Miracle-dz/UniFAR-FTUs huggingface dataset:
The Lifestyle Characteristics in Non-Alcoholic Fatty Liver Disease in the PERSIAN Guilan Cohort Study

BACKGROUND: Non-Alcoholic Fatty Liver Disease (NAFLD) is the most common cause of chronic liver disease worldwide. Since the effect and safety of pharmacotherapy for NAFLD are unknown, the proper management of lifestyle is crucial. AIM: The present study was conducted to determine the status of food, Physical Activity (PA), and sleep in patients with and without NAFLD. METHODS: In this analytical- cross-sectional study, 630 clients with 36-60 years old who referred to the PERSIAN Guilan cohort study were included through simple non-random sampling. The developed questionnaire and lifestyle characteristics, including the status of nutrition, physical activity, and sleep, were completed for all samples. BMI was also calculated by determining weight and height, and fatty liver was confirmed based on abdominal ultrasound. RESULTS: The prevalence of NAFLD in this study was by 43.7% (275 / 630). Smoking, alcohol consumption, BMI, and weight loss over the past six months, regular exercise and exercise intensity, sedentary living, speed of eating, consuming fatty food, red meat, sweets beverages, and use of saturated fatty acid (SFA), and consuming fruits and vegetables were associated with presence of NAFLD (all p < 0.05). However, no significant relationship was observed between the parameters of sleep duration, the interval between dinner and night sleep, consuming breakfast and snack during the day and NAFLD (All p > 0.05). CONCLUSION: The onset and progression of NAFLD are associated with lifestyle. Therefore, dietary therapy solutions, physical activity, and sleep and rest situations should be paid attention for people with or at risk of NAFLD.
Protective Factors and Processes Fostering Resilience and Buffering Psychosocial Distress among Later-Life Egyptian Immigrants

ABSTRACT This qualitative study explores and describes the protective factors and processes that foster resilience and buffer psychosocial distress among later-life Egyptian immigrants post immigration to the US. Open-ended structured interviews were conducted with (30) later-life Egyptian immigrants who came to the United States after turning 60 years of age. Thematic analysis was used to analyze patterns within the data. The findings of this study reveal that the availability and utilization of psychosocial resources – due to opportunities embedded in their sociocultural context and coping strategies embedded in their individual strengths and cultural or religious beliefs – play a pivotal role in buffering the losses and acculturative stressors triggered by transitioning to a new environment. The findings of this study can be used to inform psychosocial and therapeutic interventions and guide the development of appropriate social work programs and services for later-life Egyptian immigrants in particular and older Arabic-speaking immigrants in general.
Editorial: A Brief Retrospective (2013-2019)

In this editorial, we wish to offer: (1) some reflections on my experience as EIC—initially and as I got involved in the role, as well as after I retired from the role; (2) an overview of what JAIS published in the six years of my term—the credit for preparing this part of the article goes to my co-authors; and (3) heartfelt thanks to members of the community for supporting the journal and its EIC.
Identifying Table Structure in Documents using Conditional Generative Adversarial Networks

In many industries, as well as in academic research, information is primarily transmitted in the form of unstructured documents (this article, for example). Hierarchically-related data is rendered as tables, and extracting information from tables in such documents presents a significant challenge. Many existing methods take a bottom-up approach, first integrating lines into cells, then cells into rows or columns, and finally inferring a structure from the resulting 2-D layout. But such approaches neglect the available prior information relating to table structure, namely that the table is merely an arbitrary representation of a latent logical structure. We propose a top-down approach, first using a conditional generative adversarial network to map a table image into a standardised `skeleton' table form denoting approximate row and column borders without table content, then deriving latent table structure using xy-cut projection and Genetic Algorithm optimisation. The approach is easily adaptable to different table configurations and requires small data set sizes for training.
Parallel Machine Translation with Disentangled Context Transformer

State-of-the-art neural machine translation models generate a translation from left to right and every step is conditioned on the previously generated tokens. The sequential nature of this generation process causes fundamental latency in inference since we cannot generate multiple tokens in each sentence in parallel. We propose an attention-masking based model, called Disentangled Context (DisCo) transformer, that simultaneously generates all tokens given different contexts. The DisCo transformer is trained to predict every output token given an arbitrary subset of the other reference tokens. We also develop the parallel easy-first inference algorithm, which iteratively refines every token in parallel and reduces the number of required iterations. Our extensive experiments on 7 directions with varying data sizes demonstrate that our model achieves competitive, if not better, performance compared to the state of the art in non-autoregressive machine translation while significantly reducing decoding time on average.
“DEPOSITION OF CORROSION PRODUCT PARTICLES ONTO HEAT EXCHANGE SURFACES” By:

A program is continuing at UNB Nuclear to investigate the deposition of magnetite particles from suspension in water onto Alloy-800 steam generator tubes. Deposits modify the thermal hydraulic characteristics of the heat transfer surface leading to a decrease in efficiency which is often more severe when boiling or evaporation is involved. We find that the onset of boiling generally enhances the deposition rate. Experiments have been done under sub-cooled boiling conditions, in which microlayer evaporation is believed to be the dominant mechanism and local changes of the chemistry at nucleation sites may affect the particle deposition rate. A continuation of this work is to investigate the effect of bulk boiling on the deposition rate and to examine any additional mechanisms which may be involved. This entails modifying the microlayer evaporation concept to include severe local turbulence effects.
Rituximab-Containing Treatment Regimens May Imply a Long-Term Risk for Difficult-To-Treat Chronic Hepatitis E

Hepatitis E virus (HEV) infection is an emerging disease in industrialized countries which is usually characterized by a self-limited course. However, there is an increased risk of HEV persistence in immunocompromised risk populations, comprising patients following solid organ transplantation or hematological malignancies. Recently, chronic HEV infection following rituximab-containing treatment regimens has been described. Here we report five patients with chronic hepatitis E after prior rituximab therapy for various indications. We determined the immunological characteristics of these patients and analyzed the development of ribavirin (RBV) treatment failure-associated mutations in the HEV genome. One patient became chronically HEV-infected 110 months after administration of rituximab (RTX). Immunological characterization revealed that all patients exhibited significant hypogammaglobulinemia and CD4+ T cell lymphopenia. One patient permanently cleared HEV following weight-based ribavirin treatment while three patients failed to reach a sustained virological response. In depth mutational analysis confirmed the presence of specific mutations associated with RBV treatment failure in these patients. Our cases indicate that rituximab-containing treatment regimens might imply a relevant risk for persistent HEV infection even years after the last rituximab application. Moreover, we provide further evidence to prior observations suggesting that chronically HEV infected patients following RTX-containing treatment regimens might be difficult to treat.
Using elastic nets to estimate frailty burden from routinely collected national aged care data

OBJECTIVES To (1) use an elastic net (EN) algorithm to derive a frailty measure from a national aged care eligibility assessment program; (2) compare the ability of EN-based and a traditional cumulative deficit (CD) based frailty measures to predict mortality and entry into permanent residential care; (3) assess if the predictive ability can be improved by using weighted frailty measures. MATERIALS AND METHODS A Cox proportional hazard model based EN algorithm was applied to the 2003-2013 cohort of 903 996 participants for selecting items to enter an EN based frailty measure. The out-of-sample predictive accuracy was measured by the area under the curve (AUC) from Cox models fitted to 80% training and validated on 20% testing samples. RESULTS The EN approach resulted in a 178-item frailty measure including items excluded from the 44-item CD-based measure. The EN based measure was not statistically significantly different from the CD-based approach in terms of predicting mortality (AUC 0.641, 95% CI: 0.637-0.644 vs AUC 0.637, 95% CI: 0.634-0.641) and permanent care entry (AUC 0.626, 95% CI: 0.624-0.629 vs AUC 0.627, 95% CI: 0.625-0.63). However, the weighted EN based measure statistically outperforms the weighted CD measure for predicting mortality (AUC 0.774, 95% CI: 0.771-0.777 vs AUC 0.757, 95% CI: 0.754-0.760) and permanent care entry (AUC 0.676, 95% CI: 0.673-0.678 vs AUC 0.671, 95% CI: 0.668-0.674). CONCLUSIONS The weighted EN and CD-based measures demonstrated similar prediction performance. The CD-based measure items are relevant to frailty measurement and easier to interpret. We recommend using the weighted and unweighted CD-based frailty measures.
The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts

Objective: Nonsyndromic oral clefts are common birth defect with complex etiology. In the present study, we attempt to further validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. Design: We performed allelic transmission disequilibrium test analysis, on 10 eligible single nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test. Participants: The study sample consisted of 334 case–parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. Results: We found only the SNP rs560426 within the ABCA4 gene showed strong association with NSCPO (P = .03498; Permuted P = .05382). No association between other 9 selected SNPs in ABCA4-ARHGAP29 region and the risk of nonsyndromic oral clefts was found. For the haplotype analyses, we found only haplotype T-C (rs570926 and rs3789431) in ABCA4 block 2 showed significant association with nonsyndromic NSCL/P in these Taiwanese trios. Conclusions: We used a family-based analysis in 334 Taiwanese case–parent trios to validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. This study provides a new evidence for an association between the intron variant rs560426 within ABCA4 and nonsyndromic cleft palate which may contribute their regulatory role in craniofacial development.
Genetic diversity and population structure of feral rapeseed (Brassica napus L.) in Japan

Rapeseed (Brassica napus L.) is one of the most economically important oilseed crops worldwide. In Japan, it has been cultivated for more than a century and has formed many feral populations. The aim of this study was to elucidate the genetic diversity of feral rapeseeds by genotyping 537 individuals (among which 130 were determined to be genetically modified) sampled from various regions in Japan. Analysis of 30 microsatellite markers amplified 334 alleles and indicated moderate genetic diversity and high inbreeding (expected heterozygosity, 0.50; observed heterozygosity, 0.16; inbreeding coefficient within individuals, 0.68) within the feral populations. The Mantel test showed only an insignificant weak positive correlation between geographic distance and genetic distance. Analysis of molecular variance showed a greater genetic diversity among individuals than between populations. These results are in accordance with population structure assessed by using principal coordinate analysis and the program STRUCTURE, which showed that the 537 individuals could be assigned to 8 genetic clusters with very large genetic differences among individuals within the same geographic population, and that among feral individuals, many are closely related to rapeseed accessions in the NARO Genebank but some have unknown origins. These unique feral rapeseeds are likely to be affected by strong selection pressure. The results for genetically modified individuals also suggest that they have two different sources and have a considerable degree of diversity, which might be explained by hybridization with nearby individuals and separation of hybrid cultivars. The information obtained in this study could help improve the management of feral rapeseed plants in Japan.
Integrating Cognition with an Affective Lens to Better Understand Information Security Policy Compliance

Information systems security behavioral research has primarily focused on individual cognitive processes and their impact on information security policy noncompliance. However, affective processes (operationalized by affective absorption and affective flow) may also significantly contribute to misuse or information security policy noncompliance. Our research study evaluated the impact of affective absorption (i
Role of Laparotomy-based Parameters in Assessment of Optimal Primary Debulking Surgery and Long-term Outcomes in Patients with Stage IIIC Epithelial Ovarian Cancer

We evaluated the ability of our two laparotomy-based models to predict optimal primary debulking surgery (PDS) and long-term outcomes of stage IIIC epithelial ovarian cancer (EOC). Data of 400 IIIC EOC patients who underwent laparotomy were retrospectively analyzed. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and overall accuracy were calculated for 10 parameters. The parameters with a specificity ≥75%, PPV ≥50%, and NPV ≥50% were included in the final predictive index value (PIV) model. Peritoneal cancer index (PCI) was calculated summarizing lesion size scores (LSSs) of 13 regions. Receiver operating characteristic (ROC) curve was used to assessed the predictive value of PIV and PCI for optimal PDS. Univariate and multivariate analyses were performed to assess the prognostic value of PIV and PCI. After PDS, 223 (55.8%) patients with RD ≤1 cm had longer progression-free survival (PFS) and overall survival (OS) than patients with RD >1 cm (PFS: 22.4 vs. 15.4 months, respectively; P < 0.001 and OS: 48.6 vs. 35.6 months; P < 0.001). PCI better predicted optimal PDS than PIV (The area under the curve of ROC: PCI 0.79 vs. PIV 0.75). The predictive value of PIV and PCI models was verified using another cohort of 77 patients. And PIV and PCI models were demonstrated to be more powerful than the published laparoscopy-based predictive index (LPS-PI) model. Patients with a PIV ≥14 were more likely to undergo suboptimal PDS with a specificity of 100%. The median PFS and OS of patients with PIV < 3 were significantly longer than patients with PIV > 3 (PFS: 19.5 vs. 16.3 months, P = 0.007; OS: 46.1 vs. 37.0 months, P = 0.009). The median PFS and OS of patients with the PCI < 17.5 were significantly longer than patients with the PCI > 17.5 (PFS: 22.9 vs. 14.5 months, P < 0.001; OS: 54.3 vs. 31.5 months, P < 0.001). PCI could better predict optimal PDS compared with PIV. PCI was an independent prognostic factor for long-term outcome of IIIC EOC patients.
Correlations of HIV Preexposure Prophylaxis Indications and Uptake, Chicago, Illinois, 2015-2018.

Objectives. To examine gaps in identification of preexposure prophylaxis (PrEP) candidates, uptake, and use of PrEP by populations most likely to seroconvert.Methods. At a federally qualified health center in Chicago, Illinois, we used electronic medical records, prescription data, and our best approximation of Centers for Disease Control and Prevention PrEP guidelines to determine how many patients were indicated for PrEP relative to HIV diagnoses (indication:HIV), how many were on PrEP relative to indications (PrEP:indication), and how many were on PrEP relative to HIV diagnoses (PrEP:HIV). We compared these ratios across age, gender and orientation, race/ethnicity, and insurance.Results. Overall, there were 32 indications per incident diagnosis and 16 patients on PrEP per incident diagnosis. In adjusted models, Whites had higher indication:HIV and PrEP:HIV ratios compared with Blacks, men who have sex with men had higher indication:HIV and PrEP:HIV ratios compared with transwomen but lower PrEP:indication ratios, and uninsured patients had higher indication:HIV but lower PrEP:indication and PrEP:HIV ratios compared with those with insurance.Conclusions. PrEP use, relative to HIV diagnoses, differs by important patient characteristics. While improved guidelines will address some of the disparity, better approaches for determining PrEP candidates and more normalized patient-provider communication are needed to ensure better PrEP access to all individuals at high risk for HIV. (Am J Public Health. Published online ahead of print January 16, 2020: e1-e8. doi:10.2105/AJPH.2019.305469).
Interobserver Variability in the Diagnosis of High-Grade Prostatic Intraepithelial Neoplasia in a Tertiary Hospital in Northern Jordan

Prostate intraepithelial neoplasia is described as a precursor lesion to prostatic adenocarcinoma. High-grade prostate intraepithelial neoplasia (HGPIN) is classified as both grade 2 and 3 prostate intraepithelial neoplasia due to inconsistency between pathologists’ findings. In our study, we assessed the interobserver variability in the diagnosis of HGPIN among genitourinary and nongenitourinary pathologists. All cases with prostate adenocarcinoma diagnosis on needle core biopsy, radical prostatectomy, and transurethral resection of prostate (TURP) between the years 2005 and 2014 were included. In total, 191 prostate cancer cases were included: 109 needle core biopsies, 45 radical prostatectomies, and 37 TURP. All were independently reviewed by 2 urologic pathologists for the presence of HGPIN. High-grade prostate intraepithelial neoplasia was diagnosed in 65 cases (34%), among which the lesion was recognized by the reporting pathologists in 36 (55%) of the cases and was missed in 29 (45%) of the cases with a κ coefficient of 0.53. There was a moderate interobserver agreement in the diagnosis of HGPIN. Consultation with genitourinary pathologist can improve HGPIN diagnosis.
Filtering the NPP-VIIRS Nighttime Light Data for Improved Detection of Settlements in Africa

Observing and understanding changes in Africa is a hotspot in global ecological environmental research since the early 1970s. As possible causes of environmental degradation, frequent droughts and human activities attracted wide attention. Remote sensing of nighttime light provides an effective way to map human activities and assess their intensity. To identify settlements more effectively, this study focused on nighttime light in the northern Equatorial Africa and Sahel settlements to propose a new method, namely, the patches filtering method (PFM) to identify nighttime lights related to settlements from the National Polar-orbiting Partnership Visible Infrared Imaging Radiometer Suite (NPP-VIIRS) monthly nighttime light data by separating signal components induced by biomass burning, thereby generating a new annual image in 2016. The results show that PFM is useful for improving the quality of NPP-VIIRS monthly nighttime light data. Settlement lights were effectively separated from biomass burning lights, in addition to capturing the seasonality of biomass burning. We show that the new 2016 nighttime light image can very effectively identify even small settlements, notwithstanding their fragmentation and unstable power supply. We compared the image with earlier NPP-VIIRS annual nighttime light data from the National Oceanic and Atmospheric Administration (NOAA) National Center for Environmental Information (NCEI) for 2016 and the Sentinel-2 prototype Land Cover 20 m 2016 map of Africa released by the European Space Agency (ESA-S2-AFRICA-LC20). We found that the new annual nighttime light data performed best among the three datasets in capturing settlements, with a high recognition rate of 61.8%, and absolute superiority for settlements of 2.5 square kilometers or less. This shows that the method separates biomass burning signals very effectively, while retaining the relatively stable, although dim, lights of small settlements. The new 2016 annual image demonstrates good performance in identifying human settlements in sparsely populated areas toward a better understanding of human activities.
The Vibrio cholerae MARTX toxin silences the inflammatory response to cytoskeletal damage before inducing actin cytoskeleton collapse

The multifunctional MARTX toxin of Vibrio cholerae damages host cells and suppresses the innate response to that damage. Why Vibrio cholerae infection is noninflammatory The MARTX toxin of Vibrio cholerae (MARTXVc) forms a pore in the plasma membrane and translocates multiple toxin effector domains into intestinal epithelial cells (IECs). These include an actin cross-linking domain (ACD), a Rho inactivation domain (RID), and an α/β hydrolase domain (ABH), as well as a protease that releases these effectors into the host cytoplasm. Using human IECs in an in vitro model of infection, Woida and Satchell found that RID and ABH suppressed proinflammatory signaling that would otherwise have been activated by the cytoskeleton-damaging effects of ACD. These results reveal how the MARTXVc effector domains simultaneously promote virulence and suppress inflammatory responses and may explain why cholera is a noninflammatory disease. Multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are pore-forming bacterial toxins that translocate multiple functionally independent effector domains into a target eukaryotic cell. Vibrio cholerae colonizes intestinal epithelial cells (IECs) and uses a MARTX toxin with three effector domains—an actin cross-linking domain (ACD), a Rho inactivation domain (RID), and an α/β hydrolase domain (ABH)—to suppress innate immunity and enhance colonization. We investigated whether these multiple catalytic enzymes delivered from a single toxin functioned in a coordinated manner to suppress intestinal innate immunity. Using cultured human IECs, we demonstrated that ACD-induced cytoskeletal collapse activated extracellular signal–regulated kinase, p38, and c-Jun amino-terminal kinase mitogen-activated protein kinase (MAPK) signaling to elicit a robust proinflammatory response characterized by the secretion of interleukin-8 (IL-8; also called CXCL8) and the expression of CXCL8, tumor necrosis factor (TNF), and other proinflammatory genes. However, RID and ABH, which are naturally delivered together with ACD, blocked MAPK activation through Rac1 and thus prevented ACD-induced inflammation. RID also abolished IL-8 secretion induced by heat-killed bacteria, TNF, or latrunculin A. Thus, MARTX toxins use enzymatic multifunctionality to silence the host response to bacterial factors and to the damage caused by the toxins. Furthermore, these data show how V. cholerae MARTX toxin suppresses intestinal inflammation and contributes to cholera being classically defined as a noninflammatory diarrheal disease.