Miracle-dz/UniFAR-FTUs huggingface dataset:
Using X-ray images and deep learning for automated detection of coronavirus disease

Abstract Coronavirus is still the leading cause of death worldwide. There are a set number of COVID-19 test units accessible in emergency clinics because of the expanding cases daily. Therefore, it is important to implement an automatic detection and classification system as a speedy elective finding choice to forestall COVID-19 spreading among individuals. Medical images analysis is one of the most promising research areas, it provides facilities for diagnosis and making decisions of a number of diseases such as Coronavirus. This paper conducts a comparative study of the use of the recent deep learning models (VGG16, VGG19, DenseNet201, Inception_ResNet_V2, Inception_V3, Resnet50, and MobileNet_V2) to deal with detection and classification of coronavirus pneumonia. The experiments were conducted using chest X-ray & CT dataset of 6087 images (2780 images of bacterial pneumonia, 1493 of coronavirus, 231 of Covid19, and 1583 normal) and confusion matrices are used to evaluate model performances. Results found out that the use of inception_Resnet_V2 and Densnet201 provide better results compared to other models used in this work (92.18% accuracy for Inception-ResNetV2 and 88.09% accuracy for Densnet201). Communicated by Ramaswamy H. Sarma
Evaluation, Validation, and Recognition of the Point-of-Care Circulating Cathodic Antigen, Urine-Based Assay for Mapping Schistosoma mansoni Infections

Abstract. Efforts to control Schistosoma mansoni infection depend on the ability of programs to effectively detect and quantify infection levels and adjust programmatic approaches based on these levels and program goals. One of the three major objectives of the Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) has been to develop and/or evaluate tools that would assist Neglected Tropical Disease program managers in accomplishing this fundamental task. The advent of a widely available point-of-care (POC) assay to detect schistosome circulating cathodic antigen (CCA) in urine with a rapid diagnostic test (the POC-CCA) in 2008 led SCORE and others to conduct multiple evaluations of this assay, comparing it with the Kato–Katz (KK) stool microscopy assay—the standard used for more than 45 years. This article describes multiple SCORE-funded studies comparing the POC-CCA and KK assays, the pros and cons of these assays, the use of the POC-CCA assay for mapping of S. mansoni infections in areas across the spectrum of prevalence levels, and the validation and recognition that the POC-CCA, although not infallible, is a highly useful tool to detect low-intensity infections in low-to-moderate prevalence areas. Such an assay is critical, as control programs succeed in driving down prevalence and intensity and seek to either maintain control or move to elimination of transmission of S. mansoni.
Googling Allergy in Ireland: Content Analysis

Background Internet search engines are increasingly being utilized as the first port of call for medical information by the public. The prevalence of allergies in developed countries has risen steadily over time. There exists significant variability in the quality of health-related information available on the web. Inaccurately diagnosed and mismanaged allergic disease has major downstream effects on patients, general practitioners, and regional allergy services. Objective This study aimed to verify whether Ireland has a relatively high rate of web-based allergy-related searches, to establish the proportion of medically accurate web pages encountered by the public, and to compare current search results localized to Dublin, Ireland with urban centers elsewhere. Methods Google Trends was used to evaluate regional interest of allergy-related search terms over a 10-year period using terms “allergy,” “allergy test,” “food allergy,” and “food intolerance. ” These terms were then inputted into Google search, localizing them to cities in Ireland, the United Kingdom, and the United States. Output for each search was reviewed by two independent clinicians and deemed rational or nonevidence based, as per current best practice guidelines. Searches localized to Dublin were initially completed in 2015 and repeated in 2019 to assess for changes in the quality of search results over time. Results Ireland has a persistently high demand for web-based information relating to allergy and ranks first worldwide for “allergy test,” second for “food allergy” and “food intolerance,” and seventh for “allergy” over the specified 10-year timeframe. Results for each of the four subsearches in Dublin (2015) showed that over 60% of websites promoted nonevidence-based diagnostics. A marginal improvement in scientifically robust information was seen in 2019, but results for “allergy test” and “food intolerance” continued to promote alternative testing 57% (8/14) of the time. This strongly contrasted with results localized to Southampton and Rochester, where academic and hospital-affiliated web pages predominantly featured. Government-funded Department of Health websites did not feature in the top five results for Dublin searches “allergy testing,” “food allergy,” or “food intolerance” in either 2015 or 2019. Conclusions The Irish public demonstrates a keen interest in seeking allergy-related information on the web. The proportion of evidence-based websites encountered by the Irish public is considerably lower than that encountered by patients in other urban centers. Factors contributing to this are the lack of a specialist register for allergy in Ireland, inadequate funding for allergy centers currently in operation, and insufficient promotion by the health service of their web-based health database, which contains useful patient-oriented information on allergy. Increased funding of clinical allergology services will more meaningfully impact the health of patients if there is a parallel investment by the health service in information and communication technology consultancy to amplify their presence on the web.
FOODLIT-PRO: conceptual and empirical development of the food literacy wheel

Abstract Pursuing food systems’ sustainability is crucial. Given the risk constituted by unhealthy diets, scarce research on food-related adjacent fields, and inconsistency across food literacy conceptualizations, this study aims to explore the constructs’ definition and develop a conceptual and empirical framework of food literacy. A quantitative approach was taken on previously obtained qualitative outcomes from 30 interviews with experts from food-related fields. Food literacy was defined by a four-dimension model: Cooking Skills, Preserve and Analyse, Choice and Acquisition, Search and Plan. The framework Food Literacy Wheel integrates the construct definition, food literacy determinants (Internal, External) and influential factors (Nutritional, Psychological, Health, Learning Contexts, Policy, Industry, Sustainability, Social and Cultural). Allowing a broader perspective of food literacy within major food systems, this study contributes with new insights for future instruments and interventions, paving the way to develop/implement food literacy-related multi-sectorial and multilevel actions.
Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning

Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pHkcl, total nitrogen (TN), nitrate-nitrogen (NO3−), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH4+) and available phosphorus (AP) residues in the cultivated soil, among which NH4+ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO3−, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture.
Assessing the Impact of Telemonitoring-Facilitated Lifestyle Modifications on Diabetes Outcomes: A Systematic Review and Meta-Analysis.

Introduction: Lifestyle modification to promote regular physical activity and healthy eating is a key element of diabetes management. We aimed at evaluating randomized controlled trials that assess the impact of telemonitoring on diabetes outcomes with the inclusion of lifestyle change components. Methods: A systematic review search in relevant databases was conducted for studies published from January 2000 to October 2018. The search was restricted to studies published in English and included adult patients with type 2 diabetes. Study selection criteria included telehealth programs with remote monitoring of physiological data and feedback features. We further performed meta-analyses to summarize the pooled effect size (presented by the mean difference [MD]) of hemoglobin A1c (HbA1c) and weight loss outcomes. Results: Seventeen studies were included in the data synthesis (15 of them were included in the meta-analysis), with the sample size ranging from 18 to 484 and the study period ranging from 3 to 12 months. Telemonitoring achieved a significant but modest reduction in HbA1c (MD = -0.30%; 95% confidence interval [CI]: -0.31% to -0.29%) and weight loss (kg) outcomes (MD = -0.62; 95% CI: -0.78 to -0.45) compared with usual care. In the subgroup analyses, it was suggested that telemonitoring with automatic mobile transmission or with real-time feedback modality led to a greater improvement in HbA1c outcomes (MD = -0.61% and -0.77%, respectively) when compared with telemonitoring without these features. Conclusions: Telemonitoring has a great potential to further enhance diabetes management with the inclusion of a system approach for supporting patients' lifestyle changes. Features such as automatic mobile transmission and real-time feedback show promise to boost effectiveness of telemonitoring in diabetes management in the future.
The 5‐HTTLPR long allele predicts two‐year longitudinal increases in cortisol and declines in verbal memory in older adults

The short form or s‐allele variant of the serotonin transporter polymorphism (5‐HTTLPR), as compared with the long‐form or l‐allele variant, has been associated with the presence of cognitive dysfunction, and particularly memory impairment in older adults. This body of cross‐sectional work has culminated in the hypothesis that presence of the s‐allele predicts greater memory decline in older adults. Yet, to date, there are no longitudinal studies that have investigated this issue.
Considering Genomic Scans for Selection as Coalescent Model Choice

Abstract First inspired by the seminal work of Lewontin and Krakauer (1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74(1):175–195. ) and Maynard Smith and Haigh (1974. The hitch-hiking effect of a favourable gene. Genet Res. 23(1):23–35. ), genomic scans for positive selection remain a widely utilized tool in modern population genomic analysis. Yet, the relative frequency and genomic impact of selective sweeps have remained a contentious point in the field for decades, largely owing to an inability to accurately identify their presence and quantify their effects—with current methodologies generally being characterized by low true-positive rates and/or high false-positive rates under many realistic demographic models. Most of these approaches are based on Wright–Fisher assumptions and the Kingman coalescent and generally rely on detecting outlier regions which do not conform to these neutral expectations. However, previous theoretical results have demonstrated that selective sweeps are well characterized by an alternative class of model known as the multiple-merger coalescent. Taken together, this suggests the possibility of not simply identifying regions which reject the Kingman, but rather explicitly testing the relative fit of a genomic window to the multiple-merger coalescent. We describe the advantages of such an approach, which owe to the branching structure differentiating selective and neutral models, and demonstrate improved power under certain demographic scenarios relative to a commonly used approach. However, regions of the demographic parameter space continue to exist in which neither this approach nor existing methodologies have sufficient power to detect selective sweeps.
Modeling the Impact of Cardiopulmonary Irradiation on Overall Survival in NRG Oncology Trial RTOG 0617

Purpose: To quantitatively predict the impact of cardiopulmonary dose on overall survival (OS) after radiotherapy for locally advanced non–small cell lung cancer. Experimental Design: We used the NRG Oncology/RTOG 0617 dataset. The model building procedure was preregistered on a public website. Patients were split between a training and a set-aside validation subset (N = 306/131). The 191 candidate variables covered disease, patient, treatment, and dose-volume characteristics from multiple cardiopulmonary substructures (atria, lung, pericardium, and ventricles), including the minimum dose to the hottest x% volume (Dx%[Gy]), mean dose of the hottest x% (MOHx%[Gy]), and minimum, mean (Mean[Gy]), and maximum dose. The model building was based on Cox regression and given 191 candidate variables; a Bonferroni-corrected P value threshold of 0.0003 was used to identify predictors. To reduce overreliance on the most highly correlated variables, stepwise multivariable analysis (MVA) was repeated on 1000 bootstrapped replicates. Multivariate sets selected in ≥10% of replicates were fit to the training subset and then averaged to generate a final model. In the validation subset, discrimination was assessed using Harrell c-index, and calibration was tested using risk group stratification. Results: Four MVA models were identified on bootstrap. The averaged model included atria D45%[Gy], lung Mean[Gy], pericardium MOH55%[Gy], and ventricles MOH5%[Gy]. This model had excellent performance predicting OS in the validation subset (c = 0.89). Conclusions: The risk of death due to cardiopulmonary irradiation was accurately modeled, as demonstrated by predictions on the validation subset, and provides guidance on the delivery of safe thoracic radiotherapy.
Biosynthesis of Bonelike Apatite 2D Nanoplate Structures Using Fenugreek Seed Extract

An innovative, biomimetic, green synthesis approach was exploited for the synthesis of humane and environmental friendly nanomaterials for biomedical applications. Ultrafine bonelike apatite (BAp) 2D plate-like structures were prepared using fenugreek seed extract during the biosynthesis wet-chemical precipitation route. The chemical analysis, morphology and structure of the prepared 2D nanoplates were characterized by inductively coupled plasma atomic emission spectroscopy (ICP-OES), electron microscopy (SEM and TEM), X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy. A 2D plate-like nanostructure of BAp with an average width (length) of 12.67 ± 2 nm and thickness of 3.8 ± 1.2 nm was obtained. BAp 2D crystals were tuned by interaction with the fenugreek organic molecules during the fabrication process. In addition to Ca and P ions, bone mineral sources such as K, Mg, Na, SO4 and CO3 ions were incorporated into BAp nanoplates using fenugreek seed extract. The overall organic molecule concentration in the reaction process increased the effectiveness of hydroxyl groups as nucleation sites for BAp crystals. Accordingly, the size of the biosynthesized BAp plate-like structure was reduced to its lowest value. Biosynthesis BAp 2D plate-like nanocrystals showed good viability and higher growth of MC3T3 osteoblast-like structures than that of the control sample. BAp 2D nanoplates prepared by a facile, ecofriendly and cost-effective approach could be considered a favorable osteoconductive inorganic biomaterial for bone regeneration applications.
Effects of habitat mosaic on home range size of the Japanese squirrel, Sciurus lis

The Japanese squirrel, Sciurus lis Temminck, is distributed on the Honshu, Shikoku, and Kyushu islands of Japan, although local extinction of this species has recently occurred in the southwestern part of Japan. To assess the impacts of environmental change on habitat availability for the Japanese squirrel, I studied spatial responses to habitat fragmentation. Suitable habitats were defined in accordance with previous work showing that the squirrels selectively use natural or secondary forests. Studies were conducted in a natural forest on Mt. Takao, western Tokyo, and in a neighboring forest fragmented by plantation development. Home range size, mean daily range size and mean daily movement distance were estimated by radio-tracking 16 female and 17 male squirrels. Home range size in both sexes and the daily range size in females increased as the percentage of suitable habitat declined. Japanese squirrels survived by expanding home ranges, even in fragmented forests including unsuitable vegetation types, as far as habitat mosaic was small.
Such stuff as dreams are made on: John Bowlby and the interpretation of dreams

ABSTRACT In this paper, newly uncovered archival material from the Bowlby archives is presented on Bowlby’s own dreams and dream interpretation. Although he was critical of orthodox psychoanalysis, Bowlby appears to have been seriously involved in Freudian dream interpretation in the 1930s and 1940s. Here, we present in annotated form his own interpretations of several of his dreams from that time and a series of lectures on dreams. In Attachment and Loss, classic dream interpretation is absent and Bowlby used the content of dreams as a reflection of the influence of real-life experiences on the representations of attachment relations, with a clear focus on grief, loss, and mourning. Bowlby’s shift from psychoanalysis to a more behavioral approach and the introduction of the concept of “defensive exclusion” to supplant Freud’s concept of “repression” may have led him to think about how grief and mourning may affect the content of our dreams.
Relationships Between Personal Satisfaction, Cardiovascular Disease Risk, and Health Promoting Behavior Among Arab American Middle-Aged Women.

BACKGROUND Cardiovascular disease (CVD) is the leading cause of death among middle-aged women. Health-promoting behavior is essential to the prevention of CVD. During middle adulthood, women experience biopsychosocial changes that may reduce personal satisfaction and affect health-promoting behavior and CVD risk. OBJECTIVE This study aimed to examine the impact of personal satisfaction on health-promoting behavior and CVD risk in middle-aged Arab American women. METHODS A convenience sample of 114 middle-aged Arab American women was recruited from 2 clinical sites in Michigan in the United States. Participants completed a demographic questionnaire, the Health-Promoting Lifestyle Profile-II, the Multidimensional Scale of Perceived Social Support, the Satisfaction With Life Scale, the Rosenberg Self-esteem Scale, and a single item assessing health satisfaction. Risk for CVD was calculated using the 10-year atherosclerotic CVD Risk Estimator. RESULTS Health-promoting behavior was significantly correlated with self-satisfaction (r = 0.54, P < .0001), health satisfaction (r = 0.45, P < .0001), and life satisfaction (r = 0.41, P < .0001). Risk for CVD was significantly negatively correlated with self-satisfaction (r = -0.17, P = .039), health satisfaction (r = -0.18, P = .029), and life satisfaction (r = -0.27, P = .002). Self-satisfaction and health satisfaction accounted for 32% of the variance in health-promoting behavior (F = 7.568, P < .0001). Age and life satisfaction accounted for 50% of the variance in CVD risk score (F = 58.28, P < .0001). CONCLUSIONS Personal satisfaction was associated with health-promoting behavior and CVD risk. Future research would benefit from the inclusion of longitudinal data and comparative groups.
Optimizing Sample Size for Population Genomic Study in a Global Invasive Lady Beetle, Harmonia Axyridis

Finding optimal sample sizes is critical for the accurate estimation of genetic diversity of large invasive populations. Based on previous studies, we hypothesized that a minimal sample size of 3–8 individuals is sufficient to dissect the population architecture of the harlequin lady beetle, Harmonia axyridis, a biological control agent and an invasive alien species. Here, equipped with a type IIB endonuclease restriction site-associated (2b-RAD) DNA sequencing approach, we identified 13,766 and 13,929 single nucleotide polymorphisms (SNPs), respectively, among native and invasive H. axyridis populations. With this information we simulated populations using a randomly selected 3000 SNPs and a subset of individuals. From this simulation we finally determined that six individuals is the minimum sample size required for the accurate estimation of intra- and inter-population genetic diversity within and across H. axyridis populations. Our findings provide an empirical advantage for population genomic studies of H. axyridis in particular and suggest useful tactics for similar studies on multicellular organisms in general.
A descriptive cross sectional study comparing barriers and determinants of physical activity of Sri Lankan middle aged and older adults

Background Benefits of physical activities are numerous. Barriers for physical exercise may differ among middle aged and older adults. Therefore, identifying and comparing the barriers for participating in regular physical exercises among middle aged and older adults will be useful in designing age specific physical exercise programmes. Methods This descriptive cross sectional study was carried out among 206 Sri Lankan adults in the age range of 40–84 years in the Colombo North region of Sri Lanka using culturally validated questionnaires to determine and compare the barriers and factors associated with regular physical activity participation. Majority were males (56%) and 54% were < 60 years. People in the age range of 40–59 years were considered as middle age and ≥ 60 years as older adults. Bivariate analysis and multivariate analysis was carried out to determine the significant factors that are associated with regular physical activity participation. Results Lack of free time (52%), feeling too lazy (26%) and bad weather (29%) were the main barriers for the participants. In < 60 years, high level of income (p = 0.008) and in ≥ 60 years, being a male (p = 0.016), having a high level of education (P = 0.002) and a high BMI (p = 0.002) had a significant negative association with the level of physical activities. Conclusions Contrary to findings from surveys in several developed countries, this study showed that having a high level of education and being a male were strongly related with lack of physical activity participation.