Category: Statistics

Bioinformatics. 2022 Feb 16:btac098. doi: 10.1093/bioinformatics/btac098. Online ahead of print.

ABSTRACT

MOTIVATION: Drawing peaks in a data window of an MS data set happens at all time in MS data visualization applications. This asks to retrieve from an MS data set some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS data set.

RESULTS: We present mzMD, a new storage format of MS data sets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS data sets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.

AVAILABILITY: The source code is freely available at https://github.com/yrm9837/mzMD-java.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35171986 | DOI:10.1093/bioinformatics/btac098

Med Phys. 2022 Feb 16. doi: 10.1002/mp.15546. Online ahead of print.

ABSTRACT

PURPOSE: Accurately segmenting curvilinear structures, e.g., retinal blood vessels or nerve fibers, in the medical image is essential to the clinical diagnosis of many diseases. Recently, deep learning has become a popular technology to deal with the image segmentation task and it has obtained remarkable achievement. However, the existing methods still have many problems when segmenting the curvilinear structures in medical images, such as losing the details of curvilinear structures, producing many false-positive segmentation results. To mitigate these problems, we propose a novel end-to-end curvilinear structure segmentation network called Curv-Net.

METHODS: Curv-Net is an effective encoder-decoder architecture constructed based on selective kernel (SK) and multi-bidirectional convolutional LSTM (Multi-Bi-ConvLSTM). To be specific, we first employ the SK module in the convolutional layer to adaptively extract the multi-scale features of the input image, and then we design a Multi-Bi-ConvLSTM as the skip concatenation to fuse the information learned in the same stage and propagate the feature information from the deep stages to the shallow stages, which can enable the feature captured by Curv-Net to contain more detail information and high-level semantic information simultaneously to improve the segmentation performance.

RESULTS: The effectiveness and reliability of our proposed Curv-Net are verified on three public datasets: two color fundus datasets (DRIVE and CHASE_DB1) and one corneal nerve fiber dataset (CCM-2). We calculate the ACC (accuracy), SE (sensitivity), SP (specificity), Dice (Dice similarity coefficient) and AUC (area under the receiver) for the DRIVE and CHASE_DB1 datasets. The ACC, SE, SP, Dice and AUC of the DRIVE dataset are 0.9629, 0.8175, 0.9858, 0.8352 and 0.9810, respectively. For the CHASE_DB1 dataset, the values are 0.9810, 0.8564, 0.9899, 0.8143 and 0.9832, respectively. To validate the corneal nerve fiber segmentation performance of the proposed Curv-Net, we test it on the CCM-2 dataset and calculate Dice, SE and FDR (false discovery rate) metrics. The Dice, SE and FDR achieved by Curv-Net are 0.8114±0.0062, 0.8903±0.0113 and 0.2547±0.0104, respectively.

CONCLUSIONS: Curv-Net is evaluated on three public datasets. Extensive experimental results demonstrate that Curv-Net outperforms the other superior curvilinear structure segmentation methods. This article is protected by copyright. All rights reserved.

PMID:35172016 | DOI:10.1002/mp.15546

PLoS One. 2022 Feb 16;17(2):e0264021. doi: 10.1371/journal.pone.0264021. eCollection 2022.

ABSTRACT

BACKGROUND: Acanthamoeba keratitis is challenging to treat and thought to result in poor outcomes, but very few comparative studies exist to assess whether ulcers caused by Acanthamoeba are worse than those caused by bacteria or fungus.

METHODS: In a retrospective cohort study, all cases of smear- or culture-proven Acanthamoeba keratitis diagnosed from January 2006 to June 2011 at an eye hospital in South India were identified from the microbiology database. Random samples of the same number of cases of bacterial and fungal keratitis, matched by year, were identified from the same database in order to compare outcomes between the three types of organism. The main outcomes were the time until the following events: re-epithelialization, discontinuation of antimicrobials, perforation/keratoplasty, elevated intraocular pressure, and new cataract.

RESULTS: The median time until re-epithelialization was 113 days for Acanthamoeba keratitis, 30 days for fungal keratitis, and 25 days for bacterial keratitis, and the median time until discontinuation of antimicrobial therapy was 100 days for Acanthamoeba keratitis, 49 days for fungal keratitis, and 40 days for bacterial keratitis. Compared to the other two organisms, Acanthamoeba ulcers took significantly longer to re-epithelialize (adjusted HR 0.4, 95% CI 0.3 to 0.6 relative to bacterial ulcers and HR 0.3, 95% CI 0.2 to 0.5 relative to fungal ulcers; overall p<0.001) and had significantly longer courses of antimicrobials (adjusted HR 0.3, 95% CI 0.2 to 0.6 relative to bacterial ulcers and HR 0.5, 95%CI 0.3 to 0.8 relative to fungal ulcers; overall p<0.001). No statistically significant difference was observed between the three organisms for the other time-to-event outcomes.

CONCLUSIONS: Acanthamoeba keratitis was more difficult to treat and had worse clinical outcomes than bacterial or fungal ulcers, highlighting the lack of adequate treatment regimens for this infection.

PMID:35171970 | DOI:10.1371/journal.pone.0264021

PLoS One. 2022 Feb 16;17(2):e0263890. doi: 10.1371/journal.pone.0263890. eCollection 2022.

ABSTRACT

BACKGROUND: Bangladesh is a South Asian developing country trying to achieve the Sustainable Development Goals (SDG)-3 and the objective of the Rural Electrification Board (REB) regarding child mortality. Infectious diseases are leading causes of child mortality, and lack of exclusive breastfeeding (EBF) among infants aged 0-6 months increases child morbidity and mortality from various infectious diseases in developing countries. However, as per existing literature, no study has been conducted yet to determine the lack of EBF practice effect on child mortality in Bangladesh. With this backdrop, the authors intend to measure the likelihood of infectious diseases due to the lack of EBF of infants aged 0-6 months in Bangladesh.

MATERIALS AND METHODS: This study used Bangladesh Demographic and Health Survey (BDHS) data over 1996-97 to 2017-18. The mothers of infants aged 0-6 months who were willingly participated in the BDHSs were considered to include in our analysis. Initially, there were 9,133 cases in the combined dataset. After filtering, there were 5,724 cases in the final dataset. We have considered diarrhea (D), acute respiratory infection (ARI) separately as well as the presence of either D or ARI or both and named as CoDARI as outcome variables. This study used both graphical and statistical techniques (Chi-square test, Wald test, and logistic regression) to analyze the data. The odds ratio (OR) and 95% confidence interval (CI) were used to quantify the likelihood of infectious diseases due to lack of EBF practice and its elasticity, respectively.

RESULTS: The EBF practice got a conspicuous increasing trend, but the prevalence of infectious diseases was declined from 0 to 3 months of age of infants, whereas an inverse scenario is observed between 4-6 months. The significance of that inverse relationship was confirmed by p-value corresponding to the chi-square test and the Wald test of the adjusted regression coefficients after adjusting the associated factor’s effect on infectious diseases. The adjusted ORs also concluded that the lack of EBF practice up to six months of age could enhance the risk of D, ARI, and CoDARI by 2.11 [95% CI: 1.56-2.85], 1.43 [95% CI: 1.28-1.60], and 1.48 [95% CI: 1.32-1.66] times higher, respectively.

CONCLUSION: Findings of this study emphasize the importance of EBF up to six months of age of infants against diarrhea and ARI specific morbidity and mortality. Our results also agreed to the recommendation of the World Health Organization (WHO), United Nations International Children’s Emergency Fund (UNICEF), American Academy of Pediatrics (AAP), American Academy of Family Physicians (AAFP), and National Nutrition Programme of Ethiopia (NNPE) that the EBF practice for the first six months of age could be a best, cost-effective, long-lasting natural preventive way to reduce the child morbidity and mortality due to infectious diseases in developing countries. Therefore, findings would help policymakers ensuring the achievement target of REB and SDG-3 associated with the health sector in Bangladesh.

PMID:35171952 | DOI:10.1371/journal.pone.0263890

PLoS One. 2022 Feb 16;17(2):e0263817. doi: 10.1371/journal.pone.0263817. eCollection 2022.

ABSTRACT

People experience the same event but do not feel the same way. Such individual differences in emotion response are believed to be far greater than those in any other mental functions. Thus, to understand what makes people individuals, it is important to identify the systematic structures of individual differences in emotion response and elucidate how such structures relate to what aspects of psychological characteristics. Reflecting this importance, many studies have attempted to relate emotions to psychological characteristics such as personality traits, psychosocial states, and pathological symptoms across individuals. However, systematic and global structures that govern the across-individual covariation between the domain of emotion responses and that of psychological characteristics have been rarely explored previously, which limits our understanding of the relationship between individual differences in emotion response and psychological characteristics. To overcome this limitation, we acquired high-dimensional data sets in both emotion-response (8 measures) and psychological-characteristic (68 measures) domains from the same pool of individuals (86 undergraduate or graduate students) and carried out the canonical correlation analysis in conjunction with the principal component analysis on those data sets. For each participant, the emotion-response measures were quantified by regressing affective-rating responses to visual narrative stimuli onto the across-participant average responses to those stimuli, while the psychological-characteristic measures were acquired from 19 different psychometric questionnaires grounded in personality, psychosocial-factor, and clinical-problem taxonomies. We found a single robust mode of population covariation, particularly between the ‘accuracy’ and ‘sensitivity’ measures of arousal responses in the emotion domain and many ‘psychosocial’ measures in the psychological-characteristics domain. This mode of covariation suggests that individuals characterized with positive social assets tend to show polarized arousal responses to life events.

PMID:35171958 | DOI:10.1371/journal.pone.0263817

PLoS One. 2022 Feb 16;17(2):e0263557. doi: 10.1371/journal.pone.0263557. eCollection 2022.

ABSTRACT

BACKGROUND: Nursing is a profession that care for personal and private aspects of people’s lives. Therefore, nurses need to know the basic ethical aspects of nursing which is integral in nursing practices. The purpose of the study was to describe the ethical knowledge, attitude and practice of nurses in the Cape Coast Metropolis of Ghana.

METHOD: A cross-section design was used to collect data from 264 nurses in three selected healthcare facilities in the Metropolis. A structured questionnaire was administered to all the categories of these nurses in the selected facilities. Frequency counts and multiple regression statistics were used to analyze the data.

RESULTS: The results show 78% of nurses possess good ethical knowledge, 84% had a positive attitude, while 98% had good ethical practices. The results further show that nurses’ professional rank [F (1, 259), 2.35, p = .02] and academic qualification [F (1, 259), 2.67, p = .008] were significant predictors of their ethical knowledge and attitude, respectively.

CONCLUSION: Inadequate resources, poor set up of working areas and understaffing are the major barriers limiting the practice of good ethical standards among the nurses. The Regional Health Directorate, the Ministry of Health and the Managers in charge of the health facilities need to work together to eliminate these barriers as they have the potential to negatively impact quality healthcare delivery in the Metropolis.

PMID:35171946 | DOI:10.1371/journal.pone.0263557

PLoS One. 2022 Feb 16;17(2):e0263920. doi: 10.1371/journal.pone.0263920. eCollection 2022.

ABSTRACT

The aim of this study was to assess differences in cervical cancer screening and treatment outcomes by HIV status in a routine programmatic setting with a high generalized HIV prevalence. Women living with HIV (WLHIV) are at heightened risk of developing cervical cancer and the World Health Organization recommends all WLHIV who are sexually active be screened, regardless of age. In 2018, Namibia’s Ministry of Health and Social Services introduced a screen-and-treat approach using visual inspection with acetic acid (VIA) and ablative treatment with cryotherapy or thermocoagulation with a focus on screening HIV-positive women due to Namibia’s 11.5% prevalence of HIV in women aged 15-49. Using program data from October 2018 to March 2020 from seven of the country’s 14 regions, we calculated descriptive statistics and chi-square tests to test the statistical significance of differences in VIA-positivity, ineligibility for ablative treatment, treatment completion, and same day treatment completion by HIV status. Between October 2018 and March 2020, the program conducted 14,786 cervical cancer screenings. Among 8,150 women who received their first VIA screening, more WLHIV screened VIA-positive (17%) than HIV-negative women (15%). This difference was statistically significant (p = 0.02). Among 2,272 women who screened VIA-positive at any screening, 1,159 (82%) completed ablative treatment. This suggests ablative treatment is feasible and acceptable in resource-limited settings. WLHIV were also more likely to complete treatment than HIV-negative women (p<0.01). Differences in health seeking behavior of sub-populations as well as resource availability between service delivery points should be considered for further investigation. Going forward in order to strengthen program implementation and expand screening access and uptake further investigation is needed to determine cancer incidence by HIV status, age, and time since last screening to assess cases that are averted as well as potential rates of overtreatment.

PMID:35171941 | DOI:10.1371/journal.pone.0263920

PLoS One. 2022 Feb 16;17(2):e0262515. doi: 10.1371/journal.pone.0262515. eCollection 2022.

ABSTRACT

BACKGROUND: Following the full re-opening of schools in England and emergence of the SARS-CoV-2 Alpha variant, we investigated the risk of SARS-CoV-2 infection in students and staff who were contacts of a confirmed case in a school bubble (school groupings with limited interactions), along with their household members.

METHODS: Primary and secondary school bubbles were recruited into sKIDsBUBBLE after being sent home to self-isolate following a confirmed case of COVID-19 in the bubble. Bubble participants and their household members were sent home-testing kits comprising nasal swabs for RT-PCR testing and whole genome sequencing, and oral fluid swabs for SARS-CoV-2 antibodies.

RESULTS: During November-December 2020, 14 bubbles were recruited from 7 schools, including 269 bubble contacts (248 students, 21 staff) and 823 household contacts (524 adults, 299 children). The secondary attack rate was 10.0% (6/60) in primary and 3.9% (4/102) in secondary school students, compared to 6.3% (1/16) and 0% (0/1) among staff, respectively. The incidence rate for household contacts of primary school students was 6.6% (12/183) and 3.7% (1/27) for household contacts of primary school staff. In secondary schools, this was 3.5% (11/317) and 0% (0/1), respectively. Household contacts were more likely to test positive if their bubble contact tested positive although there were new infections among household contacts of uninfected bubble contacts.

INTERPRETATION: Compared to other institutional settings, the overall risk of secondary infection in school bubbles and their household contacts was low. Our findings are important for developing evidence-based infection prevention guidelines for educational settings.

PMID:35171942 | DOI:10.1371/journal.pone.0262515

PLoS One. 2022 Feb 16;17(2):e0263233. doi: 10.1371/journal.pone.0263233. eCollection 2022.

ABSTRACT

BACKGROUND: Overweight/obesity is a well-defined risk factor for a variety of chronic cardiovascular and metabolic diseases. Sleep duration has been associated with overweight/obesity and other cardio metabolic and neurocognitive problems. Notably, overweight/obesity and many of the associated comorbidities are prevalent in Indigenous Australians. Generally, sleep duration has been associated with BMI for Australian adults but information about Australian Indigenous adults’ sleep is scant. A recent report established that sleep is a weak predictor of obesity for Indigenous Australian adults.

AIM: To determine whether sleep remains a predictor of obesity when physical activity, diet and smoking status are accounted for; and to determine whether sleep duration plays a mediating role in the relationship between Indigenous status and BMI.

METHODS: Statistical analyses of 5,886 Australian adults: 5236 non-Indigenous and 650 Indigenous people aged over 18 years who participated in the Australian Health Survey 2011-2013. Demographic and lifestyle characteristics were described by χ2 and t-tests. ANOVA was used to determine the variables that significantly predicted BMI and sleep duration. Stepwise regression analyses were performed to determine the strongest significant predictors of BMI. Sleep duration was self-reported; BMI was calculated from measurement.

RESULTS: The study revealed two main findings: (i) short sleep duration was an independent predictor of obesity (adjusted-R2 = 0.056, p <0.0001); and (ii) controlling for sleep duration and other possible confounders, Indigenous status was a significant predictor of BMI overweight/obesity. Sleep duration played a weak, partial mediator role in this relationship. Increased BMI was associated with lower socioeconomic status and level of disadvantage of household locality for non-remote Indigenous and non-Indigenous people.

CONCLUSION: Indigenous status strongly predicted increased BMI. The effect was not mediated by the socioeconomic indicators but was partially mediated by sleep duration.

PMID:35171935 | DOI:10.1371/journal.pone.0263233

PLoS One. 2022 Feb 16;17(2):e0263572. doi: 10.1371/journal.pone.0263572. eCollection 2022.

ABSTRACT

INTRODUCTION: Coronavirus 2019 (COVID- 19) is an acute respiratory viral infectious disease in human being caused by RNA virus that belonged to the family of corona virus. The incidence of this disease was growing exponentially and affects millions of the world population that leads to expose thousands of peoples for death. Thus, this study was targeted to assess the practice of people on COVID-19 infections prevention strategies in the region.

METHODS: A community based cross sectional study design was conducted in Benishangul Gumuz Region from May 25 -June 15, 2020. Multistage sampling technique was carried out to select 21 kebeles/ketena and 422 study participants. Data were collected by face to face interview using semi-structured questionnaires. The collected data were entered, cleaned and analyzed using STATA software version 14.0. Descriptive, bi-variable and multivariable multilevel models were applied. Variables with p value < 0.25 in bi-variable analysis were selected as candidates for multivariable analysis. Finally, the variables with p-value < 0.5 were considered as statistically significant, then variables with odds ratio, 95% CI were used to interpret the effect of association.

RESULTS: The magnitude of good practice on prevention strategies of COVID- 19 infections was 62.1%. The most frequently practiced prevention strategies for COVID-19 infections were hand washing with water and soap (80.7%), alcohol-based hand rub (68.8%), maintaining social/physical distance (74.2%) and avoiding touching eyes. Individual and community level factors that affecting practice of COVID- 19 infection prevention strategies were discovered. Hence, community level factor was place of origin (AOR = 0.1; 95%CI: 0.03, 0.35) whereas individual level factors were able to read and write (AOR = 0.18; 95%CI: 0.04, 0.81) and being merchant (AOR = 2.07; 95%CI: 1.01, 4.28).

CONCLUSION: The level of practice of community towards COVID-19 infections prevention strategies were low as compared with the expected outcome. Individual and community level factors were identified. This implies that social mobilization and community engagement was not effective. Thus, designing appropriate strategies to improve of practice prevention strategies are strongly recommend.

PMID:35171932 | DOI:10.1371/journal.pone.0263572