Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Localization of Latent Murine Cytomegalovirus

ABSTRACT Herpesviruses typically establish latent infection in their hosts. The cell(s) responsible for harboring latent virus, in most cases, is not known. Using immunofluorescence and PCR-in situ hybridization (PISH), a technique which combines the sensitivity of PCR with the localization and specificity of in situ hybridization, we provide the first direct evidence that endothelial cells are a major site of murine cytomegalovirus (MCMV) DNA in latently infected animals. These findings are consistent with existing knowledge of the biological behavior of CMV, in particular the transmission of latent CMV by solid organ and bone marrow transplantation, in both human and animal models. In addition, we have localized MCMV DNA in the lung alveolar macrophage and in bone marrow cells. Our findings confirm that bone marrow-derived hematopoietic cells are a site of CMV latency and further suggest that bone marrow may be a reservoir of infected progeny capable of migrating into the circulation and establishing latency in various tissues. These findings provide clearly needed insight into the site of latent infection which is central to an understanding of the mechanisms of reactivation.
Modulation of Intestinal Epithelial Glycocalyx Development by Human Milk Oligosaccharides and Non‐Digestible Carbohydrates

Scope The epithelial glycocalyx development is of great importance for microbial colonization. Human milk oligosaccharides (hMOs) and non‐digestible carbohydrates (NDCs) may modulate glycocalyx development. Methods and results The effects of hMOs and NDCs on human gut epithelial cells (Caco2) are investigated by quantifying thickness and area coverage of adsorbed albumin, heparan sulfate (HS), and hyaluronic acid (HA) in the glycocalyx. Effects of hMOs (2′‐FL and 3‐FL) and NDCs [inulins with degrees of polymerization (DP) (DP3‐DP10, DP10‐DP60, DP30‐DP60) and pectins with degrees of methylation (DM) (DM7, DM55, DM69)] are tested using immunofluorescence staining at 1 and 5 days stimulation. HMOs show a significant enhancing effect on glycocalyx development but effects are structure‐dependent. 3‐FL induces a stronger albumin adsorption and increases HS and HA stronger than 2′‐FL. The DP3‐DP10, DP30‐60 inulins also increase glycocalyx development in a structure‐dependent manner as DP3‐DP10 selectively increases HS, while DP30‐DP60 specifically increases HA. Pectins have less effects, and only increase albumin adsorption. Conclusion Here, it is shown that 2′‐FL and 3‐FL and inulins stimulate glycocalyx development in a structure‐dependent fashion. This may contribute to formulation of effective hMO and NDC formulations in infant formulas to support microbial colonization and gut barrier function.
Effect of Silver Diamine Fluoride Treatment on Microbial Profiles of Plaque Biofilms from Root/Cervical Caries Lesions

Purpose: To assess the effect of silver diamine fluoride (SDF) on microbial profiles present in plaque from root/cervical carious lesions, and its association with caries lesion arrest. Materials and Methods: Twenty patients with at least one soft cavitated root/cervical carious lesion were included. One lesion/patient was randomly selected and treated with 38% SDF. Supragingival plaque samples were harvested at preintervention and 1 month postintervention. Using an MiSeq platform, 16S rDNA sequencing of the V3-V4 regions was used to determine bacterial profiles. Clinical evaluation of lesion hardness was used to evaluate arrest. t tests, principal component analysis (PCA), multidimensional scaling (MDS), and generalized linear models (GLMs) tests were used for statistical comparisons. Results: From a total of 40 plaque samples, 468 probe targets were observed. Although 60% of lesions became hard postintervention, PCA and MDS tests showed no distinct pre- and postintervention groups. In addition, pre- and postintervention differences in diversity (Shannon index) of microbial profiles between patients with and without lesion arrest were not statistically different. A likelihood ratio test for pre- versus postintervention differences within patients, i.e., adjusting for differences between patients using negative binomial GLMs, showed 17 bacterial taxa with significant differences (FDR <0.05). Conclusion: Although 60% of lesions hardened after SDF treatment, this was not directly due to either overall statistically significant differences in microbial profiles or differences in microbial diversity. Nevertheless, there was a trend with some acid-producing species in that their relative abundance was reduced postintervention. The negative binomial GLMs showed 17 bacterial taxa that were significantly different after SDF treatment.
Fighting Thyroid Cancer with Microgravity Research

Microgravity in space or simulated by special ground-based devices provides an unusual but unique environment to study and influence tumour cell processes. By investigating thyroid cancer cells in microgravity for nearly 20 years, researchers got insights into tumour biology that had not been possible under normal laboratory conditions: adherently growing cancer cells detach from their surface and form three-dimensional structures. The cells included in these multicellular spheroids (MCS) were not only altered but behave also differently to those grown in flat sheets in normal gravity, more closely mimicking the conditions in the human body. Therefore, MCS became an invaluable model for studying metastasis and developing new cancer treatment strategies via drug targeting. Microgravity intervenes deeply in processes such as apoptosis and in structural changes involving the cytoskeleton and the extracellular matrix, which influence cell growth. Most interestingly, follicular thyroid cancer cells grown under microgravity conditions were shifted towards a less-malignant phenotype. Results from microgravity research can be used to rethink conventional cancer research and may help to pinpoint the cellular changes that cause cancer. This in turn could lead to novel therapies that will enhance the quality of life for patients or potentially develop new preventive countermeasures.
Association of IL-10 (-819T/C, -592A/C and -1082A/G) and IL-6 -174G/C gene polymorphism and the risk of pneumonia-induced sepsis

Abstract Context: Association between inherited variants and the risks of sepsis is controversial. Objective: To evaluate the risk of pneumonia-induced sepsis by examining its linkage with polymorphisms of IL-6 and IL-10. Materials and methods: Samples were obtained from 188 pneumonia-induced sepsis patients, 162 pneumonia patients and 200 healthy controls. Results: Subjects with IL-10 -1082 AA genotypes and IL-6 -174 CC genotype had a higher risk of sepsis and increased mRNA levels. Conclusion: The variants of IL-10 -1082 A allele and IL-6 -174 C allele contributed to an increased risk of pneumonia-induced sepsis.
Evaluation of Methods to Measure Production Pressure

Supplemental Digital Content is Available in the Text. Background: Production pressure is a major contributor to the occurrence of medical errors. Production pressure is the demand on health care professionals to increase the quantity of work at the expense of quality. Purpose: The purpose was to summarize the state of the science on measuring production pressure in health care settings so that evidence-based strategies could be identified that minimize medical errors. Methods: This was a literature review. The electronic databases PubMed, Embase, and Scopus were queried using the keywords “work pressure” or “production pressure. ” Results: Production pressure is often measured with quantitative approaches that measure efficiency, staff workload, capacity utilization (number of hospital beds occupied), or psychometric instruments. Ethnography is a qualitative method that is also used to assess production pressure. Conclusions: There were several strategies identified to minimize the impact of production pressure on the occurrence of medical errors. These strategies can be categorized as administrator, educational, or workflow related.
Perceptions of Job Insecurity in Switzerland: Evidence Using Verbal and Numerical Descriptors

The purpose of this paper is to examine perceptions of job insecurity among employees, applying a panel model that allows us to account for the business cycle. In addition, the data will enable the comparison of two measures of job insecurity, one with a cardinal scale, and one with an ordinal scale. First of all, this paper carries out a descriptive analysis of job insecurity, taking into consideration two empirical measures, and using a panel data set from the longitudinal Swiss Household Panel (SHP). Second, an ordered probability unit (probit) model is applied, analyzing both workers’ concerns about job loss, and their subjective job security. Controlling for differences in socio-demographic and job characteristics, estimations show that perceptions of job security affect workers heterogeneously. This study contributes to the literature by revising variables that help to explain the formation of job insecurity perceptions.
Hydroxytyrosol, Tyrosol and Derivatives and Their Potential Effects on Human Health

The Mediterranean diet and olive oil as its quintessential part are almost synonymous with a healthy way of eating and living nowadays. This kind of diet has been highly appreciated and is widely recognized for being associated with many favorable effects, such as reduced incidence of different chronic diseases and prolonged longevity. Although olive oil polyphenols present a minor fraction in the composition of olive oil, they seem to be of great importance when it comes to the health benefits, and interest in their biological and potential therapeutic effects is huge. There is a growing body of in vitro and in vivo studies, as well as intervention-based clinical trials, revealing new aspects of already known and many new, previously unknown activities and health effects of these compounds. This review summarizes recent findings regarding biological activities, metabolism and bioavailability of the major olive oil phenolic compounds—hydroxytyrosol, tyrosol, oleuropein, oleocanthal and oleacein—the most important being their antiatherogenic, cardioprotective, anticancer, neuroprotective and endocrine effects. The evidence presented in the review concludes that these phenolic compounds have great pharmacological potential, however, further studies are still required.
Adherence to Dietary Approaches to Stop Hypertension (DASH)-Style Diet and the Risk of Cancer: A Systematic Review and Meta-Analysis of Cohort Studies

Abstract Objective: Several investigators have proposed a protective association between dietary approaches to stop hypertension (DASH) style diet and risk of cancers; however, they have had inconsistent results. The present study aimed to systematically review the prospective cohort studies and if possible quantify the overall effect using meta-analysis. Methods: PubMed, Scopus, and Google Scholar were searched for cohort studies published up to July 2018. Relative risks (RRs) that were reported for fully adjusted models and their confidence intervals were extracted for meta-analysis. The random effects model was used to combine the RRs. Results: Seventeen studies were eligible to be included in the systematic review, from which nine reports assessed the association between the DASH diet and risk of mortality from all cancer types, four assessed incidence of colorectal cancer, and two studies assessed the risk of colon and rectal cancer separately. Four studies examined the association with the incidence of other cancers (breast, hepatic, endometrial, and lung cancer). Meta-analysis showed that high adherence to DASH is associated with a decreased mortality from all cancer types (RR = 0.84, 95% confidence interval [95%CI]: 0.81–0.86). Participants with the highest adherence to the DASH diet had a lower risk of developing colorectal (RR = 0.79, 95%CI: 0.75–0.83), colon (RR = 0.80, 95%CI: 0.74–0.87), and rectal (RR = 0.84, 95%CI: 0.74–0.96) cancers compared to those with the lowest adherence. Conclusion: DASH-style diet should be suggested as a healthy approach associated with decreased risk of cancer in the community. Prospective studies exploring the association for other cancer types and from regions other than the United States are highly recommended.
Consumers’ Perceptions and Preferences for Bitterness in Vegetable Foods: The Case of Extra-Virgin Olive Oil and Brassicaceae—A Narrative Review

The presence of some healthy phytochemicals in food can be paired with high bitterness, and consumers have a widespread avoidance toward bitter-tasting food. This causes a gap between preferences and healthy needs of consumers. Therefore, this review collected insights from literature belonging to different discipline domains in order to have a broad view of the current state-of-the-art about biochemical aspects and consumers’ perceptions and preferences toward foods with an enhanced bitter taste. In detail, we focused on two core products of the Mediterranean diet: Extra-virgin olive oil (EVOO) and Brassicaceae, both characterized by specific phytochemicals having strong healthy properties and bitter-pungent taste. Results suggested that, although bitter taste is a general driver of dislike, some exceptions can be represented by: niches of consumers (e.g., innovators and organic buyers), foods consumed with specific purposes (e.g., coffee, chocolate, and alcoholic beverages). The level of bitterness perceived by the consumers can be modulated through exposure, information on benefits, and elements within the environment (e.g., music). Thus, these insights can be used to develop specific campaigns aimed at promoting bitter (healthy) food, considering also the key role that could be played by food pairings.
Evaluation of patients with diffuse pigmented villonodular synovitis of knee with functional scoring systems after surgery and radiosynovectomy

Aim: To evaluate the symptoms and functional status of patients with pigmented villonodular synovitis (PVNS) of the knee using the modified Marshall scoring system and musculoskeletal tumor society (MSTS) rating scale before therapy and six months after radiosynovectomy (RS). Materials and methods: Evaluation was made of 29 knee joints of 29 patients with DPVNS. Arthroscopic synovectomy was applied to all patients and additional posterior open synovectomy to five. Yittrium-90 (Y-90) citrate colloid was used in the RS procedure. RS was performed 11.8 ± 13.3 weeks after the operation. In the six months after RS, patients were evaluated with the modified Marshall scoring system and MSTS rating scale. Results: The patients were 17 females and 12 males with a mean age of 31.8 ± 12.9 years (range: 13-54 years). The preoperative modified Marshall score was poor in 24 patients and fair in five patients. In the follow-up period, the scores were excellent in 17 patients, good in 10 patients and fair in two patients. The mean modified Marshall scores increased after the operation and RS from 12.93 ± 2.93 to 25.52 ± 2.90 (p<0.001). The mean MSTS scores increased from 17.52 ± 4.82 to 26.86 ± 2.46 (p<0.001). In one of four patients with a score of 22 and three patients with a score of 24, maximum scores were obtained in the follow-up period with the effect of surgery and RS. Conclusion: RS with Y-90 citrate colloid after surgical excision in the treatment of PVNS is a reliable and efficient treatment method for the increase of functional capacity and decrease of symptoms. Correspondence to: Murat SADIC, M.D., Department of Nuclear Medicine, University of Health Science, Ankara Training and Research Hospital, Ankara/ Turkey; Tel: +903125953608; Fax: +903442240109; E-mail: mdmuratsadic@gmail.com
Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells

Splicing of mRNA precursors can occur cotranscriptionally and it has been proposed that chromatin structure influences splice site recognition and regulation. Here we have systematically explored potential links between nucleosome positioning and alternative splicing regulation upon progesterone stimulation of breast cancer cells. We confirm preferential nucleosome positioning in exons and report four distinct profiles of nucleosome density around alternatively spliced exons, with RNA polymerase II accumulation closely following nucleosome positioning. Hormone stimulation induces switches between profile classes, correlating with a subset of alternative splicing changes. Hormone-induced exon inclusion often correlates with higher nucleosome occupancy at the exon or the preceding intronic region and with higher RNA polymerase II accumulation. In contrast, exons skipped upon hormone stimulation display low nucleosome densities even before hormone treatment, suggesting that chromatin structure primes alternative splicing regulation. Skipped exons frequently harbor binding sites for hnRNP AB, a hormone-induced splicing regulator whose knock down prevents some hormone-induced skipping events. Collectively, our results argue that a variety of chromatin architecture mechanisms can influence alternative splicing decisions.
Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations

Introduction Anorectal malformations (ARM) are rare congenital malformations, resulting from disturbed hindgut development. A genetic etiology has been suggested, but evidence for the involvement of specific genes is scarce. We evaluated the contribution of rare and low-frequency coding variants in ARM etiology, assuming a multifactorial model. Methods We analyzed 568 Caucasian ARM patients and 1,860 population-based controls using the Illumina HumanExome Beadchip array, which contains >240,000 rare and low-frequency coding variants. GenomeStudio clustering and calling was followed by re-calling of ‘no-calls’ using zCall for patients and controls simultaneously. Single variant and gene-based analyses were performed to identify statistically significant associations, applying Bonferroni correction. Following an extra quality control step, candidate variants were selected for validation using Sanger sequencing. Results When we applied a MAF of ≥1.0%, no variants or genes showed statistically significant associations with ARM. Using a MAF cut-off at 0.4%, 13 variants initially reached statistical significance, but had to be discarded upon further inspection: ten variants represented calling errors of the software, while the minor alleles of the remaining three variants were not confirmed by Sanger sequencing. Conclusion Our results show that rare and low-frequency coding variants with large effect sizes, present on the exome chip do not contribute to ARM etiology.
Variational Bayesian Sparse Signal Recovery With LSM Prior

This paper presents a new sparse signal recovery algorithm using variational Bayesian inference based on the Laplace approximation. The sparse signal is modeled as the Laplacian scale mixture (LSM) prior. The Bayesian inference with the Laplacian models is a challenge because the Laplacian prior is not conjugate to the Gaussian likelihood. To solve this problem, we first introduce the inverse-gamma prior, which is conjugate to the Laplacian prior, to model the distinctive scaling parameters of the Laplacian priors. Then the posterior of the sparse signal, approximated by the Laplace approximation, is found to be Gaussian distributed with the expectation being the result of maximum a posterior (MAP) estimation. Finally the expectation-maximization (EM)-based variational Bayesian (VB) inference is utilized to accomplish the sparse signal recovery with the LSM prior. Since the proposed algorithm is a full Bayesian inference based on the MAP estimation, it achieves both the ability of avoiding structural error from the sparse Bayesian learning and the robustness to noise from the MAP estimation. Analysis on experimental results based on both simulated and measured data indicates that the proposed algorithm achieves the state-of-art performance in terms of sparse representation and de-noising.
Salivary Cortisol Awakening Response in Mild Alzheimer Disease, Caregivers, and Noncaregivers

Alterations in the hypothalamic-pituitary-adrenal axis have been noted in people with Alzheimer disease (AD) and in the people caring for them. In a case-control study, we assessed whether the cortisol response at awakening and diurnal cortisol would reflect these changes. AD patients, their caregivers, and healthy senior noncaregivers collected saliva within 5 minutes of waking, 30 minutes after waking, before lunch, 1 hour after lunch, and at 11 pm or when getting ready for bed. They also completed a Perceived Stress Scale. Total cortisol for the day after adjusting for antidepressant use revealed a group effect [F(2,39)=12.49, P<0.0001], with mild AD patients and caregivers having higher cortisol values. Unlike the noncaregivers (t=−1.15, df=14, P>0.27), both cortisol values of the AD caregivers (t=−2.96, df=16, P<0.03) and the AD patients' (t=−2.5, df=14, P<0.01) increased between awakening and 30 minutes afterward. There were also group differences at awakening [F(2,48)=4.6, P=0.012] adjusting for antidepressant use and 30 minutes after waking adjusting for antidepressant use and awakening cortisol [F(2,46)=4.7, P=0.014<0.02). AD patients (r=0.45, P=0.08) and caregivers (r=0.44, P=0.10) with higher cortisol values 30 minutes after waking also showed a trend toward higher perceived stress scores. Salivary cortisol and cortisol response on awakening may enhance future studies relating free cortisol to subjective psychologic and physiologic markers.
Linkage Between Poverty and Smoking in Philadelphia and Its Impact on Future Directions for Tobacco Control in the City

Poverty is linked to negative health consequences and harmful health behaviors such as smoking. Despite this established correlation, few comparative studies have investigated the relationship between local poverty rates and smoking in urban settings through a Social Ecological Model framework. The authors sought to examine the linkage between local poverty rates in Philadelphia, Pennsylvania and adult smoking rates by scrutinizing existing patterns and potential mediating factors via publicly accessible data in established planning districts. The authors determined several individual, interpersonal, organizational, community, and environmental factors, varying across these districts, that impact smoking in Philadelphia. Poverty rates influence the resources, demographic makeup, and number of tobacco retailers a district has, which have downstream effects. The authors recommend that further investment is allocated to planning districts in order to mitigate the risk of smoking.
Dietary Fuels in Athletic Performance.

Focusing on daily nutrition is important for athletes to perform and adapt optimally to exercise training. The major roles of an athlete's daily diet are to supply the substrates needed to cover the energy demands for exercise, to ensure quick recovery between exercise bouts, to optimize adaptations to exercise training, and to stay healthy. The major energy substrates for exercising skeletal muscles are carbohydrate and fat stores. Optimizing the timing and type of energy intake and the amount of dietary macronutrients is essential to ensure peak training and competition performance, and these strategies play important roles in modulating skeletal muscle adaptations to endurance and resistance training. In this review, recent advances in nutritional strategies designed to optimize exercise-induced adaptations in skeletal muscle are discussed, with an emphasis on mechanistic approaches, by describing the physiological mechanisms that provide the basis for different nutrition regimens. Expected final online publication date for the Annual Review of Nutrition Volume 39 is August 21, 2019. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.