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Nevin Manimala Statistics

Deep learning with robustness to missing data: A novel approach to the detection of COVID-19

PLoS One. 2021 Jul 30;16(7):e0255301. doi: 10.1371/journal.pone.0255301. eCollection 2021.

ABSTRACT

In the context of the current global pandemic and the limitations of the RT-PCR test, we propose a novel deep learning architecture, DFCN (Denoising Fully Connected Network). Since medical facilities around the world differ enormously in what laboratory tests or chest imaging may be available, DFCN is designed to be robust to missing input data. An ablation study extensively evaluates the performance benefits of the DFCN as well as its robustness to missing inputs. Data from 1088 patients with confirmed RT-PCR results are obtained from two independent medical facilities. The data includes results from 27 laboratory tests and a chest x-ray scored by a deep learning model. Training and test datasets are taken from different medical facilities. Data is made publicly available. The performance of DFCN in predicting the RT-PCR result is compared with 3 related architectures as well as a Random Forest baseline. All models are trained with varying levels of masked input data to encourage robustness to missing inputs. Missing data is simulated at test time by masking inputs randomly. DFCN outperforms all other models with statistical significance using random subsets of input data with 2-27 available inputs. When all 28 inputs are available DFCN obtains an AUC of 0.924, higher than any other model. Furthermore, with clinically meaningful subsets of parameters consisting of just 6 and 7 inputs respectively, DFCN achieves higher AUCs than any other model, with values of 0.909 and 0.919.

PMID:34329354 | DOI:10.1371/journal.pone.0255301

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Nevin Manimala Statistics

Prognostic value of high-sensitivity cardiac troponin I in heart failure patients with mid-range and reduced ejection fraction

PLoS One. 2021 Jul 30;16(7):e0255271. doi: 10.1371/journal.pone.0255271. eCollection 2021.

ABSTRACT

BACKGROUND: The identification of high-risk heart failure (HF) patients makes it possible to intensify their treatment. Our aim was to determine the prognostic value of a newly developed, high-sensitivity troponin I assay (Atellica®, Siemens Healthcare Diagnostics) for patients with HF with reduced ejection fraction (HFrEF; LVEF < 40%) and HF with mid-range EF (HFmrEF) (LVEF 40%-49%).

METHODS AND RESULTS: A total of 520 patients with HFrEF and HFmrEF were enrolled in this study. Two-year all-cause mortality, heart transplantation, and/or left ventricular assist device implantation were defined as the primary endpoints (EP). A logistic regression analysis was used for the identification of predictors and development of multivariable models. The EP occurred in 14% of the patients, and these patients had higher NT-proBNP (1,950 vs. 518 ng/l; p < 0.001) and hs-cTnI (34 vs. 17 ng/l, p < 0.001) levels. C-statistics demonstrated that the optimal cut-off value for the hs-cTnI level was 17 ng/l (AUC 0.658, p < 0.001). Described by the AUC, the discriminatory power of the multivariable model (NYHA > II, NT-proBNP, hs-cTnI and urea) was 0.823 (p < 0.001). Including heart failure hospitalization as the component of the combined secondary endpoint leads to a diminished predictive power of increased hs-cTnI.

CONCLUSION: hs-cTnI levels ≥ 17 ng/l represent an independent increased risk of an adverse prognosis for patients with HFrEF and HFmrEF. Determining a patient’s hs-cTnI level adds prognostic value to NT-proBNP and clinical parameters.

PMID:34329368 | DOI:10.1371/journal.pone.0255271

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Nevin Manimala Statistics

Intergenerational educational mobility in Bangladesh

PLoS One. 2021 Jul 30;16(7):e0255426. doi: 10.1371/journal.pone.0255426. eCollection 2021.

ABSTRACT

INTRODUCTION: Social mobility is considered as an important indicator of the economic development of a country. However, it varies widely across geographical regions and social groups in developing countries like Bangladesh. This paper intends to evaluate the intergenerational mobility in Bangladesh across generations.

METHODS AND MATERIALS: This paper considers a nationally representative sample survey of 8,403 respondents (rural: 5,436 and urban: 2,967). The male and female respondents aged 23 years and above were included in the sample. The education attainment of a son or daughter as compared to their father’s education level was considered as the measure of intergenerational mobility. Transition probability matrix and different social mobility indices were used to find out the intergenerational education mobility in Bangladesh.

RESULTS: The findings reveal that approximately three-fourth (74.5%) of the respondents attained formal education, while more than half (58.3%) of the respondents’ father was illiterate. The educational status of the respondents and their father who lived in urban areas was relatively better than who lived in rural areas. It is also observed that 91.2% and 81.6% of the intergenerational class movement was upward among sons and daughters respectively. The probability of a higher educated father will have a higher educated child is higher in urban areas than in rural areas of Bangladesh. The intergenerational mobility is higher in the primary, secondary, and higher secondary educational levels, though the illiterate and higher education levels are the least mobile classes. In addition, the limiting probabilities reveal that the chance of sending sons to schools by an illiterate father is less as compared to their daughters. Such difference is more obvious in the urban areas, i.e., it is highly likely that sons of the illiterate father are also illiterate.

CONCLUSION: Bangladesh has been progressing remarkably in recent years. To keep the pace of the ongoing economic development in the country, it is necessary to give more attention to the illiterate people especially the girls who live in rural areas. The authors anticipate that the findings will be helpful for the policymakers as the relationship between inequality and intergenerational mobility is vital for several aspects of the economic development of a country.

PMID:34329343 | DOI:10.1371/journal.pone.0255426

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Nevin Manimala Statistics

Evaluation of post-operative complications, outcome, and long-term owner satisfaction of elbow arthrodesis (EA) in 22 dogs

PLoS One. 2021 Jul 30;16(7):e0255388. doi: 10.1371/journal.pone.0255388. eCollection 2021.

ABSTRACT

The objective of this study was to report post-operative complications and outcomes in canines undergoing elbow arthrodesis (EA) with fixation techniques including bone plate fixation with a non-locking dynamic compression plate (DCP), bone plate fixation with a locking plate (LCP), and external skeletal fixator (ESF). Medical records of twenty-two cases that underwent EA between January 2009-December 2019 from 8 referral hospitals including both private practice and academic institutions were reviewed. Post-operative complications were classified as either minor or major, surgical evaluations were performed 8 weeks post operatively, and a follow-up questionnaire was sent to owners. Of the total 22 cases that met inclusion criteria, a total of 19/22 cases had complications, 12 major and 7 minor. Complications reported in 8/9, 7/9, and 4/4, for the DCP, LCP, and ESF fixation groups, respectively. Mild to moderate mechanical lameness was identified at surgical evaluation in 16/22 cases. Complete radiographic bone healing was achieved after 9 weeks in 19/22 cases. Long term owner follow up was available in 14/22 cases. Owners reported a good to normal quality of life in 13/14 cases and poor in one case. The majority of owners (11/14) reported good to excellent satisfaction with the outcome irrespective of persistent lameness. This study demonstrates that successful EA can be achieved using a variety of fixation methods, but persistent lameness is expected and complication rate is high.

PMID:34329353 | DOI:10.1371/journal.pone.0255388

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Nevin Manimala Statistics

Assessing national cervical cancer screening guidelines: Results from an HIV testing clinic also screening for cervical cancer and HPV in Soweto, South Africa

PLoS One. 2021 Jul 30;16(7):e0255124. doi: 10.1371/journal.pone.0255124. eCollection 2021.

ABSTRACT

OBJECTIVE: A screening centre in Soweto, South Africa (SA), investigated high-risk human papillomavirus (HR-HPV), HIV, cervical cancer risk amongst women.

METHODS: This cross-sectional study (June 2018-March 2019) describes screening results (Roche Linear Array HPV test and Pap smear liquid based cytology) and history of screening (known HIV status, antiretroviral therapy [ART] use, previous Pap smears). Data were stratified by age group (18-29, 30+ years), HIV status, Pap smear results and tested for statistical significance.

RESULTS: Of 280 women, 20.4% were HIV-positive, 18.2% had abnormal Pap smears, 41.8% had HR-HPV. Of older women, 48.2% (n = 78/162) had never had a Pap smear. Of younger women, 89.0% (n = 105/118) never had a Pap smear, but had significantly more low-grade squamous intraepithelial lesions (LSIL) and other HR-HPV infection than older women (12.7%[n = 15/118] vs 4.9%[n = 8/162], p = 0.0193; and 49.2%[n = 58/118] vs 29.0%[n = 47/162], p = 0.0006; respectively). HIV-positive women had more abnormal cytology results and infection with other HR-HPV types or co-infection with other HR-HPV type(s)/HPV-16 compared to HIV-negative women (35.1%[n = 20/57] vs 13.9%[n = 31/223], p = 0.0002; 56.1%[n = 32/57] vs 32.7%[n = 73/223], p = 0.001; and 12.3%[n = 7/57] vs 4.9%[n = 11/223], p = 0.044; respectively). Of 57 HIV-positive women, 45.6% (n = 26) already knew their HIV status; of which 69.2% were on ART and 34.6% never had a Pap smear.

CONCLUSION: South African women have high rates of HIV, Pap smear abnormalities and HR-HPV, with low cervical cancer screening coverage. SA cervical cancer screening policy excludes (undiagnosed) HIV-positive and HIV-negative women <30 years, both populations found to have high prevalence of HR-HPV. HPV-based primary screening from 25 years could improve outcomes.

PMID:34329334 | DOI:10.1371/journal.pone.0255124

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Nevin Manimala Statistics

Cellular responses at the application site of a high-density microarray patch delivering an influenza vaccine in a randomized, controlled phase I clinical trial

PLoS One. 2021 Jul 30;16(7):e0255282. doi: 10.1371/journal.pone.0255282. eCollection 2021.

ABSTRACT

Microarray patches (MAPs) have the potential to be a safer, more acceptable, easier to use and more cost-effective method for administration of vaccines when compared to the needle and syringe. Since MAPs deliver vaccine to the dermis and epidermis, a degree of local immune response at the site of application is expected. In a phase 1 clinical trial (ACTRN 12618000112268), the Vaxxas high-density MAP (HD-MAP) was used to deliver a monovalent, split inactivated influenza virus vaccine into the skin. HD-MAP immunisation led to significantly enhanced humoral responses on day 8, 22 and 61 compared with IM injection of a quadrivalent commercial seasonal influenza vaccine (Afluria Quadrivalent®). Here, the aim was to analyse cellular responses to HD-MAPs in the skin of trial subjects, using flow cytometry and immunohistochemistry. HD-MAPs were coated with a split inactivated influenza virus vaccine (A/Singapore/GP1908/2015 [H1N1]), to deliver 5 μg haemagglutinin (HA) per HD-MAP. Three HD-MAPs were applied to the volar forearm (FA) of five healthy volunteers (to achieve the required 15 μg HA dose), whilst five control subjects received three uncoated HD-MAPs (placebo). Local skin response was recorded for over 61 days and haemagglutination inhibition antibody titres (HAI) were assessed on days 1, 4, 8, 22, and 61. Skin biopsies were taken before (day 1), and three days after HD-MAP application (day 4) and analysed by flow-cytometry and immunohistochemistry to compare local immune subset infiltration. HD-MAP vaccination with 15 μg HA resulted in significant HAI antibody titres compared to the placebo group. Application of uncoated placebo HD-MAPs resulted in mild erythema and oedema in most subjects, that resolved by day 4 in 80% of subjects. Active, HA-coated HD-MAP application resulted in stronger erythema responses on day 4, which resolved between days 22-61. Overall, these erythema responses were accompanied by an influx of immune cells in all subjects. Increased cell infiltration of CD3+, CD4+, CD8+ T cells as well as myeloid CD11b+ CD11c+ and non-myeloid CD11b- dendritic cells were observed in all subjects, but more pronounced in active HD-MAP groups. In contrast, CD19+/CD20+ B cell counts remained unchanged. Key limitations include the use of an influenza vaccine, to which the subjects may have had previous exposure. Different results might have been obtained with HD-MAPs inducing a primary immune response. In conclusion, influenza vaccine administered to the forearm (FA) using the HD-MAP was well-tolerated and induced a mild to moderate skin response with lymphocytic infiltrate at the site of application.

PMID:34329337 | DOI:10.1371/journal.pone.0255282

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Nevin Manimala Statistics

A methodologically sound survey of Chinese consumers’ willingness to participate in courier, express, and parcel companies’ green logistics

PLoS One. 2021 Jul 30;16(7):e0255532. doi: 10.1371/journal.pone.0255532. eCollection 2021.

ABSTRACT

The environmental footprint of courier, express, and parcel (CEP) logistics is significant and growing, owing to increased e-commerce. Consumer willingness to participate in the green logistics of CEPs, however, has been understudied. This study addresses this knowledge gap by surveying 155 Chinese consumers about their willingness to participate in CEP green logistics. Additionally, this research identifies some technical issues with previous survey research. Three main factors were extracted after the data were tested for reliability and validity using exploratory factor analysis with principal axis factor extraction and confirmatory factor analysis with diagonally weighted least squares. Consumer willingness is positively correlated with economic (8 items), operational (3 items), and social (3 items) factors, with a statistical significance of p < 0.001. Of all the factors, the strongest correlation, 0.67 (95% CI = 0.57, 0.75; p < 0.001; N = 155), exists between economic factors and consumer willingness. The results of a multinomial logistic regression analysis suggest that all consumers are highly unlikely to participate in economic factors, while they are highly likely to positively commit to operational and social factors. Therefore, it is recommended that the government provides monetary incentives to CEP companies to adopt green logistics, such as tax reductions and subsidies, to reduce the costs of green logistics. Meanwhile, the CEP industry could provide some direct and indirect incentives to consumers to re-use, recycle, and share materials, and to spend time learning about express enterprises’ green logistics, to increase consumer participation in economic factors.

PMID:34329331 | DOI:10.1371/journal.pone.0255532

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Nevin Manimala Statistics

Patient delay and associated factors among tuberculosis patients in Gamo zone public health facilities, Southern Ethiopia: An institution-based cross-sectional study

PLoS One. 2021 Jul 30;16(7):e0255327. doi: 10.1371/journal.pone.0255327. eCollection 2021.

ABSTRACT

BACKGROUND: Delayed tuberculosis diagnosis and treatment increase morbidity, mortality, expenditure, and transmission in the community. Early diagnosis and initiation of treatment are essential for effective TB control. Therefore, the main objective of this study was to assess the magnitude and factors associated with patient delay among tuberculosis patients in Gamo Zone, Southern Ethiopia.

METHODS: A cross-sectional study was conducted in Gamo Zone, Southern Ethiopia from February to April 2019. Fifteen health facilities of the study area were selected randomly and 255 TB patients who were ≥18 years of age were included. Data were collected using a questionnaire through face-to-face interviews and analyzed using SPSS version 20.0. Patient delay was analyzed using the median as the cut-off value. Multivariable logistic regression analysis was fitted to identify factors associated with patient delay. A p-value of ≤ 0.05 with 95% CI was considered to declare a statistically significant association.

RESULTS: The median (inter-quartile range) of the patient delay was 30 (15-60) days. About 56.9% of patients had prolonged patients’ delay. Patient whose first contact were informal provider (adjusted odds ratio [AOR]: 2.24; 95% confidence interval [CI] 1.29, 3.86), presenting with weight loss (AOR: 2.53; 95%CI: 1.35, 4.74) and fatigue (AOR: 2.38; 95%CI: 1.36, 4.17) and body mass index (BMI) categories of underweight (AOR: 1.74; 95%CI: 1.01, 3.00) were independently associated with increased odds of patient delay. However, having good knowledge about TB (AOR: 0.44; 95% CI: 0.26, 0.76) significantly reduce patients’ delay.

CONCLUSION: In this study, a significant proportion of patients experienced more than the acceptable level for the patient delay. Knowledge about TB, the first action to illness, presenting symptoms, and BMI status were identified factors associated with patient delay. Hence, raising public awareness, regular training, and re-training of private and public healthcare providers, involving informal providers, and maintenance of a high index of suspicion for tuberculosis in the vulnerable population could reduce long delays in the management of TB.

PMID:34329333 | DOI:10.1371/journal.pone.0255327

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Nevin Manimala Statistics

Rainfall, temperature, and Classic Maya conflict: A comparison of hypotheses using Bayesian time-series analysis

PLoS One. 2021 Jul 30;16(7):e0253043. doi: 10.1371/journal.pone.0253043. eCollection 2021.

ABSTRACT

Studies published over the last decade have reached contrasting conclusions regarding the impact of climate change on conflict among the Classic Maya (ca. 250-900 CE). Some researchers have argued that rainfall declines exacerbated conflict in this civilisation. However, other researchers have found that the relevant climate variable was increasing summer temperatures and not decreasing rainfall. The goal of the study reported here was to test between these two hypotheses. To do so, we collated annually-resolved conflict and climate data, and then subjected them to a recently developed Bayesian method for analysing count-based times-series. The results indicated that increasing summer temperature exacerbated conflict while annual rainfall variation had no effect. This finding not only has important implications for our understanding of conflict in the Maya region during the Classic Period. It also contributes to the ongoing discussion about the likely impact of contemporary climate change on conflict levels. Specifically, when our finding is placed alongside the results of other studies that have examined temperature and conflict over the long term, it is clear that the impact of climate change on conflict is context dependent.

PMID:34329320 | DOI:10.1371/journal.pone.0253043

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Body shape matters: Evidence from machine learning on body shape-income relationship

PLoS One. 2021 Jul 30;16(7):e0254785. doi: 10.1371/journal.pone.0254785. eCollection 2021.

ABSTRACT

The association between physical appearance and income has been of central interest in social science. However, most previous studies often measured physical appearance using classical proxies from subjective opinions based on surveys. In this study, we use novel data, called CAESAR, which contains three-dimensional (3D) whole-body scans to mitigate possible reporting and measurement errors. We demonstrate the existence of significant nonclassical reporting errors in the reported heights and weights by comparing them with measured counterparts, and show that these discrete measurements are too sparse to provide a complete description of the body shape. Instead, we use a graphical autoencoder to obtain intrinsic features, consisting of human body shapes directly from 3D scans and estimate the relationship between body shapes and family income. We also take into account a possible issue of endogenous body shapes using proxy variables and control functions. The estimation results reveal a statistically significant relationship between physical appearance and family income and that these associations differ across genders. This supports the hypothesis on the physical attractiveness premium in labor market outcomes and its heterogeneity across genders.

PMID:34329322 | DOI:10.1371/journal.pone.0254785