Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of mechanistic and statistical methods in forecasting influenza-like illness

A variety of mechanistic and statistical methods to forecast seasonal influenza have been proposed and are in use; however, the effects of various data issues and design choices (statistical versus mechanistic methods, for example) on the accuracy of these approaches have not been thoroughly assessed. Here, we compare the accuracy of three forecasting approaches—a mechanistic method, a weighted average of two statistical methods and a super-ensemble of eight statistical and mechanistic models—in predicting seven outbreak characteristics of seasonal influenza during the 2016–2017 season at the national and 10 regional levels in the USA. For each of these approaches, we report the effects of real time under- and over-reporting in surveillance systems, use of non-surveillance proxies of influenza activity and manual override of model predictions on forecast quality. Our results suggest that a meta-ensemble of statistical and mechanistic methods has better overall accuracy than the individual methods. Supplementing surveillance data with proxy estimates generally improves the quality of forecasts and transient reporting errors degrade the performance of all three approaches considerably. The improvement in quality from ad hoc and post-forecast changes suggests that domain experts continue to possess information that is not being sufficiently captured by current forecasting approaches.
Deletion of cadherin‐17 enhances intestinal permeability and susceptibility to intestinal tumour formation

Cadherin‐17 is an adhesion molecule expressed specifically in intestinal epithelial cells. It is frequently underexpressed in human colorectal cancer. The physiological function of cadherin‐17 and its role in tumourigenesis have not yet been determined. We used the transcription activator‐like effector nuclease technique to generate a Cdh17 knockout (KO) mouse model. Intestinal tissues were analysed with histological, immunohistochemical and ultrastructural methods. Colitis was induced by oral administration of dextran sulphate sodium (DSS), and, to study effects on intestinal tumourigenesis, mice were given azoxymethane (AOM) and DSS to induce colitis‐associated cancer. Cdh17 KO mice were viable and fertile. The histology of their small and large intestines was similar to that of wild‐type mice. The junctional architecture of the intestinal epithelium was preserved. The loss of cadherin‐17 resulted in increased permeability and susceptibility to DSS‐induced colitis. The AOM/DSS model demonstrated that Cdh17 KO enhanced tumour formation and progression in the intestine. Increased nuclear translocation of Yap1, but not of β‐catenin, was identified in the tumours of Cdh17 KO mice. In conclusion, cadherin‐17 plays a crucial role in intestinal homeostasis by limiting the permeability of the intestinal epithelium. Cadherin‐17 is also a tumour suppressor for intestinal epithelia. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Use of chicken immunoglobulin Y in general virology

ABSTRACT Immunoglobulin Y (IgY), an antibody present in birds, reptiles, and amphibians, is actively transported from the serum to egg yolks, where it is stored in large quantities. The use of chicken polyclonal IgY instead of mammalian IgG antibodies for biomedical applications has ethical and economic advantages, such as the lack of a need for animal bleeding because the antibodies are extracted from eggs after hen immunization and the low cost of the production and purification methods. This article reviews the latest IgY applications in diagnostic virology and the therapeutic use of IgY in viral gastroenteritis.
Incidence of Breast Cancer in the Life Span Study of Atomic Bomb Survivors: 1958–2009

The importance of reproductive history in breast tissue development and etiology of sporadic breast cancer in females is well established. However, there is limited evidence of factors, other than age, that modify risk of radiation-related breast cancer. In this study, we evaluated breast cancer incidence in the Life Span Study cohort of atomic bomb survivors, adding 11 years of follow-up and incorporating reproductive history data. We used Poisson regression models to describe radiation risks and modifying effects of age and reproductive factors. Among 62,534 females, we identified 1,470 breast cancers between 1958 and 2009. Of 397 new cases diagnosed since 1998, 75% were exposed before age 20. We found a strong linear dose response with excess relative risk (ERR) of 1.12 per Gy [95% confidence interval (CI): 0.73 to 1.59] for females at age 70 after exposure at age 30. The ERR decreased with increasing attained age (P = 0.007) while excess absolute rate (EAR) increased with attained age up to age 70 (P < 0.001). Age at menarche was a strong modifier of the radiation effect: for a given dose, both the ERR and EAR decreased with increasing age at menarche (P = 0.007 and P < 0.001). Also, independently, age-at-exposure effects on ERR and EAR differed before and after menarche (P = 0.043 and P = 0.015, respectively, relative to log-linear trends), with highest risks for exposures around menarche. Despite the small number of male breast cancers (n = 10), the data continue to suggest a dose response (ERR per Gy = 5.7; 95% CI: 0.3 to 30.8; P = 0.018). Persistently increased risk of female breast cancer after radiation exposure and its modification pattern suggests heightened breast sensitivity during puberty.
Certified Child Life Specialists Lessen Emotional Distress of Children Undergoing Laceration Repair in the Emergency Department

Objective The objective of this study is to evaluate the impact of certified child life specialists (CCLSs) on the emotional responses of children undergoing laceration repair in the emergency department (ED). Methods Patients 4 to 12 years of age who required laceration repair by suturing were prospectively enrolled at an urban tertiary pediatric ED. Certified child life specialists are not available at all times in our institution, allowing for a priori categorization of subjects into 2 comparison groups, those with and those without CCLS involvement. Subjects requiring anxiolysis, pharmacologic sedation, narcotics, or physical restraint were excluded. The Children's Emotional Manifestation Scale, a previously validated Likert-like tool, was used to quantify the patients' distress, with a higher score reflecting a more emotional child. Just before placement of the first suture, subjects were scored by trained independent observers. Baseline data included age, sex, race, type of local anesthetic, length and location of laceration, and analgesics administered. The primary endpoint of emotional score was compared with a 2-tailed Mann-Whitney U test, with a P < 0.05 considered statistically significant. Results Two hundred one patients constituted the final study cohort, with 103 (51%) having CCLS involvement. Study groups did not differ in regards to any baseline demographic or clinical characteristics. The median emotional score for patients with child life services was 7 (interquartile range, 6–9) versus 9 (interquartile range, 7.5–12) for those without (P < 0.0005). Conclusions Certified child life specialist involvement is associated with less emotional distress for children undergoing laceration repair in the ED.
Systems protobiology: origin of life in lipid catalytic networks

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
Parents' Perception of Health-Related Quality of Life in Children With Cochlear Implants: The Impact of Language Skills and Hearing.

Purpose The study compared how parents of children with cochlear implants (CIs) and parents of children with normal hearing perceive their children's health-related quality of life (HR-QOL). Method The sample consisted of 186 Norwegian-speaking children in the age span of 5;0-12;11 (years;months): 106 children with CIs (53% boys, 47% girls) and 80 children with normal hearing (44% boys, 56% girls). No children had known additional disabilities affecting language, cognitive development, or HR-QOL. Parents completed the generic questionnaire Pediatric Quality of Life Inventory (Varni, Seid, & Kurtin, 2001), whereas children completed a test battery measuring different aspects of language and hearing. Results Parents of children with CIs reported statistically significantly poorer HR-QOL in their children, on Pediatric Quality of Life Inventory total score and the subdomains social functioning and school functioning. Roughly 50% of parents of children with CIs reported HR-QOL levels (total score) within normal limits. No significant differences between groups emerged on the physical health and emotional functioning subscales. For the children in the group with CIs, better speech perception in everyday situations was associated with higher proxy-ratings of HR-QOL. Better spoken language skills were weakly to moderately associated with higher HR-QOL. Conclusions The findings suggest that the social and school situation is not yet resolved satisfactorily for children with CIs. Habilitation focusing on spoken language skills and better sound environment may improve social interactions with peers and overall school functioning.
Feasibility trial of an unsupervised, facility-based exercise programme for depressed outpatients

ABSTRACT This pilot study examined feasibility of an unsupervised, facility-based exercise programme for promoting exercise adherence among depressed adult outpatients. The potential effect of adding physical activity counselling on depressive symptoms and physical activity was also explored. Participants were randomly assigned to a 12-week programme comprising an orientation and access to fitness centre resources (control, n = 18) or that programme plus 6 physical activity counselling sessions (intervention, n = 18). Outcome measures were feasibility (fitness centre attendance over 12 weeks); Beck Depression Inventory (BDI-II) and International Physical Activity Questionnaire (IPAQ) completed at baseline and week 12; and qualitative programme feedback. Fitness centre attendance averaged only 12 days (14% of all possible days) with no differences between study groups. No group differences were found on IPAQ or BDI-II scores at week 12. Increases from baseline in IPAQ moderate/vigorous activity minutes were associated with decreases in BDI-II scores at week 12 (p < 0.001). The most helpful programme aspect reported was connecting participants to fitness centre resources. In this pilot study of depressed outpatients, an unsupervised fitness centre based program was not feasible for promoting exercise adherence and adding physical activity counselling was not useful for increasing physical activity levels or reducing depression.
Psychometric Properties of the Child and Adolescent Mindfulness Measure (CAMM) in Racial Minority Adolescents From Low-Income Environments

No study has yet assessed the psychometric properties of scores from any mindfulness measure in racial minority adolescents from low-income environments. The present study examined the reliability and validity of Child and Adolescent Mindfulness Measure (CAMM) scores in a nonclinical sample of late adolescents (N = 92) from low-income neighborhoods who predominantly identified as African American. Findings confirmed a one-factor structure for responses to the 10 CAMM items as well as adequate internal consistency (Cronbach’s &agr; = .88). In support of validity, CAMM scores demonstrated large significant negative correlations with scores from measures of constructs that should be negatively related to mindfulness, including depressive symptoms, worry, ruminative coping, and involuntary engagement responses to stress. Thus, CAMM scores appear to reliably and validly assess mindfulness in racial minority adolescents from low-income environments. Having a psychometrically sound mindfulness measure for this population will aid in understanding the mechanisms by which mindfulness-based interventions work, which could lead to improved interventions and outcomes for this population.
Climate Variability and Dengue Hemorrhagic Fever in Hanoi, Viet Nam, During 2008 to 2015

Dengue fever/dengue hemorrhagic fever (DF/DHF) has been an important public health challenge in Viet Nam and worldwide. This study was implemented in 2016-2017 using retrospective secondary data to explore associations between monthly DF/DHF cases and climate variables during 2008 to 2015. There were 48 175 DF/DHF cases reported, and the highest number of cases occurred in November. There were significant correlations between monthly DF/DHF cases with monthly mean of evaporation (r = 0.236, P < .05), monthly relative humidity (r = −0.358, P < .05), and monthly total hours of sunshine (r = 0.389, P < .05). The results showed significant correlation in lag models but did not find direct correlations between monthly DF/DHF cases and monthly average rainfall and temperature. The study recommended that health staff in Hanoi should monitor DF/DHF cases at the beginning of epidemic period, starting from May, and apply timely prevention and intervention measures to avoid the spreading of the disease in the following months. A larger scale study for a longer period of time and adjusting for other potential influencing factors could better describe the correlations, modelling/projection, and developing an early warning system for the disease, which is important under the impacts of climate change and climate variability.
Alcohol delamination of the corneal epithelium for recurrent corneal erosion syndrome.

AIM To evaluate the outcomes of alcohol delamination (ALD) of the corneal epithelium for the treatment of recurrent corneal erosion syndrome (RCES) and to implement a standardized treatment protocol for this condition utilizing evidence based practice and the findings of an internal audit. METHODS A retrospective analysis of 42 eyes of 40 patients diagnosed with RCES who were treated with ALD between January 2006 and March 2016 was conducted. Patients had 20% alcohol applied to the cornea with the use of a well for 40s. Patients were reviewed one week later in the Outpatient Department. Outcome criteria were established based on standards from other studies in the medical literature. These included, a treatment success rate of at least 72% (defined as complete resolution of symptoms one month after treatment), a postoperative complication a rate of <5% (mainly infective keratitis, and subepithelial haze), and the absence of any detrimental effect on visual acuity in ≥95% of patients. RESULTS The mean age at the time of ALD was 41.17±13.44y. Patients were followed for an average of 12.8±15.65mo. The majority were female (52.5%, n=21) and the majority of eyes treated with ALD were left eyes (62.9%, n=26). Trauma was the primary aetiology in our study population. Treatment was successful in 73.8% (n=31) of eyes and in 75% (n=30) of patients. Recurrence occurred in 26.2% of eyes at a mean of 10.41±12.63mo post treatment. CONCLUSION ALD is an efficacious and cost-effective primary surgical intervention for RCES.
Processed and ultraprocessed food consumption pattern in the Jakarta Individual Food Consumption Survey 2014.

BACKGROUND AND OBJECTIVES Dietary patterns are undergoing a major shift worldwide. This study analysed the consumption of processed and ultraprocessed foods in Jakarta and its contribution to the energy and nutrient intake based on the Individual Food Consumption Survey 2014. METHODS AND STUDY DESIGN Food consumption data were based on 24-hour dietary recall. Foods were grouped into four food groups: nonprocessed foods, processed ingredients, processed foods, and ultraprocessed foods and subsequently categorised according to the Indonesian Food Category System. Energy and nutrient intake were calculated using Nutrisurvey 2007 software. RESULTS Nonprocessed food, processed ingredient, processed food, and ultraprocessed food consumption contributed to 57.2%, 21.6%, 1.7%, and 19.5% of total weight consumption, respectively. Ultraprocessed foods contributed to 15.7%, 16.7%, 14.2%, 12.6%, 18.4%, and 31.3% of daily energy, carbohydrate, protein, fat, sodium, and sucrose intake, respectively, and the respective contributions of nonprocessed foods were 52.2%, 58.7%, 65.8%, 32.6%, 7.9%, and 11.1%; of processed ingredients were 30.0%, 22.7%, 16.4%, 53.6%, 68.9%, and 57.6%; and of processed foods were 2.1%, 2.0%, 3.6%, 1.2%, 4.8%, and 0%. Linear regression analysis between the amount of food consumption and nutrient intake showed that at the same weight consumption, processed ingredients provided a higher intake of energy, fat, sodium, and sucrose than the other food groups. CONCLUSIONS Processed and ultraprocessed foods still have a lower contribution to energy and nutrient intake in Jakarta than nonprocessed foods and processed ingredients.
Predictive Factors for Differentiating Pancreatic Cancer-Associated Diabetes Mellitus from Common Type 2 Diabetes Mellitus for the Early Detection of Pancreatic Cancer

Background: The purpose of this study was to find the factors that may be helpful for differentiating pancreatic cancer-associated diabetes mellitus (PC + DM) from common type 2 diabetes for the early diagnosis of pancreatic cancer. Methods: From January 2008 to August 2013, 171 patients with pancreatic cancer and new-onset diabetes were recruited for the study; 242 age- and gender-matched patients with common type 2 diabetes were also identified as control during the same period. The patient’s characteristics and laboratory parameters were compared between the 2 groups. Results: By multivariate logistic regression analysis, we found that body mass index (BMI), the age of onset of diabetes, hepatitis B virus (HBV) infection, total bilirubin (TBIL), alanine aminotransferase (ALT), creatinine (Cr), apolipoprotein-A1 (APO-A1), and white blood cell (WBC) were independent predictive factors for differentiating PC + DM from common type 2 diabetes; the areas under receiver operating characteristic curves were up to 0.815 for the combination of these 8 markers. Conclusions: These results suggest that BMI, the age of onset of diabetes, HBV infection, TBIL, ALT, Cr, APO-A1, and WBC are factors that could differentiate PC + DM from common type 2 diabetes and may be used for early diagnosis of pancreatic cancer.
The plasma Epstein–Barr virus DNA level guides precision treatment for nasopharyngeal carcinoma in the intensity-modulated radiotherapy era: a large population-based cohort study from an endemic area

Background: In the intensity-modulated radiotherapy (IMRT) era, the survival benefit of concurrent chemotherapy for locoregionally advanced nasopharyngeal carcinoma (LA-NPC) remains undetermined. This study aimed to evaluate the benefits of IMRT with concurrent chemotherapy compared with IMRT alone for LA-NPC patients with different plasma Epstein–Barr virus (EBV) DNA levels. Methods: Patients were identified from a prospectively maintained database in an endemic area between November 2002 and December 2013. Cox proportional hazards models, propensity score matching, and inverse probability weighting models were established for survival analysis. Stratification analysis was performed based on interaction effects analysis. Finally, sensitivity analysis was performed considering unmeasured confounders. Results: A total of 1357 eligible patients were enrolled (median follow up 62.4 months; range 3.5–155.8 months). No significant survival differences were observed between groups in the entire cohort. Notably, a significant interaction effect was observed between treatment regimens and EBV DNA levels. In patients with high EBV DNA levels (>4000 copies/ml), all three models showed that IMRT with concurrent chemotherapy significantly improved overall survival [hazard ratio (HR) 2.521, 95% confidence interval (CI) 1.218–5.216], disease-free survival (HR 2.168, 95% CI 1.349–3.483), and distant metastasis-free survival (HR 2.331, 95% CI 1.194–4.551) compared with IMRT alone. No differences were found in patients with low EBV DNA levels. Sensitivity analysis confirmed the robustness of the results. Conclusion: In the IMRT era, concurrent chemotherapy treatment of LA-NPC patients with high EBV DNA levels is reasonable. However, the optimal regimen for LA-NPC patients with low EBV DNA levels needs further validation in randomized clinical trials.