes the characteristics of the first 102 severe COVID-19 in-patients treated with Convalescent Plasma (CP) therapy or Tocilizumab or both at Al-Nahdha hospital in Muscat, Oman. Additionally, differences in requiring critical care were explored across the treatment groups.

METHODS: Data of all the positive cases in Al-Nahdha hospital were retrieved from the electronic health information system retrospectively from April 1st to July 31st 2020. The required information was recorded in a bespoke sheet and exported to SPSS for further analysis. The primary outcome was defined as improved (discharged home) vs worsening (requiring critical care).

RESULTS: Out of the 102 severe cases of COVID-19 admissions, 20.6%, 59.8% and 20.6% received CP, Tocilizumab and both respectively. In average, CP was introduced at day 3.7(4.8) whereas Tocilizumab at day 7.8(5.1) from admission. The between-group differences in the proportion of patient who improved vs worsened were not significant (P = 0.7). However, the within-group difference in the proportion of patient who improved vs worsened was significant in the Tocilizumab treatment group (P = 0.03). All socio-demographics were not significantly different across the treatment groups. Most improvements in the studies parameters [CBC (total WBC, Lymph and neutrophil counts), oxygen and immune response “cytokine storm” parameters] post-treatment was attributed to the use of Tocilizumab. There was a statistically significant difference in the mean hospital stay between the improved and worsened cases across all treatment categories [at the population level: 8.2(5.0) improved vs 4.7(3.7) worsened-P < 0.001].

CONCLUSIONS: Results from this study provided baseline information about the characteristics of confirmed COVID-19 cases in Al-Nahdha hospital who received CP, Tocilizumab or both. Results obtained seems to be promising in preventing critical care, especially for Tocilizumab. However, further randomized studies are needed.

PMID:33623809 | PMC:PMC7878948 | DOI:10.1177/2333392820986639

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Count Models Analysis of Factors Associated with Under-Five Mortality in Ethiopia

Glob Pediatr Health. 2021 Feb 10;8:2333794X21989538. doi: 10.1177/2333794X21989538. eCollection 2021.

ABSTRACT

Background. Under-five mortality has continued a key challenge to public health in Ethiopia, and other sub-Saharan Africa countries. The threat of under-five mortality is incessant and more studies are needed to generate new scientific evidence. This study aimed to model the number of under-five deaths a mother has experienced in her lifetime and factors associated with it in Ethiopia. Method. A retrospective cross-sectional study based on data obtained from the Ethiopian Demographic and Health Survey (DHS), 2016 was used. The response variable was the total number of under-five children died per mother in her lifetime. Variables such as maternal socioeconomic and demographic characteristics, health, and environmental factors were considered as risk factors of under-five mortality. Hurdle negative binomial (HNB) regression analysis was employed to determine the factors associated with under-five mortality. Results. The data showed that 27.2% (95%CI: 0263, 0.282) of women experienced under-five deaths. The study revealed the age of mother at first birth, the age of mother at the time of under-five mortality occurred, number of household members, household access to electricity, region, educational level of the mother, sex of household head, wealth index, mother residing with husband/partner at the time of under-five mortality occurred as factors associated with under-five mortality. Age of mother at first birth 18 to 24 (IRR = .663; 95%CI: 0.587, 0.749), 25 or higher years old (IRR = 0.424; 95%CI: 0.306, 0.588), access to electricity (IRR = 0.758; 95%CI: 0.588, 0.976), primary education level of the mother (IRR = 0.715; 95%CI: 0.584, 0.875) and the richer wealth index (IRR = 0.785; 95%CI: 0.624, 0.988) were associated with reduced incidence of under-five mortality controlling for other variables in the model. Whereas older age of mother 35 to 39 (IRR = 5.252; 95%CI: 2.992, 9.218), 40 to 44 (IRR = 7.429; 95%CI: 4.188, 13.177), 45 to 49 (IRR = 8.697; 95%CI: 4.853, 15.585), being a resident of the Benishangul-gumuz region (IRR = 1.781; 95%CI: 1.303, 2.434), female household head (IRR = 1.256; 95%CI: 1.034, 1.525) were associated with an increased incidence of under-five mortality. Conclusion. The findings suggested that early age of mothers’ at first birth and old ages of mothers’, female household head and being uneducated were found to increase the incidence of the under-five mortality, whereas access to electricity and living with husband was statistically associated with reduced incidence of under-five mortality. The implication of this study is that policymakers and stakeholders should provide health education for mothers not to give birth at an earlier age and improve living standards to achieve sustainable development goals.

PMID:33623812 | PMC:PMC7878955 | DOI:10.1177/2333794X21989538

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Nevin Manimala Statistics

Toolbox to simulate and mitigate COVID-19 propagation

SoftwareX. 2021 Feb 18:100673. doi: 10.1016/j.softx.2021.100673. Online ahead of print.

ABSTRACT

In this paper we present an age-and-migration-dependent Markov-chain-based model for the propagation of the COVID-19, together with a user-friendly MatLab-based toolbox. We present several examples to estimate the propagation of the virus worldwide and in a particular country.

PMID:33623815 | PMC:PMC7891107 | DOI:10.1016/j.softx.2021.100673

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E-learning Readiness among Dental Students and Faculty Members Pre-COVID-19 Pandemic

J Microsc Ultrastruct. 2020 Nov 9;8(4):168-174. doi: 10.4103/JMAU.JMAU_40_20. eCollection 2020 Oct-Dec.

ABSTRACT

PURPOSE: The purpose was to assess students’ and faculty readiness toward online dental education in Saudi Arabia.

MATERIALS AND METHODS: This is a cross-sectional study using a 5-point Likert scale questionnaire distributed to students (undergraduates and postgraduates) and faculty at King Abdulaziz University, Faculty of Dentistry, Jeddah, Saudi Arabia, in 2018. It assessed individual characteristics, system competency needs, social influence, institutional support, overall readiness, and the needed technical support in using e-learning for personal as well as teaching and learning (T&L) purposes. The readiness response scale for each domain was categorized as follows: low (mean value = 1-<3), acceptable/moderate (mean value = 3-<4), and high readiness level (mean value = 4-5). Descriptive and group comparisons were conducted using Pearson’s Chi-square test, paired sample t-test, independent sample t-test, one-way ANOVA, and Tukey’s post hoc test. The statistical significance level was set at P < 0.05.

RESULTS: the total completed response rate was 400/550 (72.7%) comprising undergraduates (n = 312), postgraduates (n = 38), and faculty (n = 50). The results showed an acceptable level of online skills with no statistically significant difference between the groups (P > 0.05). A statistically significant difference between the two categories of uses, personal and T&L, was found (P < 0.05). The undergraduate students reported statistically significantly lower readiness level in online English literacy, perceived impact of online technology on education, technology accessibility, importance of institutional support, overall readiness, and the need for technical support (P < 0.05).

CONCLUSION: Significant differences between students’ and faculty readiness for e-learning adoption in dental education were reported. The current study captured the prepandemic e-readiness of students and faculty as a baseline for future assessment of pandemic effect on education.

PMID:33623743 | PMC:PMC7883505 | DOI:10.4103/JMAU.JMAU_40_20

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Students’ Awareness as an Underlying Factor for Satisfaction and Compliance

J Microsc Ultrastruct. 2020 Dec 10;8(4):198-204. doi: 10.4103/JMAU.JMAU_77_20. eCollection 2020 Oct-Dec.

ABSTRACT

INTRODUCTION: As soon as the WHO declared COVID-19 a pandemic, many higher education facilities had to change their educational and teaching strategies to cope with the lockdown. Some medical schools decided to rely on online teaching while others depended on students’ self-learning abilities. Methods of assessment also changed as some medical schools implemented pass/fail exams, online examinations, and research projects while others postponed their final exams. In Egypt, medical schools started delivering their lectures online and changed the assessment criteria of the preclinical academic years to depend mainly on research and online exams while postponed the clinical rotations and final exams of the clinical years.

AIM: This study assesses medical students’ awareness of the current situation regarding the safety guidelines and their satisfaction with the solutions provided by their schools for the plans to continue their learning and the new assessment methods and criteria.

METHODOLOGY: The method used for data collection is an online survey filled by medical students from around Egypt. Moreover, data were statistically analyzed using IBM statistical package SPSS for doing a Chi-squared test on two variables.

RESULTS: After collecting the data and analyzing responses, we found that 66.2% of students who answered the survey do not think that the safety measures taken by their universities after the return back will be enough.

CONCLUSION: This shows that the basic knowledge of COVID-19 among medical students is average and there is a need to start programs for infection control practices against COVID-19 for all medical students and professionals.

PMID:33623747 | PMC:PMC7883500 | DOI:10.4103/JMAU.JMAU_77_20

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Challenges encountered in a South African school nutrition programme

J Public Health Res. 2021 Jan 29;10(1):1982. doi: 10.4081/jphr.2021.1982. eCollection 2021 Jan 14.

ABSTRACT

Background: School Nutritional Programmes (SNP) provide meals at school to reduce hunger, nutrient deficiencies and improve class alertness among children in poor communities. The purpose of the research was to determine the challenges encountered in implementing the SNP in KwaZulu-Natal Province, South Africa in 2017. Design and methods: A cross-sectional study underpinned by a concurrent triangulation research design where interviews were used to collect qualitative data from stakeholders, and a questionnaire collected quantitative data from students. The set of qualitative data was thematically analysed. Descriptive and inferential statistics were used to analyse the quantitative data. Analysis of variance (ANOVA) and Tukey HSD test were used to compare the mean scores for food quality on different days of the week. Results: Both the quality and quantity of food were affected by delays in payment of food suppliers, lack of training of stakeholders, and poor kitchen facilities. Health problems experienced by students after eating the food made them reluctant to consume meals on some days. The Tukey HSD test indicated that the mean score for the quality of food served on Wednesday (3.2 ± 1.3) was significantly higher than the mean score for the quality of the meal served on Friday (2.5 ± 1.3). Conclusions: Late payment of food-suppliers and inadequate training of food-handlers affected the quality and quantity of the meals. The researcher recommends that the programme administrators should improve the frequency of payment for food suppliers, training of food handlers, and find alternative meals for students who do not consume the regular meals due to various reasons.

PMID:33623777 | PMC:PMC7883013 | DOI:10.4081/jphr.2021.1982

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Impact of Pangolin Bootleg Market on the Dynamics of COVID-19 Model

Results Phys. 2021 Feb 19:103913. doi: 10.1016/j.rinp.2021.103913. Online ahead of print.

ABSTRACT

In this paper we consider ant-eating pangolin as a possible source of the novel corona virus (COVID-19) and propose a new mathematical model describing the dynamics of COVID-19 pandemic. Our new model is based on the hypotheses that the pangolin and human populations are divided into measurable partitions and also incorporates pangolin bootleg market or reservoir. First we study the important mathematical properties like existence, boundedness and positivity of solution of the proposed model. After finding the threshold quantity for the underlying model, the possible stationary states are explored. We exploit linearization as well as Lyapanuv function theory to exhibit local stability analysis of the model in terms of the threshold quantity. We then discuss the global stability analyses of the newly introduced model and found conditions for its stability in terms of the basic reproduction number. It is also shown that for certain values of

R0

, our model exhibits a backward bifurcation. Numerical simulations are performed to verify and support our analytical findings.

PMID:33623730 | PMC:PMC7892304 | DOI:10.1016/j.rinp.2021.103913