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Nevin Manimala Statistics

AutomAl 6000: Semi-automatic structural labelling of HAADF-STEM images of precipitates in Al-Mg-Si(-Cu) alloys

Ultramicroscopy. 2022 Mar 10;236:113493. doi: 10.1016/j.ultramic.2022.113493. Online ahead of print.

ABSTRACT

When the Al-Mg-Si(-Cu) alloy system is subjected to age hardening, different types of precipitates nucleate depending on the composition and thermomechanical treatment. The main hardening precipitates extend as needles, laths or rods along the <100> directions in the aluminium matrix. It has been found that the structures of all metastable precipitates may be generalized as stacks of <100> columns, where most of these columns are replaced by solute elements. In the precipitates, a column relates to neighbour columns by a set of simple structural principles, which allows identification of species and relative longitudinal displacement over the (100) cross-section. Aberration-corrected high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) is an important tool for studying such precipitates. With the goal of analysing atomic resolution HAADF-STEM images of precipitate cross-sections in the Al-Mg-Si(-Cu) system, we have developed the stand-alone software AutomAl 6000, which features a column characterization algorithm based on the symbiosis of a statistical model and the structural principles formulated in a digraph-like framework. The software can semi-autonomously determine the 3D column positions in the image, as well as column species. In turn, AutomAl 6000 can then display, analyse and/or export the structure data. This paper describes the methodology of AutomAl 6000 and applies it on three different HAADF-STEM images, which demonstrate the methodology. The software, as well as other resources, are available at http://automal.org. The source code is also directly available from https://github.com/Haawk666/AutomAl-6000.

PMID:35349939 | DOI:10.1016/j.ultramic.2022.113493

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Nevin Manimala Statistics

Modeling the impact of interventions during an outbreak of HIV infection among people who inject drugs in 2012-2013 in Athens, Greece

Drug Alcohol Depend. 2022 Mar 5;234:109396. doi: 10.1016/j.drugalcdep.2022.109396. Online ahead of print.

ABSTRACT

BACKGROUND: A large HIV outbreak in People Who Inject Drugs (PWID) occurred in Athens, Greece in 2011-2013. In response, opioid substitution treatment (OST) and needle and syringe programs (NSP) were scaled-up and a seek-test-treat program was introduced in mid-2012. We aim to assess the impact of these interventions.

METHODS: A mathematical model of HIV transmission among PWID was calibrated to data available over time (2009-2013) on HIV prevalence, NSP/antiretroviral treatment (ART) coverage and high-risk injection. A combined interventions scenario, including decrease in high-risk injection through linkage to OST and modification of risk behaviours and access to NSP and ART, was compared to a counterfactual scenario (no improvement at the levels of these interventions), with HIV incidence being the main outcome.

RESULTS: HIV incidence increased from <0.1 new cases/100 person-years (in 2099) to 11.0 new cases/100 person-years (in 2012). Under both models, a subsequent decline was projected following early 2012, with incidence at the end of 2013 in the combined interventions scenario being lower by 77% compared to the counterfactual. The projected reduction in incidence under the intervention scenario was in agreement with empirical data. HIV prevalence would have escalated to 20.4% (95% CrI: 16.9%, 23.6%) in 2013 under the counterfactual scenario (vs. 16.8% (95% CrI: 11.2%, 23.0%) under the combined interventions scenario). In total, 31.4% of HIV cases (392) were averted over 2012-2013.

CONCLUSION: These results underline the importance of high-coverage harm reduction programs and of community-based interventions to rapidly reach PWID most in need.

PMID:35349919 | DOI:10.1016/j.drugalcdep.2022.109396

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Nevin Manimala Statistics

Prevalence and associated factors of depressive symptoms among the young adults during the post-epidemic period – Evidence from the first wave of COVID-19 in Hubei Province, China

Acta Psychol (Amst). 2022 Mar 26;226:103577. doi: 10.1016/j.actpsy.2022.103577. Online ahead of print.

ABSTRACT

INTRODUCTION: China emerged from the first wave of COVID-19 in a short period of time and returned to normal economic and living order nationwide, making China’s entry into the post-COVID-19 epidemic period since April 2020. However, the COVID-19 epidemic had a great impact on young adults’ psychological status and may continue into the post-epidemic period. The enormous economic, employment and entrepreneurship pressures of this period may exacerbate this negative impact. This study investigated the depression status of the young adults and put forward the suggestions on how to strengthen the psychological crisis intervention and social security to cultivate the resilience of the young adults after major public health emergencies.

METHODS: This study conducted a questionnaire survey to identify the prevalence of depressive symptoms and explore the associated factors of depressive symptoms among 1069 young adults in X City, Hubei province in September 2020. And the multistage stratified random sampling method was used for sampling. Depressive symptoms were measured using the 10-item version of the Center for Epidemiological Studies Depression Scale (CES-D-10). Descriptive statistics and logistic regression analysis were adopted for statistical analysis.

RESULTS: 1069 respondents (67.68% male; mean age = 28.87 ± 4.18 years; age range = 18-35 years) were included in final analyses. About 25.9% of the respondents reported depressive symptoms (CES-D-10 score = 7.28 ± 3.85). Age, marital status, employment status, monthly disposable income, the cognition, experience and social relationship of the COVID-19 epidemic, and regional discrimination were significantly associated with depressive symptoms. Being male (P = 0.025), age of 25-29 years (P = 0.011), having a household size with 4-5 (P = 0.01) and more than 8 (P = 0.012) family members, a little pessimism about the prospect of COVID-19 epidemic prevention and control (P = 0.044), often (P = 0.018) or always (P = 0.009) participation in anti-epidemic volunteer work were likely to lead to depressive symptoms.

CONCLUSIONS: In the post-COVID-19 epidemic period, the psychological status of young people is generally stable, but some of them are depressed. Life, work and mental stress affect the generation of depressive symptoms among the young adults.

PMID:35349926 | DOI:10.1016/j.actpsy.2022.103577

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Nevin Manimala Statistics

Arsenic in private well water and birth outcomes in the United States

Environ Int. 2022 Mar 26;163:107176. doi: 10.1016/j.envint.2022.107176. Online ahead of print.

ABSTRACT

BACKGROUND: Prenatal exposure to drinking water with arsenic concentrations >50 μg/L is associated with adverse birth outcomes, with inconclusive evidence for concentrations ≤50 μg/L. In a collaborative effort by public health experts, hydrologists, and geologists, we used published machine learning model estimates to characterize arsenic concentrations in private wells-federally unregulated for drinking water contaminants-and evaluated associations with birth outcomes throughout the conterminous U.S.

METHODS: Using several machine learning models, including boosted regression trees (BRT) and random forest classification (RFC), developed from measured groundwater arsenic concentrations of ∼20,000 private wells, we characterized the probability that arsenic concentrations occurred within specific ranges in groundwater. Probabilistic model estimates and private well usage data were linked by county to all live birth certificates from 2016 (n = 3.6 million). We evaluated associations with gestational age and term birth weight using mixed-effects models, adjusted for potential confounders and incorporated random intercepts for spatial clustering.

RESULTS: We generally observed inverse associations with term birth weight. For instance, when using BRT estimates, a 10-percentage point increase in the probability that private well arsenic concentrations exceeded 5 μg/L was associated with a -1.83 g (95% CI: -3.30, -0.38) lower term birth weight after adjusting for covariates. Similarly, a 10-percentage point increase in the probability that private well arsenic concentrations exceeded 10 μg/L was associated with a -2.79 g (95% CI: -4.99, -0.58) lower term birth weight. Associations with gestational age were null.

CONCLUSION: In this largest epidemiologic study of arsenic and birth outcomes to date, we did not observe associations of modeled arsenic estimates in private wells with gestational age and found modest inverse associations with term birth weight. Study limitations may have obscured true associations, including measurement error stemming from a lack of individual-level information on primary water sources, water arsenic concentrations, and water consumption patterns.

PMID:35349912 | DOI:10.1016/j.envint.2022.107176

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Nevin Manimala Statistics

Structural connectivity in children after total corpus callosotomy

Epilepsy Res. 2022 Mar 15;182:106908. doi: 10.1016/j.eplepsyres.2022.106908. Online ahead of print.

ABSTRACT

OBJECTIVES: To investigate structural connectivity after total callosotomy.

METHODS: Deterministic fiber tracking (tractography) of whole brain white matter was performed on 13 epilepsy patients pre- and post-callosotomy. The analysis of structural connectivity was based on graph theory and network-based analysis with a focus on the inter- and intrahemispheric networks. Clinical demographic data including seizure patterns and outcomes were scored for the identification of correlations.

RESULTS: After total callosotomy, structural interhemispheric networks were significantly interrupted. Specific changes were observed in the structural intrahemispheric networks in both hemispheres: 3 edges presented with significant decreases in the left hemisphere, whereas 2 edges presented with significant decreases in the right hemisphere. No global changes were observed in the network density, average weighted strength, average characteristic path length, or global efficiency of intrahemispheric networks. The intrahemispheric hubs and nodal efficiency were minimal changed after callosotomy.

CONCLUSION: While there was a significant decrease in structural interhemispheric connectivity post-callosotomy, we observed synchronously decremented changes of intrahemispheric edges in each hemisphere. This study suggests that white matter maintains the structural connectivity intrahemispherically although functional connectivity recovered after total callosotomy.

PMID:35349891 | DOI:10.1016/j.eplepsyres.2022.106908

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Nevin Manimala Statistics

Multimorbidity patterns and their relationships with incident disability and frailty among older adults in Taiwan: A 16-year, population-based cohort study

Arch Gerontol Geriatr. 2022 Mar 20;101:104688. doi: 10.1016/j.archger.2022.104688. Online ahead of print.

ABSTRACT

BACKGROUND: Multimorbidity has negative impacts on the health outcomes of older adults. Previous research has discovered different patterns of multimorbidity. However, evidence is scarce for associations between multimorbidity patterns and disability/frailty, especially evidence from longitudinal studies. This study aimed to explore the relationship between multimorbidity patterns and disability/frailty among older adults in Taiwan.

METHODS: This population-based cohort study used data from the Taiwan Longitudinal Study on Aging. It included 2,194 older adults (age >50 years) who were followed from 1996 to 2011. The participants’ multimorbidity patterns in 1996 were determined by latent class analysis; their incident disability and frailty were ascertained in 2011. Multivariate logistic regression was used to analyze the relationship between multimorbidity patterns and disability/frailty.

RESULTS: In 1996, the participants’ average age was 62 years. Four multimorbidity patterns were discovered through latent class analysis, as follows: (1) Cardiometabolic group (n = 222), (2) Arthritis-cataract group (n = 112), (3) Multimorbidity group (n = 189), and (4) Relatively healthy group (n = 1671). After adjusting for age, sex, social participation, alcohol consumption, self-rated health, admission in the past year, and depression, participants in the Cardiometabolic group had a greater risk of incident disability (odds ratio: 1.78; 95% confidence interval: 1.26-2.52), compared with the Relatively healthy group. No statistically significant relationships were found between multimorbidity patterns and frailty. Subgroup analysis showed that females in the Cardiometabolic and Multimorbidity groups had greater risks of developing disability.

CONCLUSION: This 16-year, population-based cohort study showed that distinct multimorbidity patterns among older adults in Taiwan were associated with incident disability during later life but were not related to frailty.

PMID:35349876 | DOI:10.1016/j.archger.2022.104688

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Nevin Manimala Statistics

Are we underestimating floating microplastic pollution? A quantitative analysis of two sampling methodologies

Mar Pollut Bull. 2022 Mar 26;178:113592. doi: 10.1016/j.marpolbul.2022.113592. Online ahead of print.

ABSTRACT

Microplastics (MPs) are widespread in the water column of several aquatic ecosystems. Thus, the sampling methodology is considered as a basic factor influencing MPs abundance. In this baseline, a total of 67 investigations were chosen to conduct a quantitative analysis between two sampling methods: Trawl and bulk. The aim is to report a general overview of the MPs abundance and characteristic differences based on the sampling procedures and provide methodological recommendations. MPs abundance reported by bulk studies is 3500 higher than trawl studies. Furthermore, the morphological types and polymers abundances were statistically affected by the type of sampling tool. Conversely, MPs size ranges were significantly different between sampling procedures, suggesting that trawling underestimates the smaller MPs fractions. The analysis confirms that the sampling methods should be selected based on the research objectives. In this sense, it is recommended to combine both types of sampling procedures to obtain comprehensive data.

PMID:35349867 | DOI:10.1016/j.marpolbul.2022.113592

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Nevin Manimala Statistics

Health literacy and quality of life in Iranian persons with COPD

Heart Lung. 2022 Mar 26;54:61-67. doi: 10.1016/j.hrtlng.2022.02.009. Online ahead of print.

ABSTRACT

BACKGROUND: Chronic obstructive pulmonary disease is a progressive disorder with significant physical, psychological, and social consequences and adversely affects the persons’ quality of life (QOL).

OBJECTIVES: This study aimed to determine the health literacy (HL) and QOL of persons with COPD and some of the contributing factors.

METHODS: A cross-sectional study was conducted from May to December 2019 on 270 persons with COPD referring to Shahid-Beheshti Hospital of Kashan, Iran. Data were collected using a demographic questionnaire, the 33-item Health Literacy Questionnaire of the Urban Population of Iran (with a total score ranging from 33 to 165, higher score indicates higher HL) and the 50-item St. George’s Respiratory Questionnaire for assessing the QOL (with a total score ranging from zero to 100, greater score means lower QOL). Descriptive statistics, Pearson and Spearman correlation coefficient, Chi-square test, t-test, analysis of variance, and linear regression analysis were used to analyze the data.

RESULTS: The mean age and the mean duration of COPD were 59.48±13.31 and 3.85±3.47 years, respectively. The mean HL score and the mean QOL were 81.44±23.89 and 57.41±10.70, respectively. A significant correlation was found between HL and QOL (r=-0.21, p<0.001).

CONCLUSION: Participants had moderate levels of HL and QOL. There was a significant correlation between HL and QOL. Health care providers are recommended to take effective steps to improve the HL of persons with COPD by developing comprehensive educational programs for them.

PMID:35349857 | DOI:10.1016/j.hrtlng.2022.02.009

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Nevin Manimala Statistics

DNA methylation of Nuclear Factor of Activated T Cells 1 mediates the prospective relation between exposure to different traumatic event types and post-traumatic stress disorder

Psychiatry Res. 2022 Mar 19;311:114510. doi: 10.1016/j.psychres.2022.114510. Online ahead of print.

ABSTRACT

The mechanisms through which exposure to differing trauma types become biologically embedded to shape the risk for post-traumatic stress disorder (PTSD) is unclear. DNA methylation (5-mC), particularly in stress-relevant genes, may play a role in this relationship. Here, we conducted path analysis using generalized structural equation modeling to investigate whether blood-derived 5-mC in Nuclear Factor of Activated T Cells 1 (NFATC1) mediates the prospective association between each of five different trauma types (“assaultive violence”, “other injury or shocking experience”, “learning of trauma to loved one”, “sudden, unexpected death of a close friend or relative”, and “other”) and lifetime PTSD. All five trauma types were significantly associated with reduced methylation at NFATC1 CpG site, cg17057218. Two of the five trauma types were significantly associated with increased methylation at NFATC1 CpG site, cg22324981. Moreover, methylation at cg17057218 significantly mediated 21-32% of the total effect for four of the five trauma types, while methylation at cg22324981 mediated 27-40% of the total effect for two of the five trauma types. These CpG sites were differentially associated with transcription factor binding sites and chromatin state signatures. NFATC1 5-mC may be a potential mechanism in the relationship between some trauma types and prospective risk for PTSD.

PMID:35349860 | DOI:10.1016/j.psychres.2022.114510

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Nevin Manimala Statistics

Polar transform network for prostate ultrasound segmentation with uncertainty estimation

Med Image Anal. 2022 Mar 17;78:102418. doi: 10.1016/j.media.2022.102418. Online ahead of print.

ABSTRACT

Automatic and accurate prostate ultrasound segmentation is a long-standing and challenging problem due to the severe noise and ambiguous/missing prostate boundaries. In this work, we propose a novel polar transform network (PTN) to handle this problem from a fundamentally new perspective, where the prostate is represented and segmented in the polar coordinate space rather than the original image grid space. This new representation gives a prostate volume, especially the most challenging apex and base sub-areas, much denser samples than the background and thus facilitate the learning of discriminative features for accurate prostate segmentation. Moreover, in the polar representation, the prostate surface can be efficiently parameterized using a 2D surface radius map with respect to a centroid coordinate, which allows the proposed PTN to obtain superior accuracy compared with its counterparts using convolutional neural networks while having significantly fewer (18%∼41%) trainable parameters. We also equip our PTN with a novel strategy of centroid perturbed test-time augmentation (CPTTA), which is designed to further improve the segmentation accuracy and quantitatively assess the model uncertainty at the same time. The uncertainty estimation function provides valuable feedback to clinicians when manual modifications or approvals are required for the segmentation, substantially improving the clinical significance of our work. We conduct a three-fold cross validation on a clinical dataset consisting of 315 transrectal ultrasound (TRUS) images to comprehensively evaluate the performance of the proposed method. The experimental results show that our proposed PTN with CPTTA outperforms the state-of-the-art methods with statistical significance on most of the metrics while exhibiting a much smaller model size. Source code of the proposed PTN is released at https://github.com/DIAL-RPI/PTN.

PMID:35349838 | DOI:10.1016/j.media.2022.102418