Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the basic reproduction number for the 2015 bubonic plague outbreak in Nyimba district of Eastern Zambia

Background Plague is a re-emerging flea-borne infectious disease of global importance and in recent years, Zambia has periodically experienced increased incidence of outbreaks of this disease. However, there are currently no studies in the country that provide a quantitative assessment of the ability of the disease to spread during these outbreaks. This limits our understanding of the epidemiology of the disease especially for planning and implementing quantifiable and cost-effective control measures. To fill this gap, the basic reproduction number, R0, for bubonic plague was estimated in this study, using data from the 2015 Nyimba district outbreak, in the Eastern province of Zambia. R0 is the average number of secondary infections arising from a single infectious individual during their infectious period in an entirely susceptible population. Methodology/Principal findings Secondary epidemic data for the most recent 2015 Nyimba district bubonic plague outbreak in Zambia was analyzed. R0 was estimated as a function of the average epidemic doubling time based on the initial exponential growth rate of the outbreak and the average infectious period for bubonic plague. R0 was estimated to range between 1.5599 [95% CI: 1.382–1.7378] and 1.9332 [95% CI: 1.6366–2.2297], with average of 1.7465 [95% CI: 1.5093–1.9838]. Further, an SIR deterministic mathematical model was derived for this infection and this estimated R0 to be between 1.4 to 1.5, which was within the range estimated above. Conclusions/Significance This estimated R0 for bubonic plague is an indication that each bubonic plague case can typically give rise to almost two new cases during these outbreaks. This R0 estimate can now be used to quantitatively analyze and plan measurable interventions against future plague outbreaks in Zambia.
Associations between Stress and Physical Activity in Korean Adolescents with Atopic Dermatitis Based on the 2018–2019 Korea Youth Risk Behavior Web-Based Survey

This study aimed to confirm the associations between stress and physical activity (PA) in Korean adolescents with atopic dermatitis (AD) based on data from the 2018–2019 Korea Youth Risk Behavior Web-Based Survey. The AD groups were divided into adolescents who were not diagnosed with AD, adolescents who were diagnosed with AD more than one year ago, and adolescents who were diagnosed with AD within one year. We defined the regular PA group and the non-PA group using the American College of Sports Medicine guidelines for children and adolescents: moderate to vigorous PA ≥5 times per week, including vigorous PA ≥3 days per week and muscle strengthening exercises ≥3 times per week. We performed logistic regression analysis to calculate the stress odds ratio (OR) and 95% confidence interval (CI) by group using model 1, adjusted for age, sex, and body mass index, and model 2, additionally adjusted for drinking, smoking, economic statuses, academic achievement, asthma, and rhinitis. In the group diagnosed with AD within one year, stress was 41% and 32% higher according to models 1 (1.41 (1.31–1.52)) and 2 (1.34 (1.20–1.50)), respectively. However, the stress OR was 30% lower in adolescents who completed regular PA than in the non-PA group (model 1: 0.71 (0.58–0.87); model 2: 0.68 (0.57–0.84)), even if diagnosed with AD within one year. In conclusion, the stress of adolescents with AD was significantly higher than that of adolescents without AD. The stress was significantly lower in the group with regular PA, and it was more robust in adolescents diagnosed with AD within one year.
Subtask Segmentation of Timed Up and Go Test for Mobility Assessment of Perioperative Total Knee Arthroplasty †

Total knee arthroplasty (TKA) is one of the most common treatments for people with severe knee osteoarthritis (OA). The accuracy of outcome measurements and quantitative assessments for perioperative TKA is an important issue in clinical practice. Timed up and go (TUG) tests have been validated to measure basic mobility and balance capabilities. A TUG test contains a series of subtasks, including sit-to-stand, walking-out, turning, walking-in, turning around, and stand-to-sit tasks. Detailed information about subtasks is essential to aid clinical professionals and physiotherapists in making assessment decisions. The main objective of this study is to design and develop a subtask segmentation approach using machine-learning models and knowledge-based postprocessing during the TUG test for perioperative TKA. The experiment recruited 26 patients with severe knee OA (11 patients with bilateral TKA planned and 15 patients with unilateral TKA planned). A series of signal-processing mechanisms and pattern recognition approaches involving machine learning-based multi-classifiers, fragmentation modification and subtask inference are designed and developed to tackle technical challenges in typical classification algorithms, including motion variability, fragmentation and ambiguity. The experimental results reveal that the accuracy of the proposed subtask segmentation approach using the AdaBoost technique with a window size of 128 samples is 92%, which is an improvement of at least 15% compared to that of the typical subtask segmentation approach using machine-learning models only.
A Full-Spectrum Registration Method for Zhuhai-1 Satellite Hyperspectral Imagery

Accurate registration is an essential prerequisite for analysis and applications involving remote sensing imagery. It is usually difficult to extract enough matching points for inter-band registration in hyperspectral imagery due to the different spectral responses for land features in different image bands. This is especially true for non-adjacent bands. The inconsistency in geometric distortion caused by topographic relief also makes it inappropriate to use a single affine transformation relationship for the geometric transformation of the entire image. Currently, accurate registration between spectral bands of Zhuhai-1 satellite hyperspectral imagery remains challenging. In this paper, a full-spectrum registration method was proposed to address this problem. The method combines the transfer strategy based on the affine transformation relationship between adjacent spectrums with the differential correction from dense Delaunay triangulation. Firstly, the scale-invariant feature transform (SIFT) extraction method was used to extract and match feature points of adjacent bands. The RANdom SAmple Consensus (RANSAC) algorithm and the least square method is then used to eliminate mismatching point pairs to obtain fine matching point pairs. Secondly, a dense Delaunay triangulation was constructed based on fine matching point pairs. The affine transformation relation for non-adjacent bands was established for each triangle using the affine transformation relation transfer strategy. Finally, the affine transformation relation was used to perform differential correction for each triangle. Three Zhuhai-1 satellite hyperspectral images covering different terrains were used as experiment data. The evaluation results showed that the adjacent band registration accuracy ranged from 0.2 to 0.6 pixels. The structural similarity measure and cosine similarity measure between non-adjacent bands were both greater than 0.80. Moreover, the full-spectrum registration accuracy was less than 1 pixel. These registration results can meet the needs of Zhuhai-1 hyperspectral imagery applications in various fields.
Specular highlights improve color constancy when other cues are weakened

Abstract Previous studies suggest that to achieve color constancy, the human visual system makes use of multiple cues, including a priori assumptions about the illumination (“daylight priors”). Specular highlights have been proposed to aid constancy, but the evidence for their usefulness is mixed. Here, we used a novel cue-combination approach to test whether the presence of specular highlights or the validity of a daylight prior improves illumination chromaticity estimates, inferred from achromatic settings, to determine whether and under which conditions either cue contributes to color constancy. Observers made achromatic settings within three-dimensional rendered scenes containing matte or glossy shapes, illuminated by either daylight or nondaylight illuminations. We assessed both the variability of these settings and their accuracy, in terms of the standard color constancy index (CCI). When a spectrally uniform background was present, neither CCIs nor variability improved with specular highlights or daylight illuminants (Experiment 1). When a Mondrian background was introduced, CCIs decreased overall but were higher for scenes containing glossy, as opposed to matte, shapes (Experiments 2 and 3). There was no overall reduction in variability of settings and no benefit for scenes illuminated by daylights. Taken together, these results suggest that the human visual system indeed uses specular highlights to improve color constancy but only when other cues, such as from the local surround, are weakened.
Natural compounds as inhibitors of SARS-CoV-2 endocytosis: A promising approach against COVID-19

Background and aim: The recent COVID-19 pandemic caused by SARS-CoV-2 affected more than six million people and caused thousands of deaths. The lack of effective drugs or vaccines against SARS-CoV-2 further worsened the situation. This review is focused on the identification of molecules that may inhibit viral entry into host cells by endocytosis. Methods: We performed the literature search for these natural compounds in the articles indexed in PubMed. Results: Natural products against viral infections have been gaining importance in recent years. Specific natural compounds like phytosterols, polyphenols, flavonoids, citrus, galangal, curcuma and hydroxytyrosol are being analyzed to understand whether they could inhibit SARS-CoV-2. Conclusions: We reviewed natural compounds with potential antiviral activity against SARS-CoV-2 that could be used as a treatment for COVID-19. (www.actabiomedica.it)
A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes

Genome‐wide association studies (GWAS) have identified single‐nucleotide polymorphisms (SNPs) associated with glioma risk on 20q13.33, but the biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 20q13.33 impacted the activity of an enhancer, leading to an altered expression of nearby genes. To identify candidate functional SNPs, we identified all SNPs in linkage disequilibrium with the risk‐associated SNP rs2297440 that mapped to putative enhancers. Putative enhancers containing candidate functional SNPs were tested for allele‐specific effects in luciferase enhancer activity assays against glioblastoma multiforme (GBM) cell lines. An enhancer containing SNP rs3761124 exhibited allele‐specific effects on activity. Deletion of this enhancer by CRISPR‐Cas9 editing in GBM cell lines correlated with an altered expression of multiple genes, including STMN3, RTEL1, RTEL1‐TNFRSF6B, GMEB2, and SRMS. Expression quantitative trait loci (eQTL) analyses using nondiseased brain samples, isocitrate dehydrogenase 1 (IDH1) wild‐type glioma, and neurodevelopmental tissues showed STMN3 to be a consistent significant eQTL with rs3761124. RTEL1 and GMEB2 were also significant eQTLs in the context of early CNS development and/or in IDH1 wild‐type glioma. We provide evidence that rs3761124 is a functional variant on 20q13.33 related to glioma/GBM risk that modulates the expression of STMN3 and potentially other genes across diverse cellular contexts.
Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Pogostemon Desf. , the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth. ). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.
Mobile Application-Based Interventions for Chronic Pain Patients: A Systematic Review and Meta-Analysis of Effectiveness

Chronic pain is one of the major causes of disability in the general population. Even though there are effective treatment options available for reducing symptoms, these treatments often do not have consistent lasting effects. As the usage of mobile devices has increased enormously during the last few years, mobile application-based treatment options are widespread. Such app-based programs are not yet empirically proven but might enable patients to become more independent in their pain management in order to prevent relapse. The aim of this meta-analysis was to summarize the literature on mobile application-based interventions for chronic pain patients. Therefore, three electronic bibliographic databases, PubMed, PsycINFO, and Web of Science, were searched for studies that investigated the effectiveness of mobile application-based intervention for chronic pain on pain intensity. The final sample comprised twenty-two studies, with a total of 4679 individuals. Twelve of these twenty-two studies used a randomized control trial (RCT) design, while ten studies only used an observational design. For all twenty-two studies, a small but significant effect (d = −0.40) was found when compared to baseline measures or control groups. The results suggest that apps-based treatment can be helpful in reducing pain, especially in the long-term.
The Bacillus cereus Food Infection as Multifactorial Process

The ubiquitous soil bacterium Bacillus cereus presents major challenges to food safety. It is responsible for two types of food poisoning, the emetic form due to food intoxication and the diarrheal form emerging from food infections with enteropathogenic strains, also known as toxico-infections, which are the subject of this review. The diarrheal type of food poisoning emerges after production of enterotoxins by viable bacteria in the human intestine. Basically, the manifestation of the disease is, however, the result of a multifactorial process, including B. cereus prevalence and survival in different foods, survival of the stomach passage, spore germination, motility, adhesion, and finally enterotoxin production in the intestine. Moreover, all of these processes are influenced by the consumed foodstuffs as well as the intestinal microbiota which have, therefore, to be considered for a reliable prediction of the hazardous potential of contaminated foods. Current knowledge regarding these single aspects is summarized in this review aiming for risk-oriented diagnostics for enteropathogenic B. cereus.
Development and preliminary validation of a brief household food insecurity screening tool for paediatric health services in Australia.

Children from food insecure households are more likely to have substandard food and nutritional intakes, and experience developmental delays, behaviour issues and increased use of health services. In Australia, screening for household food insecurity (HFI) within health services is not undertaken routinely, limiting opportunities to optimise nutrition and healthcare. This research aimed to (a) identify the prevalence, potential determinants and outcomes of HFI among paediatric outpatients in two Queensland hospitals; and (b) identify questions suitable for screening households at risk of HFI. A cross-sectional survey collected data from caregivers of children attending paediatric appointments at two hospitals in Brisbane, Australia (n = 148). Sociodemographic, health and household-related characteristics were collected, and food security status was assessed using four HFI measures. Chi-square, independent t-tests, ANOVA and logistic regression explored associations between HFI and health-related characteristics. A potential HFI screener was identified based on the most frequently endorsed questions from any HFI measure, and its validity was assessed through calculation of sensitivity and specificity. Prevalence of HFI was 41%, with 16% experiencing very low food security. Households with a child of 'fair/poor' health had 5.59 times greater odds of being food insecure than being food secure, compared to households with a child of 'excellent/good' health (aOR 5.59, 95% CI: 1.3-23.5). HFI was also positively associated with household chaos (p = .006). A combination of two questions was identified as a possible screening tool, with a sensitivity of 96% and a specificity of 90%. This study demonstrated HFI may be highly prevalent in a paediatric outpatient population, which may result in difficulties in being able to follow nutrition prescriptions. A highly sensitive and specific two-question screening tool was identified and may assist practitioners in paediatric healthcare settings in identifying clients who are at risk of HFI.
Physical activity for people living with cancer: Knowledge, attitudes, and practices of general practitioners in Australia

Background Healthcare professionals’ (Oncologists, doctors, and nurses) physical activity (PA) recommendations impact patients living with cancer PA levels. General practitioners (GPs) monitor the overall health of patients living with cancer throughout their treatment journey. This is the first study to explore GP’s knowledge, attitudes and practices of PA for patients living with cancer. Methods GPs who see patients living with cancer regularly (n = 111) completed a survey based on The Theory of Planned Behaviour (TPB). Participants (GP’s) reported knowledge, attitudes, perceived behaviour control and subjective norms of PA within the cancer population. GP recommendation and referral rates of PA were reported. Principal component analysis was conducted to establish a set of survey items aligned to TPB constructs (attitude, subjective norms, perceived control), and multiple regression analyses characterised associations between these predictor variables and (a) recommendation; and (b) referral–of PA to cancer patients. Results GPs (n = 111) recommended PA to 41–60% of their patients and referred 1–20% to PA programs. Multiple regression models significantly predicted the percent of patients recommended PA, p < . 0005 adj. R2 = 0.40 and referred PA, p < . 0005, adj. R2 = 0.21. GP attitudes and perceived behavioural control and GP’s own activity levels were significant predictors of whether patients were recommended and referred for PA, p<0.05. Conclusion GPs reported positive attitudes and perceptions towards promoting PA for their patients living with cancer. Despite having a positive correlation between PA recommendations and referral rates, a gap was evident between GP’s PA beliefs and their individual referral practices. More GP’s willing to promote and refer their patients for PA, would improve the physical and mental health outcomes of the cancer population.
The ERP, frequency, and time-frequency correlates of feedback processing: Insights from a large sample study.

Human learning, at least in part, appears to be dependent on the evaluation of how outcomes of our actions align with our expectations. Over the past 23 years, electroencephalography (EEG) has been used to probe the neural signatures of feedback processing. Seminal work demonstrated a difference in the human event-related potential (ERP) dependent on whether people were processing correct or incorrect feedback. Since then, these feedback evoked ERPs have been associated with reinforcement learning and conflict monitoring, tied to subsequent behavioral adaptations, and shown to be sensitive to a wide range of factors (e.g., Parkinson's disease). Recently, research has turned to frequency decomposition techniques to examine how changes in the EEG power spectra are related to underlying learning mechanisms. Although the literature on the neural correlates of feedback processing is vast, there are still methodological discrepancies and differences in results across studies. Here, we provide reference results and an investigation of methodological considerations for the ERP (reward positivity) and frequency (delta and theta power) correlates of feedback evaluation with a large sample size. Specifically, participants (n = 500) performed a two-armed bandit task while we recorded EEG. Our findings provide key information about the data characteristics and relationships that exist between the neural signatures of feedback evaluation. Additionally, we conclude with selected methodological recommendations for standardization of future research. All data and scripts are freely provided to facilitate open science.
Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary Th17 Response that Mitigates Susceptibility to Streptococcus pneumoniae.

Rationale Cross-sectional human data suggest that enrichment of oral anaerobic bacteria in the lung is associated with increased Th17 inflammatory phenotype. In this study we evaluated the microbial and host immune response dynamics after aspiration with a oral commensals using a preclinical mouse model. Methods Aspiration with a mixture of human oral commensals (MOC; Prevotella melaninogenica, Veillonella parvula, and Streptococcus mitis) was modeled in mice followed by variable time of sacrifice. Genetic background of mice included WT, MyD88 knock out and STAT3C. Measurements 16S rRNA gene sequencing characterized changes in microbiota. Flow cytometry, cytokine measurement via Luminex and RNA host transcriptome sequencing was used to characterize host immune phenotype. Main Results While MOC aspiration correlated with lower airway dysbiosis that resolved within five days, it induced an extended inflammatory response associated with IL17-producing T-cells lasting at least 14 days. MyD88 expression was required for the IL-17 response to MOC aspiration, but not for T-cell activation or IFN-γ expression. MOC aspiration prior to a respiratory challenge with S. pneumoniae led to a decreased in host's susceptibility to this pathogen. Conclusions Thus, in otherwise healthy mice, a single aspiration event with oral commensals are rapidly cleared from the lower airways, but induce a prolonged Th17 response that secondarily decreased susceptibility to respiratory pathogens. Translationally, these data implicate an immuno-protective role of episodic microaspiration of oral microbes in the regulation of the lung immune phenotype and mitigation of host susceptibility to infection with lower airway pathogens.