Nevin Manimala

PLoS One. 2021 Sep 7;16(9):e0256612. doi: 10.1371/journal.pone.0256612. eCollection 2021.

ABSTRACT

This study aims to explore whether higher education and science popularization can achieve coordinated growth with temporal and spatial characteristics. Selecting the provincial regions of the Yangtze River Economic Belt in China as cases with data from the national statistics administrations (such as China Statistical Yearbook), this study uses entropy weight analysis, TOPSIS, GM(1,1) gray prediction methods and coupling coordination degree model to evaluate the coordinated growth status. The key findings are: (1) the annual budget per student, and the number of science and technology museums affect both systems more obviously; (2) the overall performances of science popularization fluctuate more obviously than those of higher education; (3) the coordinated growth performances of the two systems in most regions remain mild fluctuations and keep relatively stable coordinated status, however, temporal and spatial variation tendencies do exist among regions. Therefore, corresponding countermeasures should be implemented: generally, national authority needs to involve in coordination activities among regions; the regions with satisfactory coordinated growth performances need more creative approaches to maintain the coordinated growth interactions; the regions at the transitioning status need to prevent the grade decline and upgrade the performances; the regions with lagging performances need to stop the decline and reduce the gaps with others. The novelties include analyzing the coordinated growth interaction mechanism between the two, selecting indices to assess the abstract interaction mechanism precisely, proposing suggestions based on temporal and spatial comparisons of the coordinated growth performances, etc.

PMID:34492057 | DOI:10.1371/journal.pone.0256612

PLoS One. 2021 Sep 7;16(9):e0256630. doi: 10.1371/journal.pone.0256630. eCollection 2021.

ABSTRACT

Pneumonia is a respiratory infection caused by bacteria or viruses; it affects many individuals, especially in developing and underdeveloped nations, where high levels of pollution, unhygienic living conditions, and overcrowding are relatively common, together with inadequate medical infrastructure. Pneumonia causes pleural effusion, a condition in which fluids fill the lung, causing respiratory difficulty. Early diagnosis of pneumonia is crucial to ensure curative treatment and increase survival rates. Chest X-ray imaging is the most frequently used method for diagnosing pneumonia. However, the examination of chest X-rays is a challenging task and is prone to subjective variability. In this study, we developed a computer-aided diagnosis system for automatic pneumonia detection using chest X-ray images. We employed deep transfer learning to handle the scarcity of available data and designed an ensemble of three convolutional neural network models: GoogLeNet, ResNet-18, and DenseNet-121. A weighted average ensemble technique was adopted, wherein the weights assigned to the base learners were determined using a novel approach. The scores of four standard evaluation metrics, precision, recall, f1-score, and the area under the curve, are fused to form the weight vector, which in studies in the literature was frequently set experimentally, a method that is prone to error. The proposed approach was evaluated on two publicly available pneumonia X-ray datasets, provided by Kermany et al. and the Radiological Society of North America (RSNA), respectively, using a five-fold cross-validation scheme. The proposed method achieved accuracy rates of 98.81% and 86.85% and sensitivity rates of 98.80% and 87.02% on the Kermany and RSNA datasets, respectively. The results were superior to those of state-of-the-art methods and our method performed better than the widely used ensemble techniques. Statistical analyses on the datasets using McNemar’s and ANOVA tests showed the robustness of the approach. The codes for the proposed work are available at https://github.com/Rohit-Kundu/Ensemble-Pneumonia-Detection.

PMID:34492046 | DOI:10.1371/journal.pone.0256630

PLoS One. 2021 Sep 7;16(9):e0254287. doi: 10.1371/journal.pone.0254287. eCollection 2021.

ABSTRACT

Dog importation data from 2018-2020 were evaluated to ascertain whether the dog importation patterns in the United States changed during the COVID-19 pandemic, specifically with regard to denial of entry. Dog denial of entry reports from January 1, 2018, to December 31, 2020, stored within the Centers for Disease Control and Prevention (CDC) Quarantine Activity Reporting System (QARS), were reviewed. Basic descriptive statistics were used to analyze the data. Reason for denial, country of origin, and month of importation were all examined to determine which countries of origin resulted in the largest number of denials, and whether there was a seasonal change in importations during the COVID-19 pandemic (2020), compared to previous years (2018 and 2019). During 2020, CDC denied entry to 458 dogs. This represents a 52% increase in dogs denied entry compared to the averages in 2018 and 2019. Dogs were primarily denied entry for falsified rabies vaccination certificates (56%). Three countries exported 74% of all dogs denied entry into the United States, suggesting that targeted interventions may be needed for certain countries. Increased attempts to import inadequately vaccinated dogs from countries with canine rabies in 2020 may have been due to the increased demand for domestic pets during the COVID-19 pandemic. Educational messaging should highlight the risk of rabies and the importance of making informed pet purchases from foreign entities to protect pet owners, their families, and the public.

PMID:34492037 | DOI:10.1371/journal.pone.0254287

PLoS Negl Trop Dis. 2021 Sep 7;15(9):e0009762. doi: 10.1371/journal.pntd.0009762. Online ahead of print.

ABSTRACT

BACKGROUND: Entamoeba infections have major impact on millions of the people worldwide. Entamoeba histolytica has long been accepted as the only pathogenic species. However, recent reports of other Entamoeba spp. in symptomatic cases have raised questions on their pathogenicity.

METHODOLOGY/PRINCIPAL FINDINGS: Total 474 stool samples and 125 liver aspirates from patients with intestinal and extra intestinal manifestations and from community were included. Sewage samples from the hospital and the city were also included. Microscopic examination and molecular detection were performed to detect presence of E. histolytica/ dispar/ moshkovskii/ bangladeshi. The associated demographic and socioeconomic factors were statistically analyzed with the presence of Entamoeba. Microscopy detected Entamoeba spp. in 5.4% stool and 6.4% liver aspirate samples. Through nested multiplex PCR, prevalence of Entamoeba spp. in intestinal and extra-intestinal cases was 6.6% (20/301) and 86.4% (108/125) respectively and in asymptomatic population was 10.5% (13/123). Sewage samples did not show presence of any Entamoeba spp. Uneducated subjects, low economic conditions, untreated drinking water, consumption of raw vegetables and habit of not washing hands before meals were significantly associated with presence of Entamoeba spp.

CONCLUSIONS: E. histolytica still remains the only Entamoeba spp. in invasive extra intestinal infections. E. dispar was detected in both asymptomatic and symptomatic intestinal infections. Routine identification of Entamoeba spp. should incorporate PCR based detection methods.

PMID:34492023 | DOI:10.1371/journal.pntd.0009762

PLoS One. 2021 Sep 7;16(9):e0255375. doi: 10.1371/journal.pone.0255375. eCollection 2021.

ABSTRACT

OBJECTIVE: Lung cancer patients with interstitial lung disease (ILD) are prone for higher morbidity and mortality and their treatment is challenging. The purpose of this study is to investigate whether the survival of lung cancer patients is affected by the presence of ILD documented on CT.

MATERIALS AND METHODS: 146 patients with ILD at initial chest CT were retrospectively included in the study. 146 lung cancer controls without ILD were selected. Chest CTs were evaluated for the presence of pulmonary fibrosis which was classified in 4 categories. Presence and type of emphysema, extent of ILD and emphysema, location and histologic type of cancer, clinical staging and treatment were evaluated. Kaplan-Meier estimates and Cox regression models were used to assess survival probability and hazard of death of different groups. P value < 0.05 was considered significant.

RESULTS: 5-year survival for the study group was 41% versus 48% for the control group (log-rank test p = 0.0092). No significant difference in survival rate was found between the four different categories of ILD (log-rank test, p = 0.195) and the different histologic types (log-rank test, p = 0.4005). A cox proportional hazard model was used including presence of ILD, clinical stage and age. The hazard of death among patients with ILD was 1.522 times that among patients without ILD (95%CI, p = 0.029).

CONCLUSION: Patients with lung cancer and CT evidence of ILD have a significantly shorter survival compared to patients with lung cancer only. Documenting the type and grading the severity of ILD in lung cancer patients will significantly contribute to their challenging management.

PMID:34492020 | DOI:10.1371/journal.pone.0255375

PLoS One. 2021 Sep 7;16(9):e0254577. doi: 10.1371/journal.pone.0254577. eCollection 2021.

ABSTRACT

BACKGROUND: Circulating levels of the endogenous inhibitor of nitric oxide synthase, asymmetric dimethylarginine (ADMA), are positively associated with the prevalence of metabolic syndrome (MetS) in cross-sectional investigations. It is unclear if circulating ADMA and other methylarginines are associated with incident MetS prospectively.

METHODS: We related circulating ADMA, symmetric dimethylarginine (SDMA), L-arginine (ARG) concentrations (measured with a validated tandem mass spectrometry assay) and the ARG/ADMA ratio to MetS and its components in 2914 (cross-sectional analysis, logistic regression; mean age 58 years, 55% women) and 1656 (prospective analysis, Cox regression; mean age 56 years, 59% women) individuals from the Framingham Offspring Study who attended a routine examination.

RESULTS: Adjusting for age, sex, smoking, and eGFR, we observed significant associations of ADMA (direct) and ARG/ADMA (inverse) with odds of MetS (N = 1461 prevalent cases; Odds Ratio [OR] per SD increment 1.13, 95%CI 1.04-1.22; and 0.89, 95%CI 0.82-0.97 for ADMA and ARG/ADMA, respectively). Upon further adjustment for waist circumference, systolic and diastolic blood pressure, glucose, high-density lipoprotein cholesterol, and triglycerides, we observed a positive relation between SDMA and MetS (OR per SD increment 1.15, 95% CI 1.01-1.30) but the other associations were rendered statistically non-significant. We did not observe statistically significant associations between any of the methylarginines and the risk of new-onset MetS (752 incident events) over a median follow-up of 11 years.

CONCLUSION: It is unclear whether dimethylarginines play an important role in the incidence of cardiometabolic risk in the community, notwithstanding cross-sectional associations. Further studies of larger samples are needed to replicate our findings.

PMID:34492019 | DOI:10.1371/journal.pone.0254577

PLoS Comput Biol. 2021 Sep 7;17(9):e1009347. doi: 10.1371/journal.pcbi.1009347. Online ahead of print.

ABSTRACT

We construct a recursive Bayesian smoother, termed EpiFilter, for estimating the effective reproduction number, R, from the incidence of an infectious disease in real time and retrospectively. Our approach borrows from Kalman filtering theory, is quick and easy to compute, generalisable, deterministic and unlike many current methods, requires no change-point or window size assumptions. We model R as a flexible, hidden Markov state process and exactly solve forward-backward algorithms, to derive R estimates that incorporate all available incidence information. This unifies and extends two popular methods, EpiEstim, which considers past incidence, and the Wallinga-Teunis method, which looks forward in time. We find that this combination of maximising information and minimising assumptions significantly reduces the bias and variance of R estimates. Moreover, these properties make EpiFilter more statistically robust in periods of low incidence, where several existing methods can become destabilised. As a result, EpiFilter offers improved inference of time-varying transmission patterns that are advantageous for assessing the risk of upcoming waves of infection or the influence of interventions, in real time and at various spatial scales.

PMID:34492011 | DOI:10.1371/journal.pcbi.1009347

PLoS Comput Biol. 2021 Sep 7;17(9):e1009323. doi: 10.1371/journal.pcbi.1009323. Online ahead of print.

ABSTRACT

The B cells in our body generate protective antibodies by introducing somatic hypermutations (SHM) into the variable region of immunoglobulin genes (IgVs). The mutations are generated by activation induced deaminase (AID) that converts cytosine to uracil in single stranded DNA (ssDNA) generated during transcription. Attempts have been made to correlate SHM with ssDNA using bisulfite to chemically convert cytosines that are accessible in the intact chromatin of mutating B cells. These studies have been complicated by using different definitions of “bisulfite accessible regions” (BARs). Recently, deep-sequencing has provided much larger datasets of such regions but computational methods are needed to enable this analysis. Here we leveraged the deep-sequencing approach with unique molecular identifiers and developed a novel Hidden Markov Model based Bayesian Segmentation algorithm to characterize the ssDNA regions in the IGHV4-34 gene of the human Ramos B cell line. Combining hierarchical clustering and our new Bayesian model, we identified recurrent BARs in certain subregions of both top and bottom strands of this gene. Using this new system, the average size of BARs is about 15 bp. We also identified potential G-quadruplex DNA structures in this gene and found that the BARs co-locate with G-quadruplex structures in the opposite strand. Using various correlation analyses, there is not a direct site-to-site relationship between the bisulfite accessible ssDNA and all sites of SHM but most of the highly AID mutated sites are within 15 bp of a BAR. In summary, we developed a novel platform to study single stranded DNA in chromatin at a base pair resolution that reveals potential relationships among BARs, SHM and G-quadruplexes. This platform could be applied to genome wide studies in the future.

PMID:34491985 | DOI:10.1371/journal.pcbi.1009323

PLoS Comput Biol. 2021 Sep 7;17(9):e1008363. doi: 10.1371/journal.pcbi.1008363. Online ahead of print.

ABSTRACT

Although combination antiretroviral therapies seem to be effective at controlling HIV-1 infections regardless of the viral subtype, there is increasing evidence for subtype-specific drug resistance mutations. The order and rates at which resistance mutations accumulate in different subtypes also remain poorly understood. Most of this knowledge is derived from studies of subtype B genotypes, despite not being the most abundant subtype worldwide. Here, we present a methodology for the comparison of mutational networks in different HIV-1 subtypes, based on Hidden Conjunctive Bayesian Networks (H-CBN), a probabilistic model for inferring mutational networks from cross-sectional genotype data. We introduce a Monte Carlo sampling scheme for learning H-CBN models for a larger number of resistance mutations and develop a statistical test to assess differences in the inferred mutational networks between two groups. We apply this method to infer the temporal progression of mutations conferring resistance to the protease inhibitor lopinavir in a large cross-sectional cohort of HIV-1 subtype C genotypes from South Africa, as well as to a data set of subtype B genotypes obtained from the Stanford HIV Drug Resistance Database and the Swiss HIV Cohort Study. We find strong support for different initial mutational events in the protease, namely at residue 46 in subtype B and at residue 82 in subtype C. The inferred mutational networks for subtype B versus C are significantly different sharing only five constraints on the order of accumulating mutations with mutation at residue 54 as the parental event. The results also suggest that mutations can accumulate along various alternative paths within subtypes, as opposed to a unique total temporal ordering. Beyond HIV drug resistance, the statistical methodology is applicable more generally for the comparison of inferred mutational networks between any two groups.

PMID:34491984 | DOI:10.1371/journal.pcbi.1008363

J Drugs Dermatol. 2021 Sep 1;20(9):996-1003. doi: 10.36849/jdd.5818.

ABSTRACT

BACKGROUND: Skin aging is a multifactorial process induced by intrinsic factors such as metabolic processes and senescence as well as environmental factors, including smoking, air pollution, and solar radiation. UV-induced production of reactive oxygen species induces skin photoaging. Antioxidants, including vitamin C and E and green tea polyphenols represent a promising strategy for the aesthetic improvement of clinical features associated with aging.

OBJECTIVE: To assess the safety, tolerability, and efficacy of a novel vitamin C and E and green tea polyphenols (CE-GTP) combination serum on photoaged facial skin.

METHODS: 31 healthy females aged 43 to 65 years (mean age, 57.9) participated in this single-center, 12-week clinical trial. Subjects applied CE-GTP serum twice daily for the duration of the study. Clinical grading of efficacy parameters, safety and tolerability evaluations, ultrasound measurements, and self-assessment questionnaires were conducted at several study milestones.

RESULTS: Statistically significant improvements were observed in all clinically graded efficacy parameters. Highlights include reduction in fine lines around the eye area and facial wrinkles and enhanced skin smoothness and radiance. Ultrasound measurements showed a statistically significant increase in skin density at week 12 compared with baseline, indicating thickening of the epidermal and dermal tissue, associated with youthful, healthier skin. Subjects self-reported numerous improvements, including reduction of fine lines and wrinkles, improved skin tone and texture, diminished look of dark spots, and improved skin elasticity.

CONCLUSION: Novel CE-GTP serum is safe and effective, as shown by statistically significant improvements in multiple aesthetically important objective, subjective, and patient reported outcomes. J Drugs Dermatol. 2021;20(9):996-1003. doi:10.36849/JDD.5818.

PMID:34491027 | DOI:10.36849/jdd.5818