Miracle-dz/UniFAR-FTUs huggingface dataset:
Methodological approach to create an atlas using a commercial auto‐contouring software

Abstract Purpose The aim of this work was to establish a methodological approach for creation and optimization of an atlas for auto‐contouring, using the commercial software MIM MAESTRO (MIM Software Inc. Cleveland OH). Methods A computed tomography (CT) male pelvis atlas was created and optimized to evaluate how different tools and options impact on the accuracy of automatic segmentation. Pelvic lymph nodes (PLN), rectum, bladder, and femurs of 55 subjects were reviewed for consistency by a senior consultant radiation oncologist with 15 yr of experience. Several atlas and workflow options were tuned to optimize the accuracy of auto‐contours. The deformable image registration (DIR), the finalization method, the k number of atlas best matching subjects, and several post‐processing options were studied. To test our atlas performances, automatic and reference manual contours of 20 test subjects were statistically compared based on dice similarity coefficient (DSC) and mean distance to agreement (MDA) indices. The effect of field of view (FOV) reduction on auto‐contouring time was also investigated. Results With the optimized atlas and workflow, DSC and MDA median values of bladder, rectum, PLN, and femurs were 0.91 and 1.6 mm, 0.85 and 1.6 mm, 0.85 and 1.8 mm, and 0.96 and 0.5 mm, respectively. Auto‐contouring time was more than halved by strictly cropping the FOV of the subject to be contoured to the pelvic region. Conclusion A statistically significant improvement of auto‐contours accuracy was obtained using our atlas and optimized workflow instead of the MIM Software pelvic atlas.
Immunogenetic Association Underlying Severe COVID-19

SARS-CoV2 has caused the current pandemic of new coronavirus disease 2019 (COVID-19) worldwide. Clinical outcomes of COVID-19 illness range broadly from asymptotic and mild to a life-threatening situation. This casts uncertainties for defining host determinants underlying the disease severity. Recent genetic analyses based on extensive clinical sample cohorts using genome-wide association studies (GWAS) and high throughput sequencing curation revealed genetic errors and gene loci associated with about 20% of life-threatening COVID-19 cases. Significantly, most of these critical genetic loci are enriched in two immune signaling pathways, i.e., interferon-mediated antiviral signaling and chemokine-mediated/inflammatory signaling. In line with these genetic profiling studies, the broad spectrum of COVID-19 illness could be explained by immuno-pathological regulation of these critical immunogenetic pathways through various epigenetic mechanisms, which further interconnect to other vital components such as those in the renin–angiotensin–aldosterone system (RAAS) because of its direct interaction with the virus causing COVID-19. Together, key genes unraveled by genetic profiling may provide targets for precisely early risk diagnosis and prophylactic design to relieve severe COVID-19. The confounding epigenetic mechanisms may be key to understanding the clinical broadness of COVID-19 illness.
HRN: A Holistic Approach to One Class Learning

Existing neural network based one-class learning methods mainly use various forms of auto-encoders or GAN style adversarial training to learn a latent representation of the given one class of data. This paper proposes an entirely different approach based on a novel regularization, called holistic regularization (or H-regularization ), which enables the system to consider the data holistically, not to produce a model that biases towards some features. Combined with a proposed 2-norm instance-level data normalization , we obtain an effective one-class learning method, called HRN. To our knowledge, the proposed regularization and the normalization method have not been reported before. Experimental evaluation using both benchmark image classiﬁcation and traditional anomaly detection datasets show that HRN markedly outperforms the state-of-the-art existing deep/non-deep learning models. The code of HRN can be found here 3 .
What Factors Are Associated With Recent Changes in Men’s Attitudes Towards Intimate Partner Violence Across Regional, Rural, and Urban Spaces of Ghana? Findings From Three Waves of Ghana National Surveys From 2003 to 2014

Numerous studies have shown that men’s attitudes towards intimate partner violence (IPV) remain a strong predictor of its actual perpetration. Very few trend studies available have also reported that IPV-acceptance is gradually declining globally. However, almost none of these trend studies have included men in their samples, nor have investigated factors associated with changes in men’s attitudes towards IPV. To supplement this sparse knowledge, the current study employed three waves of the Ghana Demographic and Health Survey (GDHS): 2003 (n=4,901), 2008 (n = 4,481), and 2014 (n = 4,333) data, and reports trends and patterns in men’s attitudes towards wife-beating at national, regional, and rural-urban residences of Ghana. Multivariable logistic regression models were fitted to further examine the key socioeconomic and cultural factors significantly associated with men’s acceptance of IPV at 95% confidence interval. The results show that men’s acceptance of wife-beating declined largely at the national level by 60.8% between 2003 and 2014: from 31.7% in 2003 to 12.4% in 2014. However, when disaggregated by region, data revealed a slight increase in men’s IPV-acceptance in two regions between 2008 and 2014—the Western and Upper East regions, by 2.1% and 3.8%, respectively. Having less than secondary education, being in a polygynous union, and residence in certain regions, was significantly associated with justification of wife-beating. Whereas having access to media was not consistently significant in influencing men’s attitudes against wife-beating, especially in the rural areas. The decreasing significance of education, household wealth, and religion in the 2014 wave (especially in urban areas) seem to suggest that recent decline in men’s acceptance of wife-beating may not have been driven by a single isolated factor, but by complex interactions of several exogenous factors including those not captured in the current data. Study implications and need for further studies are discussed.
A Blended Cognitive–Behavioral Intervention for the Treatment of Postpartum Depression: Study Protocol for a Randomized Controlled Trial

Despite the existence of effective treatment for postpartum depression, few women seek professional help, indicating the need for a new and innovative format of treatment that can overcome help-seeking barriers. This article presents the study protocol for a blended cognitive–behavioral intervention for the treatment of postpartum depression, by integrating face-to-face sessions with a web-based program (Be a Mom) into one treatment protocol. This study will be a two-arm, noninferiority randomized controlled trial comparing blended intervention to usual treatment for postpartum depression provided in healthcare centers. Portuguese postpartum adult women diagnosed with postpartum depression (according to the DSM-5 diagnostic criteria for major depressive disorder) will be recruited during routine care appointments in local healthcare centers and will be eligible to participate. Measures will be completed at baseline, postintervention, and at three- and six-month follow-ups. The primary outcome will be depressive symptoms. Secondary outcomes will include anxiety symptoms, fatigue, quality of life, marital satisfaction, maternal self-efficacy, and mother–child bonding. Cost-effectiveness analysis and mediator and moderator analysis will be conducted. This study will provide insight into the efficacy and cost-effectiveness of a blended psychological intervention in the Portuguese context and increase the empirically validated treatment options for postpartum depression.
Drug therapy problems and health related quality of life among patients with colorectal cancer in a Kenyan tertiary health facility

Background Colorectal cancer is the third most common form of cancer in males and the second in females globally. The ill-health due to cancer and use of multiple therapies may result in drug related problems and also affect the health-related quality of life of the patients. Objective To characterize drug therapy problems and health-related quality of life among patients with colorectal cancer at Kenyatta National Hospital. Methodology: A descriptive prospective cross-sectional study design was used and simple random sampling utilized to select seventy- one participants. The participants were interviewed and their responses captured using World Health Organisation Quality of Life-BREF and a structured questionnaire. The data were analysed using STATA version 15.0. Data was summarized using descriptive statistic such as mean, range and standard deviation. Association between variables was determined using linear regression model at 0.05% level of significance. Ethical approval was granted by the relevant authorities to conduct the study. Results Patients were predominantly females (52.1%), had a mean age of 55.9± 14.4 years. The main drug therapy problems were adverse drug reactions (45.1%). Approximately two thirds (67.6%) of the participants complained of gastrointestinal problems followed by cardiovascular diseases (29.6%). Quality of life assessment indicated that psychological health had the highest score at 60.5%. On linear regression analysis, the presence of anemia (p = 0.021), coverage (p = 0.038), and cardiovascular problems (p = 0.034) were significantly associated with the overall health-related quality of life. Conclusion The health-related quality of life was is dependent on several patient related factors. Interventions regarding prevention of drug therapy problems should be considered alongside other measures used to manage colorectal cancer.
Clinical challenges in cancer patients with COVID-19: Aging, immunosuppression, and comorbidities

COVID-19 caused by severe acute respiratory syndrome coronavirus 2 has developed into a global pandemic. COVID-19 poses a huge threat to health care, and the shortage of medical resources caused by COVID-19 brought serious secondary disasters to elderly cancer patients who are particularly dependent on medical resources. The clinical challenges of cancer management, including aging, immunosuppression, and comorbidities, make cancer patients more vulnerable to COVID-19 with different clinical manifestations, disease severity, and outcomes. The review comprehensively analyzed the characteristics of the cancer patients under the pandemic and concluded that cancer patients were more susceptible to COVID-19, and also concluded that they were more likely to develop poor outcomes and the severe form of the disease. Three basic management strategies have been proposed to protect susceptible elderly cancer patients, find reliable indicators to monitor the course of disease, and implement effective prevention measures.
The Burden of Potentially Inappropriate Medications in Chronic Polypharmacy

We aimed to describe the burden represented by potentially inappropriate medications (PIMs) in chronic polypharmacy in France. We conducted a nationwide cross-sectional study using data from the French National Insurance databases. The study period was from 1 January 2016 to 31 December 2016. Chronic drug use was defined as uninterrupted daily use lasting ≥6 months. Chronic polypharmacy was defined as the chronic use of ≥5 medications, and chronic hyperpolypharmacy as the chronic use of ≥10 medications. For individuals aged ≥65 (older adults), PIMs were defined according to the Beers and Laroche lists, and for individuals aged 45–64 years (middle-aged) PIMs were defined according to the PROMPT (Prescribing Optimally in Middle-aged People’s Treatments) list. Among individuals with chronic polypharmacy, 4009 (46.2%) middle-aged and 18,036 (64.8%) older adults had at least one chronic PIM. Among individuals with chronic hyperpolypharmacy, these figures were, respectively, 570 (75.0%) and 2544 (88.7%). The most frequent chronic PIM were proton pump inhibitors (43.4% of older adults with chronic polypharmacy), short-acting benzodiazepines (older adults: 13.7%; middle-aged: 16.1%), hypnotics (6.1%; 7.4%), and long-acting sulfonylureas (3.9%; 12.3%). The burden of chronic PIM appeared to be very high in our study, concerning almost half of middle-aged adults and two-thirds of older adults with chronic polypharmacy. Deprescribing interventions in polypharmacy should primarily target proton pump inhibitors and hypnotics.
Analysing Better Work Data from a Gender Perspective: A Preliminary Exploration of Worker Surveys with a Focus on Vietnam

The literature on the feminisation of the labour force associated with labour-intensive manufacturing exports is characterised by lively discussions and differing viewpoints on its implications for women’s empowerment. This paper contributes to the debate by presenting insights from an exploration of the Better Work baseline worker survey for Vietnam. Confirming patterns found in many other parts of the world, the analysis shows marked differences between male workers and female workers at the time that the garment factories joined the Better Work programme. Occupational segmentation by gender is pronounced. Women workers are less likely to be promoted and to receive training than men workers. And most of them report having less free time than male workers. An interesting finding is that differences between female workers with varying levels of education are also significant, in particular with regard to awareness and voice. The paper concludes by reflecting on implications for Better Work and suggesting areas for further research.
Association of Val158Met polymorphism in COMT gene with attention-deficit hyperactive disorder

Abstract Background: The results of published articles on the relationship between the Val158Met polymorphism in the (Catechol-O-methyltransferase) COMT gene and the susceptibility of attention-deficit hyperactive disorder (ADHD) are controversial. We conducted an updated meta-analysis of case-control studies to assess the relationship between Val158Met polymorphism in COMT gene and ADHD susceptibility. Methods: A comprehensive literature search was conducted to identify all the case-control studies on the relationship between the COMT gene Val158Met polymorphism and ADHD susceptibility. According to the heterogeneity test results among studies evaluated with I2, the fixed effect model or random effect model was selected as the pooling method. Meta-regression as well as sensitive analysis were used to explore possible causes of between-study heterogeneity. The funnel plot and Harbord test were used to estimate publication bias. Results: Finally, seventeen studies that met the inclusion criteria were included. The Val158Met genotype distributions of COMT gene in controls were in Hardy–Weinberg equilibrium in all studies. In general, there was no significant association between the COMT gene Val158Met polymorphism and ADHD susceptibility in dominant, recessive, and codominant models. The recessive genetic model (I2 = 60.8%) showed strong heterogeneity among studies, and still no significant association was found after sensitivity analysis. Subgroup analysis stratified by ethnicity (Asian and Caucasian) also showed that there was no significant association in the above-mentioned three models. Conclusions: This updated meta-analysis indicated that the Val158Met polymorphism in the COMT gene may not be related to the risk of ADHD. Further researches are needed to confirm these results.
Regional and global contributions of air pollution to risk of death from COVID-19

Abstract Aims The risk of mortality from the coronavirus disease that emerged in 2019 (COVID-19) is increased by comorbidity from cardiovascular and pulmonary diseases. Air pollution also causes excess mortality from these conditions. Analysis of the first severe acute respiratory syndrome coronavirus (SARS-CoV-1) outcomes in 2003, and preliminary investigations of those for SARS-CoV-2 since 2019, provide evidence that the incidence and severity are related to ambient air pollution. We estimated the fraction of COVID-19 mortality that is attributable to the long-term exposure to ambient fine particulate air pollution. Methods and results We characterized global exposure to fine particulates based on satellite data, and calculated the anthropogenic fraction with an atmospheric chemistry model. The degree to which air pollution influences COVID-19 mortality was derived from epidemiological data in the USA and China. We estimate that particulate air pollution contributed ∼15% (95% confidence interval 7–33%) to COVID-19 mortality worldwide, 27% (13 – 46%) in East Asia, 19% (8–41%) in Europe, and 17% (6–39%) in North America. Globally, ∼50–60% of the attributable, anthropogenic fraction is related to fossil fuel use, up to 70–80% in Europe, West Asia, and North America. Conclusion Our results suggest that air pollution is an important cofactor increasing the risk of mortality from COVID-19. This provides extra motivation for combining ambitious policies to reduce air pollution with measures to control the transmission of COVID-19.
Effects of combined calcium and vitamin D supplementation on osteoporosis in postmenopausal women: a systematic review and meta-analysis of randomized controlled trials.

OBJECTIVE The aim of the present study was to explore whether combined calcium and vitamin D supplementation is beneficial for osteoporosis in postmenopausal women. METHODS We searched the PubMed, Cochrane library, Web of science and Embase databases and reference lists of eligible articles up to Feb, 2020. Randomized controlled trials (RCTs) evaluating the effect of combined calcium and vitamin D on osteoporosis in postmenopausal women were included in the present study. RESULTS Combined calcium and vitamin D significantly increased total bone mineral density (BMD) (standard mean differences (SMD) = 0.537; 95% confidence interval (CI): 0.227 to 0.847), lumbar spine BMD (SMD = 0.233; 95% CI: 0.073 to 0.392; P < 0.001), arms BMD (SMD = 0.464; 95% CI: 0.186 to 0.741) and femoral neck BMD (SMD = 0.187; 95% CI: 0.010 to 0.364). It also significantly reduced the incidence of hip fracture (RR = 0.864; 95% CI: 0.763 to 0.979). Subgroup analysis showed that combined calcium and vitamin D significantly increased femoral neck BMD only when the dose of the vitamin D intake was no more than 400 IU d-1 (SMD = 0.335; 95% CI: 0.113 to 0.558), but not for a dose more than 400 IU d-1 (SMD = -0.098; 95% CI: -0.109 to 0.305), and calcium had no effect on the femoral neck BMD. Subgroup analysis also showed only dairy products fortified with calcium and vitamin D had a significant influence on total BMD (SMD = 0.784; 95% CI: 0.322 to 1.247) and lumbar spine BMD (SMD = 0.320; 95% CI: 0.146 to 0.494), but not for combined calcium and vitamin D supplement. CONCLUSION Dairy products fortified with calcium and vitamin D have a favorable effect on bone mineral density. Combined calcium and vitamin D supplementation could prevent osteoporosis hip fracture in postmenopausal women.
Need for hepatitis A prevention in patients with chronic liver disease in the changing epidemiological setting of India

ABSTRACT The burden of chronic liver disease (CLD) in India is high, particularly among middle-aged men, with nearly 220,000 deaths due to cirrhosis in 2017. CLD increases the risk of infection, severe disease (e.g. hepatitis A virus or HAV superinfection, acute-on-chronic liver failure, fulminant hepatic failure), and mortality. Hence, various countries recommend HAV vaccination for CLD patients. While historic Indian studies showed high seroprevalences of protective HAV antibodies among Indian adults with CLD, the most recent ones found that nearly 7% of CLD patients were susceptible to HAV infection. Studies in healthy individuals have shown that HAV infection in childhood is decreasing in India, resulting in an increasing population of adults susceptible to HAV infection. As patients with CLD are at increased risk of severe HAV infection, now may be the time to recommend HAV vaccination among people with CLD in India. PLAIN LANGUAGE SUMMARY What is the context? Patients with chronic liver diseases have progressive liver deterioration. Hepatitis A virus infection, while generally mild in childhood, can cause acute liver deterioration in adulthood, and be particularly severe in patients with chronic liver diseases. We conducted a review of the scientific literature on the status of hepatitis A virus infection and chronic liver diseases in India, including the associated health impacts of liver failure and mortality. What is new? We found that chronic liver diseases are common, mostly affecting middle-aged men as a result of hepatitis viruses, alcohol, and non-alcoholic fatty liver disease. Also, the number of children naturally infected by hepatitis A virus is decreasing due to improved sanitation; The population reaching adulthood with acquired immunity is therefore decreasing. This is likely also the case for patients with chronic liver diseases, putting them at risk of severe disease What is the impact? Evidence presented in this review supports the potential benefit of vaccination of individuals with chronic liver diseases. A potential next step is to recommend hepatitis A virus vaccination for chronic liver disease patients in India, particularly for those without protective antibodies. This could reduce morbidity, mortality, and healthcare costs of hepatitis A virus infection among chronic liver disease patients.
Protection of Galacto-Oligosaccharide against E. coli O157 Colonization through Enhancing Gut Barrier Function and Modulating Gut Microbiota

Galacto-oligosaccharide (GOS) has been added to infant formula as prebiotics and can bring many benefits to human health. This study proved the effect of GOS in prevention and alleviation against E. coli O157 invasion and colonization and the mechanism behind this was explored in a mice model. The results showed that the expression of Muc2 and Occlaudin were both significantly down-regulated (p < 0.05) by E. coli O157 infection, while GOS alleviated this phenomenon, which means that GOS can reduce the colonization of E. coli O157 by enhancing the gut barrier function. Through the determination of inflammatory cytokines, we found that GOS can relieve inflammation caused by pathogens. At the same time, GOS can promote the growth of probiotics such as Akkermansia, Ruminococcaceae and Bacteroides, thus modulating microorganism environments and improving short chain fatty acid (SCFA) levels in the intestine. This study provides an explanation for the mechanism behind the protection of GOS against pathogen infection.