Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a risk management framework to improve public health outcomes by enumerating Salmonella in ground turkey

Abstract Salmonella spp. continue to be a leading cause of foodborne morbidity worldwide. To assess the risk of foodborne disease, current national regulatory schemes focus on prevalence estimates of Salmonella and other pathogens. The role of pathogen quantification as a risk management measure and its impact on public health is not well understood. To address this information gap, a quantitative risk assessment model was developed to evaluate the impact of pathogen enumeration strategies on public health after consumption of contaminated ground turkey in the USA. Public health impact was evaluated by using several dose–response models for high- and low-virulent strains to account for potential under- or overestimation of human health impacts. The model predicted 2705–21 099 illnesses that would result in 93–727 reported cases of salmonellosis. Sensitivity analysis predicted cooking an unthawed product at home as the riskiest consumption scenario and microbial concentration the most influential input on the incidence of human illnesses. Model results indicated that removing ground turkey lots exceeding contamination levels of 1 MPN/g and 1 MPN in 25 g would decrease the median number of illnesses by 86–94% and 99%, respectively. For a single production lot, contamination levels higher than 1 MPN/g would be needed to result in a reported case to public health officials. At contamination levels of 10 MPN/g, there would be a 13% chance of detecting an outbreak, and at 100 MPN/g, the likelihood of detecting an outbreak increases to 41%. Based on these model prediction results, risk management strategies should incorporate pathogen enumeration. This would have a direct impact on illness incidence linking public health outcomes with measurable food safety objectives.
Biological Fixed Film

The review includes literature published during the year 2012 regarding the use of biofilms and bioreactors to treat wastewater. Topics considered are: biofilm formation and factors that impact biofilm formation; extracellular polymeric substance and its extraction from biofilms; biofilm consortia and quorum sensing; biofilm imaging techniques; biofilm reactors and modeling.
Long term outcome of EUS-based strategy for suspected choledocholithiasis but negative CT finding

Abstract Objectives: The American Society for Gastrointestinal Endoscopy (ASGE) guidelines offered the risk-stratified approach in suspected choledocholithiasis. Previous studies have raised concern about the insufficient accuracy of the guideline, especially in high probability group. The purposes of this study were to authenticate the stratification and clinical predictors of the guidelines for suspected choledocholithiasis with no visible choledocholithiasis on computed tomography (CT) and to make clear the clinical strategy of endoscopic ultrasonography (EUS). Materials and methods: We carried out the retrospective single-center study of 156 patients with suspected choledocholithiasis but negative findings on CT who underwent EUS for about 8 years at Samsung Medical Center. We assessed the clinical predictors of the ASGE guidelines in predicting the presence of choledocholithiasis and the outcome of the EUS. Results: Fifty-three of the 156 patients had positive findings on EUS that included choledocholithiasis (n = 43, 27.6%) or obstructive papillitis (n = 10, 6.4%). Among the 53 patients, 51 (96.2%) had choledocholithiasis or obstructive papillitis on ERCP. The 101 patients of 103 patients with negative finding on EUS did not show biliary events during follow-up period. EUS accuracy was 98.7% (sensitivity 100%; specificity 98.1%). Among the 49 patients with high probability, 21 (42.9%) had choledocholithiasis on ERCP. In 107 patients who were classified as intermediate probability, 30 (27.3%) had choledocholithiasis. There were no complications related to EUS. Conclusions: Not only intermediate probability group but also high probability group without definite acute cholangitis may require EUS. Application of EUS for suspected choledocholithiasis is highly accurate, safe and reduces unnecessary invasive ERCP in 57.1% of patients with high probability group.
Effect of Quercetin Monoglycosides on Oxidative Stress and Gut Microbiota Diversity in Mice with Dextran Sodium Sulphate-Induced Colitis

The pathogenesis of inflammatory bowel disease (IBD) is linked to an intricate association of environmental, microbial, and host-related factors. This study examined the potential effects of dietary addition of two preparations from onion, one comprising quercetin aglycone alone (Q: 0.15% polyphenols, quercetin aglycone:quercetin monoglycosides, 98:2) and another comprising quercetin aglycone with monoglycosides (Q+MQ: 0.15% total polyphenols, quercetin aglycone:quercetin monoglycosides, 69:31), on dextran sodium sulphate- (DSS-) induced colitis in mice. The results revealed a significant decrease in the body weight gain of the mice with DSS-induced colitis, which was counteracted by the dietary Q or Q+MQ supplementation. Meanwhile, the oxidative stress indicated by myeloperoxidase (MPO), reduced glutathione (GSH), malondialdehyde (MDA), and serum nitrate (NO) concentrations was higher in mice with DSS-induced colitis than in the control group mice, but dietary Q or Q+MQ supplementation counteracted this trend. The colitis mice demonstrated reduced Chao1, angiotensin-converting enzyme (ACE), and Shannon indices and an increased Simpson index, but the colitis mice receiving dietary Q or Q+MQ exhibited higher Chao1, ACE, and Shannon indices and a reduced Simpson index. In conclusion, this research showed that even at a low dose, dietary Q or Q+MQ supplementation counteracts DSS-induced colitis in mice, indicating that Q or Q+MQ may be used as an adjuvant therapy for IBD patients.
Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm

Reassortment of influenza viral RNA (vRNA) segments in co-infected cells can lead to the emergence of viruses with pandemic potential. Replication of influenza vRNA occurs in the nucleus of infected cells, while progeny virions bud from the plasma membrane. However, the intracellular mechanics of vRNA assembly into progeny virions is not well understood. Here we used recent advances in microscopy to explore vRNA assembly and transport during a productive infection. We visualized four distinct vRNA segments within a single cell using fluorescent in situ hybridization (FISH) and observed that foci containing more than one vRNA segment were found at the external nuclear periphery, suggesting that vRNA segments are not exported to the cytoplasm individually. Although many cytoplasmic foci contain multiple vRNA segments, not all vRNA species are present in every focus, indicating that assembly of all eight vRNA segments does not occur prior to export from the nucleus. To extend the observations made in fixed cells, we used a virus that encodes GFP fused to the viral polymerase acidic (PA) protein (WSN PA-GFP) to explore the dynamics of vRNA assembly in live cells during a productive infection. Since WSN PA-GFP colocalizes with viral nucleoprotein and influenza vRNA segments, we used it as a surrogate for visualizing vRNA transport in 3D and at high speed by inverted selective-plane illumination microscopy. We observed cytoplasmic PA-GFP foci colocalizing and traveling together en route to the plasma membrane. Our data strongly support a model in which vRNA segments are exported from the nucleus as complexes that assemble en route to the plasma membrane through dynamic colocalization events in the cytoplasm.
Validation of a Questionnaire for Personality Profiling using Cognitive Diagnostic Modeling

Abstract This article describes the development of the ENCUIST (Extroversion, Neuroticism, Callous-Unemotional, Instability, Short-Test) questionnaire, which has been created to provide a personality profiling method based on a cognitive diagnostic modeling framework. The ENCUIST measures the attributes of extroversion, neuroticism, callous unemotionality and overt expressions of anger that are relevant in a forensic context. The scores provided by the ENCUIST are binary classifications of the individuals (high/low) in these attributes. The ENCUIST was developed using a sample of 516 subjects to study its validation through psychometric procedures, including factor analysis, cognitive diagnostic modeling and structural equation modeling. The results supported a four-factor structure. Linear regressions were used to evaluate the predictive validity of the scores provided by ENCUIST with respect to two external criteria that are relevant in the forensic context, namely behavioral activation and behavioral inhibition. The results showed that the extroversion dimension is positively related to behavioral activation, although the effect size is modest and the proportion of explained variance is only 11%. Moreover, the dimensions of neuroticism and anger expression are positively related to behavioral inhibition, with 7% of the variance explained. Together, these results suggest that cognitive diagnostic models are useful tools for the elaboration of personality profiles based on classifying subjects along binary attributes.
Measuring Dynamic Leg Length during Normal Gait

Dynamic leg length [DLL] is a resultant factor of anatomic leg length and lower limb movement that is measured by the distance from the hip to the heel, ankle, and forefoot during the gait cycle. The aim of this study was to present DLL measurement during normal gait. Forty healthy participants underwent a gait evaluation using a motion analysis system. The average DLLs were compared between sides during the gait cycle using the paired t-test at 51 sample points. Time of maximal and minimal DLLs and the ratio between maximal and minimal DLLs during the gait cycle were calculated. DLLs were found to be consistent, indicated by a within standard deviation of <6.65 mm and by being symmetrical with no significant differences between sides [p > 0.103]. DLL patterns and time of maximal and minimal DLLs were established. The ratio between maximal DLLs during the stance phase and minimal DLLs during the swing phase was also defined and found to be symmetrical. Normative data of DLL measures were set with respect to magnitude and pattern during the gait cycle. These data might serve as a reference for abnormal gait deviation reflected by abnormal DLLs, thus promoting a new perspective in gait analysis.
Role of FGF signalling in neural crest cell migration during early chick embryo development

Summary Fibroblast growth factor (FGF) signalling acts as one of modulators that control neural crest cell (NCC) migration, but how this is achieved is still unclear. In this study, we investigated the effects of FGF signalling on NCC migration by blocking this process. Constructs that were capable of inducing Sprouty2 (Spry2) or dominant-negative FGFR1 (Dn-FGFR1) expression were transfected into the cells making up the neural tubes. Our results revealed that blocking FGF signalling at stage HH10 (neurulation stage) could enhance NCC migration at both the cranial and trunk levels in the developing embryos. It was established that FGF-mediated NCC migration was not due to altering the expression of N-cadherin in the neural tube. Instead, we determined that cyclin D1 was overexpressed in the cranial and trunk levels when Sprouty2 was upregulated in the dorsal neural tube. These results imply that the cell cycle was a target of FGF signalling through which it regulates NCC migration at the neurulation stage.
Association of the human aryl hydrocarbon receptor repressor (AhRR)‐c.565C>G transversion with male infertility: A case‐control study from Iran

Dioxins (eg, 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin/TCDD), as environmental endocrine disruptors and toxic carcinogens, can affect male reproductive health. The influence of dioxins is mediated via the aryl hydrocarbon receptor (AhR) pathway and its repressor (AhRR). In this study, we investigated the association of AhRR‐c.565C>G transversion polymorphism with male infertility. In a hospital‐based case‐control study, 221 semen samples (111 infertile and 110 healthy controls) based on World Health Organization guidelines were collected from in vitro fertilization centers of Babol, Iran. The AhRR‐c.565C>G (rs2292596) polymorphism was genotyped using a polymerase chain reaction‐restriction fragment length polymorphism analysis. The difference in the allele frequency of AhRR‐c.565C>G transversion polymorphism did not reach a significant level. The genotype frequency was statistically significantly different between fertile and infertile men. We found that polymorphism rs2292596 (Pro185Ala) was statistically significantly associated with the risk of male infertility. In addition, the statistical difference became more significant when the frequency was compared between the Pro/Pro genotype and the Pro/Ala plus Ala/Ala genotype. The 185 Pro wild‐type alleles of AhRR may be associated with the risk of male infertility. The proallele also may diminish inhibition of AhR‐mediated signaling of exposure to environmental pollutants.
From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data.

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies.
Transplanting HCV-Infected Kidneys into Uninfected Recipients.

n engl j med 377;11 nejm.org September 14, 2017 facilitate rapid implementation of the intervention in large numbers of patients by the clinical staff at different institutions, all in the chaos of emergency departments; and to avoid potential responder bias in the outcome assessments of patients (or surrogates) who may have thought they had received “nonstandard” care. Our decision to view the matter of head position as involving “low risk” was based on several considerations: the insufficient amount of level 1 evidence specifying the benefits and harms of head positioning for patients with acute stroke; the fact that people change their head position within the ranges being tested during routine hospital care and in daily life, as they shift from activity during the day to rest and sleep at night; and the view that patient care would not be compromised by either of the interventions. Finally, Taito and Yamauchi raise an important point regarding an unresolved issue that should be addressed in another trial — that of the appropriate timing (and intensity) of early mobilization after acute stroke that follows from the unexpected results of the AVERT trial.2 Unfortunately, we did not collect data on the specific time that patients began to move outside the confines of the bed.
DoseNet: a volumetric dose prediction algorithm using 3D fully-convolutional neural networks

The goal of this study is to demonstrate the feasibility of a novel fully-convolutional volumetric dose prediction neural network (DoseNet) and test its performance on a cohort of prostate stereotactic body radiotherapy (SBRT) patients. DoseNet is suggested as a superior alternative to U-Net and fully connected distance map-based neural networks for non-coplanar SBRT prostate dose prediction. DoseNet utilizes 3D convolutional downsampling with corresponding 3D deconvolutional upsampling to preserve memory while simultaneously increasing the receptive field of the network. DoseNet was implemented on 2 Nvidia 1080 Ti graphics processing units and utilizes a 3 phase learning protocol to help achieve convergence and improve generalization. DoseNet was trained, validated, and tested with 151 patients following Kaggle completion rules. The dosimetric quality of DoseNet was evaluated by comparing the predicted dose distribution with the clinically approved delivered dose distribution in terms of conformity index, heterogeneity index, and various clinically relevant dosimetric parameters. The results indicate that the DoseNet algorithm is a superior alternative to U-Net and fully connected methods for prostate SBRT patients. DoseNet required ~50.1 h to train, and ~0.83 s to make a prediction on a 128 × 128 × 64 voxel image. In conclusion, DoseNet is capable of making accurate volumetric dose predictions for non-coplanar SBRT prostate patients, while simultaneously preserving computational efficiency.
Spectral clustering with distinction and consensus learning on multiple views data

Since multi-view data are available in many real-world clustering problems, multi-view clustering has received considerable attention in recent years. Most existing multi-view clustering methods learn consensus clustering results but do not make full use of the distinct knowledge in each view so that they cannot well guarantee the complementarity across different views. In this paper, we propose a Distinction based Consensus Spectral Clustering (DCSC), which not only learns a consensus result of clustering, but also explicitly captures the distinct variance of each view. It is by using the distinct variance of each view that DCSC can learn a clearer consensus clustering result. In order to optimize the introduced optimization problem effectively, we develop a block coordinate descent algorithm which is theoretically guaranteed to converge. Experimental results on real-world data sets demonstrate the effectiveness of our method.
Patient and provider perceptions of a comprehensive care program for HIV-positive adults over 50 years of age: The formation of the Golden Compass HIV and aging care program in San Francisco

Objective People living with HIV (PLWH) are living longer and developing comorbidities and aging-related syndromes. New care models are needed to address the combined burden and complexity of HIV and its comorbidities in this group. The goal of this study is to describe qualitative data from patients and providers that informed the development of a comprehensive care model for older PLWH. Methods Patient and provider perspectives on the clinical care and service needs of patients living and aging with HIV were explored via surveys and focus groups at a safety net HIV clinic in San Francisco. We surveyed 77 patients and 26 providers and conducted separate focus groups of older patients living with HIV (n = 31) and staff (n = 20). Transcripts were analyzed using thematic analysis. Themes for a care program were additionally explored using findings from the literature on HIV and aging. Findings Themes from surveys and focus groups emphasized (a) the need for knowledge expertise in HIV and aging, (b) focus on medical conditions and determinants of health of particular import (e.g. marginal housing) among older PLWH, (c) co-locating specialty services (e.g. cardiology, geriatrics) with primary care, and (d) addressing social isolation. Findings informed the design of a comprehensive, multidisciplinary care model for PLWH called the Golden Compass program composed of four “points”: Heart and Mind (North), Bones and Strength (East), Network and Navigation (South), and Dental, Hearing, and Vision (West). Conclusion Based on patient and clinic staff perspectives from surveys and focus groups, we designed a multidisciplinary program of integrated primary and specialty care, as well as housing and social support, to address the needs of older PLWH within a safety-net infrastructure. Golden Compass launched in 2017 for PLWH older than 50 years. Future research to evaluate the effectiveness of this care program in improving patient outcomes and satisfaction is ongoing.
Diosmetin inhibits osteoclast formation and differentiation and prevents LPS‐induced osteolysis in mice

Osteolytic bone diseases are closely linked to the over‐activation of osteoclasts and enhancement of bone resorption. It has become a major health issue in orthopedic practice worldwide. Inhibition of osteoclasts is proposed to be the main treatment for osteolytic disorders. Diosmetin (DIO) is a natural flavonoid with properties of antioxidant, anti‐infection, and antishock. The effect of DIO on osteoclast differentiation is poorly understood. In this study project, we found that DIO could inhibit osteoclastic formation induced by receptor activator of nuclear factor kappa‐B ligand (RANKL) in a dose‐dependent manner. The expression of the osteoclast differentiation marker genes, cathepsin K, nuclear factor of activated T‐cells 1 (NFATc1), Acp5, Ctr, Atp6v0d2, and Mmp9 were also decreased by the treatment of DIO. In addition, DIO attenuated the formation of actin ring and the ability of bone resorption. Further, the western blotting showed that DIO inhibits the phosphorylation of the mitogen‐activated protein kinases signaling pathway induced by RANKL, accompanied by the downregulation of NFATc1 and c‐Fos expression. We also found that DIO could reduce the accumulation of reactive oxygen species (ROS) induced by RANKL. In vivo, the study revealed that DIO can significantly reduce LPS‐induced osteolysis in mice. Collectively, our study shows that DIO can inhibit osteoclast formation and activation, and could serve as a potential therapeutic drug for osteolytic bone diseases.
Significantly more intense pain in methadone-maintained patients who are addicted to nicotine

Pain and cigarette smoking are very common in heroin-dependent patients (HDPs) receiving methadone maintenance treatment (MMT) and both have substantial negative effects on HDPs' physical and mental health. Nevertheless, very few studies have assessed the relationship between the two in HDPs. This study examined the association between pain intensity and smoking in Chinese methadone-maintained HDPs. A total of 603 HDPs were consecutively recruited from three MMT clinics in Wuhan, China, and administered with a socio-demographic and drug use questionnaire, a smoking questionnaire concerning average number of cigarettes smoked daily and Heaviness of Smoking Index, and Zung's Self-rating Depression Scale. We used a five-point Verbal Rating Scale to rate the intensity of pain. To determine whether pain's associations with smoking and nicotine dependence were independent, an analysis of covariance was adopted to control for the potential confounding effects of socio-demographic variables, drug use characteristics, and depressive symptoms. Net of potential confounders, in methadone-maintained HDPs, pain intensity was significantly higher in smoker than non-smokers (F = 11.836, P = 0.002) but the pain intensity did not differ significantly across patients with various levels of cigarette consumption (F = 1.992, P = 0.137), while the pain intensity significantly differed across patients with different levels of nicotine dependence (F = 3.252, P = 0.013). Pain is significantly associated with smoking in HDPs receiving MMT, this phenomenon may be explained by the association between nicotine dependence and pain.