Nevin Manimala

PLoS One. 2022 Apr 14;17(4):e0264839. doi: 10.1371/journal.pone.0264839. eCollection 2022.

ABSTRACT

INTRODUCTION: The emergence of novel SARS-CoV-2 has caused a pandemic of Coronavirus Disease 19 (COVID-19) which has spread exponentially worldwide. A robust surveillance system is essential for correct estimation of the disease burden and containment of the pandemic. We evaluated the performance of COVID-19 case-based surveillance system in FCT, Nigeria and assessed its key attributes.

METHODS: We used a cross-sectional study design, comprising a survey, key informant interview, record review and secondary data analysis. A self-administered, semi-structured questionnaire was administered to key stakeholders to assess the attributes and process of operation of the surveillance system using CDC’s Updated Guidelines for Evaluation of Public Health Surveillance System 2001. Data collected alongside surveillance data from March 2020 to January 2021 were analyzed and summarized using descriptive statistics.

RESULTS: Out of 69,338 suspected cases, 12,595 tested positive with RT-PCR with a positive predictive value (PPV) of 18%. Healthcare workers were identified as high-risk group with a prevalence of 23.5%. About 82% respondents perceived the system to be simple, 85.5% posited that the system was flexible and easily accommodates changes, 71.4% reported that the system was acceptable and expressed willingness to continue participation. Representativeness of the system was 93%, stability 40%, data quality 56.2% and timeliness 45.5%, estimated result turnaround time (TAT) was suboptimal.

CONCLUSION: The system was found to be useful, simple, flexible, sensitive, acceptable, with good representativeness but the stability, data quality and timeliness was poor. The system meets initial surveillance objectives but rapid expansion of sample collection and testing sites, improvement of TAT, sustainable funding, improvement of electronic database, continuous provision of logistics, supplies and additional trainings are needed to address identified weaknesses, optimize the system performance and meet increasing need of case detection in the wake of rapidly spreading pandemic. More risk-group persons should be tested to improve surveillance effectiveness.

PMID:35421123 | DOI:10.1371/journal.pone.0264839

PLoS One. 2022 Apr 14;17(4):e0264207. doi: 10.1371/journal.pone.0264207. eCollection 2022.

ABSTRACT

Bioplastics, synthesized by several microbes, accumulates inside cells under stress conditions as a storage material. Several microbial enzymes play a crucial role in their degradation. This research was carried to test the biodegradability of poly-β-hydroxybutyrate (PHB) utilizing PHB depolymerase, produced by bacteria isolated from sewage waste soil samples. Potent PHB degrader was screened based on the highest zone of hydrolysis followed by PHB depolymerase activity. Soil burial method was employed to check their degradation ability at different incubation periods of 15, 30, and 45 days at 37±2°C, pH 7.0 at 60% moisture with 1% microbial inoculum of Aeromonas caviae Kuk1-(34) (MN414252). Without optimized conditions, 85.76% of the total weight of the PHB film was degraded after 45 days. This degradation was confirmed with Fourier-transform infrared spectroscopy (FTIR) and Scanning electron microscope (SEM) analysis. The presence of bacterial colonies on the surface of the degraded film, along with crest, holes, surface erosion, and roughness, were visible. Media optimization was carried out in statistical mode using Plackett Burman (PB) and Central Composite Design (CCD) of Response Surface Methodology (RSM) by considering ten different factors. Analysis of Variance (ANOVA), Pareto chart, response surface plots, and F-value of 3.82 implies that the above statistical model was significant. The best production of PHB depolymerase enzyme (14.98 U/mL) was observed when strain Kuk1-(34) was grown in a media containing 0.1% PHB, K2HPO4 (1.6 gm/L) at 27 ℃ for seven days. Exploiting these statistically optimized conditions, the culture was found to be a suitable candidate for the management of solid waste, where 94.4% of the total weight of the PHB film was degraded after 45 days of incubation.

PMID:35421107 | DOI:10.1371/journal.pone.0264207

PLoS Comput Biol. 2022 Apr 14;18(4):e1009898. doi: 10.1371/journal.pcbi.1009898. Online ahead of print.

ABSTRACT

Pertussis has resurfaced in the UK, with incidence levels not seen since the 1980s. While the fundamental causes of this resurgence remain the subject of much conjecture, the study of historical patterns of pathogen diffusion can be illuminating. Here, we examined time series of pertussis incidence in the boroughs of Greater London from 1982 to 2013 to document the spatial epidemiology of this bacterial infection and to identify the potential drivers of its percolation. The incidence of pertussis over this period is characterized by 3 distinct stages: a period exhibiting declining trends with 4-year inter-epidemic cycles from 1982 to 1994, followed by a deep trough until 2006 and the subsequent resurgence. We observed systematic temporal trends in the age distribution of cases and the fade-out profile of pertussis coincident with increasing national vaccine coverage from 1982 to 1990. To quantify the hierarchy of epidemic phases across the boroughs of London, we used the Hilbert transform. We report a consistent pattern of spatial organization from 1982 to the early 1990s, with some boroughs consistently leading epidemic waves and others routinely lagging. To determine the potential drivers of these geographic patterns, a comprehensive parallel database of borough-specific features was compiled, comprising of demographic, movement and socio-economic factors that were used in statistical analyses to predict epidemic phase relationships among boroughs. Specifically, we used a combination of a feed-forward neural network (FFNN), and SHapley Additive exPlanations (SHAP) values to quantify the contribution of each covariate to model predictions. Our analyses identified a number of predictors of a borough’s historical epidemic phase, specifically the age composition of households, the number of agricultural and skilled manual workers, latitude, the population of public transport commuters and high-occupancy households. Univariate regression analysis of the 2012 epidemic identified the ratio of cumulative unvaccinated children to the total population and population of Pakistan-born population to have moderate positive and negative association, respectively, with the timing of epidemic. In addition to providing a comprehensive overview of contemporary pertussis transmission in a large metropolitan population, this study has identified the characteristics that determine the spatial spread of this bacterium across the boroughs of London.

PMID:35421101 | DOI:10.1371/journal.pcbi.1009898

PLoS One. 2022 Apr 14;17(4):e0264208. doi: 10.1371/journal.pone.0264208. eCollection 2022.

ABSTRACT

Vacuum pump oil (VPO) is used as a lubricant in pumps of different machines. The rate of heat transport is a fundamental requirement of all phenomena. To enhance the rate of heat transmission and reduce the amount of energy consumed as a result of high temperatures. For this reason, the vacuum pump oil (VPO) is taken as a base fluid and Fe3O4 is the nanoparticles suspended in VPO. That’s why, the present study inspected the consequence of Hall current, Joule heating effect and variable thickness on these three-dimensional magnetohydrodynamics bidirectional flow of nanoliquid past on a stretchable sheet. Further, the Cattaneo-Christove heat flux and radiation impacts are also considered. The VPO-Fe3O4 nanofluid model is composed of momentum equations in x-direction, y-direction and temperature equations. The leading higher-order non-linear PDEs of the current study have been changed into non-linear ODEs with the implementation of appropriate similarity transformations. The procedure of the homotopy analysis method is hired on the resulting higher-order non-linear ODEs along with boundary conditions for the analytical solution. The significance of distinct flow parameters on the velocities in x-direction, y-direction and temperature profiles of the nanofluid have been encountered and briefly explained in a graphical form. Some important findings of the present modelling are that with the increment of nanoparticles volume fraction the nanofluid velocities in x-direction and y-direction are increased. It is also detected that higher estimations of magnetic field parameter, Prandtl number and thermal relaxation time parameter declined the nanofluid temperature. During this examination of the model, it is found that the Fe3O4-Vacuum pump oil (VPO) nanofluid enhanced the rate of heat transfer. Also, the vacuum pump oil (VPO) has many industrial and engineering applications. The current study will help to improve the rate of heat transmission by taking this into account due to which working machines will do better performance and the loss of useful energy will be decayed. Lastly, the skin friction coefficient and Nusselt number are also illustrated in a tabular form. Some major findings according to the numerical computation of the problem are that the enhancing estimations of magnetic parameter, nanoparticles volume fraction and wall thickness parameter augmented the skin friction coefficient in x-direction and Nusselt number. The reduction in skin friction coefficient of the nanofluid in y-direction is examined for Hall current and shape parameter.

PMID:35421096 | DOI:10.1371/journal.pone.0264208

PLoS Biol. 2022 Apr 14;20(4):e3001600. doi: 10.1371/journal.pbio.3001600. eCollection 2022 Apr.

ABSTRACT

The risk of accidental or deliberate misuse of biological research is increasing as biotechnology advances. As open science becomes widespread, we must consider its impact on those risks and develop solutions that ensure security while facilitating scientific progress. Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. Increasing the availability of computational tools, datasets, and protocols could increase risks from research with misuse potential. For instance, in the context of viral engineering, open code, data, and materials may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. While preprints accelerate dissemination of findings, their increased use could challenge strategies for risk mitigation at the publication stage. This highlights the importance of oversight earlier in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research. Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.

PMID:35421093 | DOI:10.1371/journal.pbio.3001600

PLoS Comput Biol. 2022 Apr 14;18(4):e1010028. doi: 10.1371/journal.pcbi.1010028. Online ahead of print.

ABSTRACT

Genome wide association studies (GWASs) for complex traits have implicated thousands of genetic loci. Most GWAS-nominated variants lie in noncoding regions, complicating the systematic translation of these findings into functional understanding. Here, we leverage convolutional neural networks to assist in this challenge. Our computational framework, peaBrain, models the transcriptional machinery of a tissue as a two-stage process: first, predicting the mean tissue specific abundance of all genes and second, incorporating the transcriptomic consequences of genotype variation to predict individual abundance on a subject-by-subject basis. We demonstrate that peaBrain accounts for the majority (>50%) of variance observed in mean transcript abundance across most tissues and outperforms regularized linear models in predicting the consequences of individual genotype variation. We highlight the validity of the peaBrain model by calculating non-coding impact scores that correlate with nucleotide evolutionary constraint that are also predictive of disease-associated variation and allele-specific transcription factor binding. We further show how these tissue-specific peaBrain scores can be leveraged to pinpoint functional tissues underlying complex traits, outperforming methods that depend on colocalization of eQTL and GWAS signals. We subsequently: (a) derive continuous dense embeddings of genes for downstream applications; (b) highlight the utility of the model in predicting transcriptomic impact of small molecules and shRNA (on par with in vitro experimental replication of external test sets); (c) explore how peaBrain can be used to model difficult-to-study processes (such as neural induction); and (d) identify putatively functional eQTLs that are missed by high-throughput experimental approaches.

PMID:35421087 | DOI:10.1371/journal.pcbi.1010028

J Cancer Res Clin Oncol. 2022 Apr 14. doi: 10.1007/s00432-022-03997-0. Online ahead of print.

ABSTRACT

PURPOSE: Therapy decision for patients with metastatic renal cell carcinoma (mRCC) is highly dependent on disease monitoring based on radiological reports. The purpose of the study was to compare non-standardized, common practice free text reporting (FTR) on disease response with reporting based on response evaluation criteria in solid tumors modified for immune-based therapeutics (iRECIST).

METHODS: Fifty patients with advanced mRCC were included in the retrospective, single-center study. CT scans had been evaluated and FTR prepared in accordance with center’s routine practice. For study purposes, reports were re-evaluated using a dedicated computer program that applied iRECIST. Patients were followed up over a period of 22.8 ± 7.9 months in intervals of 2.7 ± 1.8 months. Weighted kappa statistics was run to assess strength of agreement. Logistic regression was used to identify predictors for different rating.

RESULTS: Agreement between FTR and iRECIST-based reporting was moderate (kappa 0.38 [95% CI 0.2-0.6] to 0.70 [95% CI 0.5-0.9]). Tumor response or progression according to FTR were not confirmed with iRECIST in 19 (38%) or 11 (22%) patients, respectively, in at least one follow-up examination. With FTR, new lesions were frequently not recognized if they were already identified in the recent prior follow-up examination (odds ratio for too favorable rating of disease response compared to iRECIST: 5.4 [95% CI 2.9-10.1].

CONCLUSIONS: Moderate agreement between disease response according to FTR or iRECIST in patients with mRCC suggests the need of standardized quantitative radiological assessment in daily clinical practice.

PMID:35420348 | DOI:10.1007/s00432-022-03997-0

Environ Sci Pollut Res Int. 2022 Apr 14. doi: 10.1007/s11356-022-20097-1. Online ahead of print.

ABSTRACT

The agriculture sector creates nearly a quarter of the total GHG emissions globally as production and transportation activities in the agriculture sector mostly use fossil fuels, creating carbon emissions. In this regard, it is highly important to study the environmental sustainability of agriculture sector growth by using the theory of environmental Kuznets curve (EKC). Furthermore, this research study is aimed to assess the moderation role of transportation competitiveness in determining the carbon emissions of transportation sector by using agriculture sector value addition. The study uses panel quantile regression technique for data analysis of 121 countries by covering time period from 2008 to 2018. The study results validated the agricultural EKC across four different quantile groups based on carbon emissions of transport sector. The moderation of transportation competitiveness is observed in changing the turning point and flattening of agricultural EKC indicating the early achievement of maturity. The quality of institutions and planned increase of population can help reduce carbon emissions of transportation sector. The moderation of transportation competitiveness implicates the importance of planning and efficiently operating the transportation sector to mitigate carbon emissions.

PMID:35420341 | DOI:10.1007/s11356-022-20097-1

Support Care Cancer. 2022 Apr 14. doi: 10.1007/s00520-022-07052-z. Online ahead of print.

ABSTRACT

PURPOSE: Patients receiving cancer treatments experience many treatment-related symptoms. Telehealth is increasingly being used to support symptom management. The overall aim was to determine the effectiveness of nurse-led telehealth symptom management interventions for patients with cancer receiving systemic or radiation therapy compared to usual care on health service use, quality of life, and symptom severity.

METHODS: A systematic review was conducted following the Cochrane Handbook and PRISMA reporting guidelines. Five electronic databases were searched. Two independent reviewers screened articles and extracted data. Meta-analysis was performed if data were clinically and methodologically homogeneous. Subanalysis was conducted on reactive and scheduled telehealth interventions.

RESULTS: Of 7749 citations screened, 10 studies were included (8 randomized control trials, 2 quasi-experimental). Five were reactive telehealth interventions with patient-initiated contact and five evaluated scheduled telehealth interventions initiated by nurses. Compared to usual care (typically patient-initiated calls), nurse-led telehealth interventions for symptom management showed no statistically significant difference in hospitalizations, emergency department visits, or unscheduled clinic visits. Two of three studies of reactive telehealth interventions showed improved quality of life. All telehealth interventions showed reduction in the severity of most symptoms. Pain severity was significantly reduced (standard mean difference – 0.54; 95% CI – 0.88, – 0.19). Significant heterogeneity prevented meta-analysis for most outcomes.

CONCLUSION: Few studies evaluated nurse-led telehealth interventions for cancer symptom management. Compared to usual care, patients exposed to telehealth interventions had reduced symptom severity and no difference in health services use. Future research should focus on better reporting intervention characteristics and consistently measuring outcomes.

PMID:35420331 | DOI:10.1007/s00520-022-07052-z

Breast Cancer Res Treat. 2022 Apr 14. doi: 10.1007/s10549-022-06582-8. Online ahead of print.

ABSTRACT

BACKGROUND: There are limited data on breast surgery completion rates and prevalence of care-continuum delays in breast cancer treatment programs in low-income countries.

METHODS: This study analyzes treatment data in a retrospective cohort of 312 female patients with non-metastatic breast cancer in Haiti. Descriptive statistics were used to summarize patient characteristics; treatments received; and treatment delays of > 12 weeks. Multivariate logistic regressions were performed to identify factors associated with receiving surgery and with treatment delays. Exploratory multivariate survival analysis examined the association between surgery delays and disease-free survival (DFS).

RESULTS: Of 312 patients, 249 (80%) completed breast surgery. The odds ratio (OR) for surgery completion for urban vs. rural dwellers was 2.15 (95% confidence interval [CI]: 1.19-3.88) and for those with locally advanced vs. early-stage disease was 0.34 (95%CI: 0.16-0.73). Among the 223 patients with evaluable surgery completion timelines, 96 (43%) experienced delays. Of the 221 patients eligible for adjuvant chemotherapy, 141 (64%) received adjuvant chemotherapy, 66 of whom (47%) experienced delays in chemotherapy initiation. Presentation in the later years of the cohort (2015-2016) was associated with lower rates of surgery completion (75% vs. 85%) and with delays in adjuvant chemotherapy initiation (OR [95%CI]: 3.25 [1.50-7.06]). Exploratory analysis revealed no association between surgical delays and DFS.

CONCLUSION: While majority of patients obtained curative-intent surgery, nearly half experienced delays in surgery and adjuvant chemotherapy initiation. Although our study was not powered to identify an association between surgical delays and DFS, these delays may negatively impact long-term outcomes.

PMID:35420316 | DOI:10.1007/s10549-022-06582-8