Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of tacrolimus on skin microbiome in atopic dermatitis

1. Carey MA, Card JW, Voltz JW, et al. It's all about sex: gender, lung development and lung disease. Trends Endocrinol Metab. 2007;18:308‐313. 2. Wolterink R, Kleinjan A, van Nimwegen M, et al. Pulmonary innate lymphoid cells are major producers of IL‐5 and IL‐13 in murine models of allergic asthma. Eur J Immunol. 2012;42:1106‐1116. 3. Laffont S, Blanquart E, Savignac M, et al. Androgen signaling negatively controls group 2 innate lymphoid cells. J Exp Med. 2017;214: 1581‐1592. 4. Kadel S, Ainsua-Enrich E, Haripoglu I, et al. A major population of functional KLRG1– ILC2s in female lungs contributes to a sex bias in ILC2 numbers. Immunohorizons. 2018;2:74‐86. 5. Cephus JY, Stier MT, Fuseini H, et al. Testosterone attenuates group 2 innate lymphoid cell‐mediated airway inflammation. Cell Rep. 2017;21:2487‐2499. 6. Chen R, Smith SG, Salter B, et al. Allergen‐induced increases in sputum levels of group 2 innate lymphoid cells in subjects with asthma. Am J Respir Crit Care Med. 2017;196:700‐712. 7. Smith SG, Chen R, Kjarsgaard M, et al. Increased numbers of activated group 2 innate lymphoid cells in the airways of patients with severe asthma and persistent airway eosinophilia. J Allergy Clin Immunol. 2016;137:75‐86. 8. Morrison D, Capewell S, Reynolds P, et al. Testosterone levels during systemic and inhaled corticosteroid therapy. Respir Med. 1994;88 (9):659‐663. 9. Brestoff JR, Kim BS, Saenz SA, et al. Group 2 innate lymphoid cells promote beiging of white adipose tissue and limit obesity. Nature. 2014;519:242.
Nutritional Regime, Post-Slaughter Conditioning Temperature, and Vacuum Packaging Effects on Bacteriology of Beef Carcasses and Retail Meat Cuts 1.

Thirty-eight crossbred steers were used to evaluate effects of nutritional regime (grass-, short-, long-, and forage-fed) and post-slaughter chilling (3 C) and conditioning temperature (13 C) on carcass psychrotrophic and mesophilic bacterial counts. Inside chucks from right halves of carcasses chilled at 3 C for 48 h were used to evaluate effects of nutritional regime and vacuum packaging on total aerobic and anaerobic bacterial counts. Psychrotrophic and mesophilic mean bacterial counts tended to decrease from 1 to 46 h postmortem regardless of temperature treatment. At 46 h postmortem, the forage-fed group mean psychrotrophic count was significantly lower (P < 0.05) than that for any of the other feeding regimes. Mesophilic mean counts were significantly different (P < 0.05) at 46 h postmortem (grass-fed >short-fed >long-fed > forage-fed). Carcass halves chilled at 3 C for 46 h had lower total psychrotrophic and mesophilic mean bacterial counts than did corresponding halves conditioned at 13 C for 8 h then chilled at 3 C for 38 h. Total aerobic and anaerobic counts tended to remain constant or decrease slightly during vacuum storage for 21 days at 0 to 1 C. Both aerobic and anaerobic counts on vacuum-stored cuts from carcasses of grass-fed steers were significantly higher (P < 0.05) than other feeding-regime means. Aerobic and anaerobic counts on vacuum-stored cuts from carcasses of short-, long-, and forage-fed steers were statistically similar. All carcass and inside-chuck bacterial counts were well within acceptable limits. Scalpel-template sampling was considered to be a significant improvement over previously used methods.
An Efficient Approximation Algorithm for Finding a Maximum Clique Using Hopfield Network Learning

In this article, we present a solution to the maximum clique problem using a gradient-ascent learning algorithm of the Hopfield neural network. This method provides a near-optimum parallel algorithm for finding a maximum clique. To do this, we use the Hopfield neural network to generate a near-maximum clique and then modify weights in a gradient-ascent direction to allow the network to escape from the state of near-maximum clique to maximum clique or better. The proposed parallel algorithm is tested on two types of random graphs and some benchmark graphs from the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS). The simulation results show that the proposed learning algorithm can find good solutions in reasonable computation time.
High-throughput Automated Single Cell Imaging Analysis Reveals Dynamics Of Glioblastoma Stem Cell Population During State Transition

Cancer stem cells (CSCs) are a heterogeneous and dynamic population that stands at the top of tumor cellular hierarchy and is responsible for maintenance of the tumor microenvironment. As methods of CSC isolation and functional interrogation advance, there is a need for a reliable and accessible quantitative approach to assess heterogeneity and state transition dynamics in CSCs. We developed a High-throughput Automated Single Cell Imaging Analysis (HASCIA) approach for quantitative assessment of protein expression with single cell resolution and applied the method to investigate spatiotemporal factors that influence CSC state transition using glioblastoma (GBM) CSC as a model system. We were able to validate the quantitative nature of this approach through comparison of the protein expression levels determined by HASCIA to those determined by immunoblotting. A virtue of HASCIA was exemplified by detection of a subpopulation of SOX2-low cells, which expanded in fraction size during state transition. HASCIA also revealed that CSCs were committed to loose stem cell state at an earlier time point than the average SOX2 level decreased. Functional assessment of stem cell frequency in combination with quantification of SOX2 expression by HASCIA defined a stable cut-off of SOX2 expression level for stem cell state. We also developed an approach to assess local cell density and found that denser monolayer areas possess higher average levels of SOX2, higher cell diversity and a presence of a sub-population of slowly proliferating SOX2-low CSCs. HASCIA is an open source software that facilitates understanding the dynamics of heterogeneous cell population such as that of CSCs and their progeny. It is a powerful and easy-to-use image analysis and statistical analysis tool available at https://hascia.lerner. ccf.org.
Endogenous and Antipsychotic-Related Risks for Diabetes Mellitus in Young People With Schizophrenia: A Danish Population-Based Cohort Study.

OBJECTIVE Diabetes mellitus contributes to excessive cardiovascular deaths and reduced life expectancy in schizophrenia. This population-based cohort study investigated the endogenous risk for diabetes in antipsychotic-naive schizophrenia and evaluated the risks added by starting antipsychotic treatment in people with schizophrenia. METHOD The study followed all people born in Denmark on or after Jan. 1, 1977, until Jan. 1, 2013 (N=2,736,510). The Danish Psychiatric Central Research Register ascertained schizophrenia diagnoses. The Danish National Prescription Registry provided data on prescriptions of antipsychotics. Diabetes was ascertained from the Danish National Patient Register and Danish National Prescription Registry. The authors estimated the endogenous and antipsychotic-related risks for diabetes by using Cox proportional hazards regression models, while accounting for potential confounders. RESULTS Of the cohort members, 14,118 (0.52%) developed diabetes, and 8,945 (0.33%) developed schizophrenia during follow-up (49,582,279 person-years). The adjusted hazard ratio for diabetes was 3.07 (95% confidence interval [CI], 1.71-5.41) in antipsychotic-naive schizophrenia compared with the general population. The risk for diabetes after starting antipsychotic treatment was significantly higher (adjusted hazard ratio, 3.64; 95% CI, 1.95-6.82) than the risk in antipsychotic-naive schizophrenia, after adjustment for family history of diabetes and other potential confounders. First-line treatment with either first-generation antipsychotics (adjusted hazard ratio, 3.06; 95% CI, 1.32-7.05) or second-generation antipsychotics (adjusted hazard ratio, 3.44; 95% CI, 1.73-6.83) increased the risk for diabetes without a statistically significant difference. Appropriate sensitivity analyses limited to type 2 diabetes corroborated these results. CONCLUSIONS Schizophrenia confers a high endogenous risk for diabetes, and the risk is further increased by both first-generation and second-generation antipsychotics. Early detection and effective treatment of diabetes should be an integral part of multidisciplinary management of schizophrenia regardless of antipsychotic drug exposure.
Prevalence and associated physical symptoms of depressive and anxiety symptoms in neurology outpatient clinic

The co-occurrence of depressive and anxiety symptoms in a variety of neurological conditions are widely common and disabling. Furthermore, it could persist for a long time and interfere in the development of neurological disorders, and affect the prognosis of neurological disorders.1 However, despite their high incidence and jeopardy, depressive and anxiety symptoms remain under-recognised and undertreated.2 Most previous studies focused on depressive and anxiety symptoms in specific neurological diseases such as stroke, Parkinson’s disease, epilepsy and multiple sclerosis. However, the prevalence of depressive and anxiety symptoms in neurological diseases were reported differently, and few studies reported the situation in Asia. Furthermore, a number of outpatients are newly referred to general neurology clinics for different symptoms such as headache, dizziness, cerebrovascular diseases and insomnia. Hence, the prevalence of depressive and anxiety symptoms in these new patients at the neurology outpatient clinic remains unclear, and the symptoms which predict the experience of depressive and anxiety symptoms are still ambiguous. We aimed to investigate the prevalence of depressive and anxiety symptoms in newly referred patients at the general neurology outpatient clinics and determine the correlates for occurrence of these symptoms. Patients newly referred at the general neurology outpatient clinics were recruited from three centres in Shanghai (Shanghai Huashan, Shanghai Changhai, and Shanghai Zhongshan Hospital) during 17 January 2009 to 21 January 2011. Patients were screened randomly using random number table by resident neurologists followed by interview of attending doctors. Demographic information was collected and the Patient Health Questionnaire Depression (PHQ-9) as well as Generalized Anxiety Disorder Questionnaire scale (GAD-7) were used for assessing depressive and anxiety symptoms, respectively. When the patients with score of …
Role of transient receptor potential channels in adipocyte biology

The transient receptor potential (TRP) channel superfamily is a family of 28 nonselective cation channels expressed on the plasma membrane with a high permeability to calcium. Role of TRP channels, especially TRP vanilloid 1, TRP ankyrin 1 and TRP melastatin 8, is widely documented in nociception. During the last few years, there has been a consistent increase in reports indicating the presence and significance of these channels in different tissues including bladder, skin, respiratory system and brain. Based on calcium permeability of these channels and the much published role of calcium and its signaling in adipogenesis, there is a potential for importance of these ion channels in adipocyte biology. This review provides insight into the involvement of TRP channels in adipocyte differentiation, obesity and associated complications. Furthermore, the authors will focus to evaluate these channels as potential therapeutic targets for the management of obesity.
TRAIL pathway targeting therapeutics

ABSTRACT Introduction: Despite decades of focused research efforts, cancer remains a significant cause of morbidity and mortality. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is capable of inducing cell death selectively in cancer cells while sparing normal cells. Areas covered: In this review, the authors cover TRA therapy and strategies that have been undertaken to improve their efficacy, as well as unconventional approaches to TRAIL pathway activation including TRAIL-inducing small molecules. They also discuss mechanisms of resistance to TRAIL and the use of combination strategies to overcome it. Expert commentary: Targeting the TRAIL pathway has been of interest in oncology, and although initial clinical trials of TRAIL receptor agonists showed limitations, novel approaches represent the future of TRAIL-based therapy.
Edible Coatings Enriched with Essential Oils on Apples Impair the Survival of Bacterial Pathogens through a Simulated Gastrointestinal System

Edible coatings supplemented with essential oil components have been investigated to control spoilage microorganisms. In this study, the survival of Listeria monocytogenes and Salmonella enterica serovar Typhimurium on apples treated with edible coatings based on sodium alginate (2%) (ECs) and supplemented with essential oil components, namely eugenol (Eug) at 0.2% or in combination with 0.1% (v/v) of Eug and citral (Cit) at 0.15% was determined. Both bacterial pathogens were exposed on apples treated with ECs supplemented with Eug or Eug + Cit and challenged with gastrointestinal fluids and their survival was examined. Both pathogens were able to survive on the surface of ‘Bravo de Esmolfe’ apple. The use of ECs in fresh-cut fruits impaired the survival of both bacterial populations over 72 h at 4 °C. The exposure of the pathogens on apples with ECs supplemented with Eug and Cit and challenged with gastrointestinal fluids significantly reduced their survival. This study evidences that the use of alginate edible coating enriched with Eug or the combination of Eug and Cit can contribute to the safer consumption of minimally processed fruits.
Extracellular Vesicles in Metabolic Syndrome

Metabolic syndrome defines a cluster of interrelated risk factors for cardiovascular disease and diabetes mellitus. These factors include metabolic abnormalities, such as hyperglycemia, elevated triglyceride levels, low high-density lipoprotein cholesterol levels, high blood pressure, and obesity, mainly central adiposity. In this context, extracellular vesicles (EVs) may represent novel effectors that might help to elucidate disease-specific pathways in metabolic disease. Indeed, EVs (a terminology that encompasses microparticles, exosomes, and apoptotic bodies) are emerging as a novel mean of cell-to-cell communication in physiology and pathology because they represent a new way to convey fundamental information between cells. These microstructures contain proteins, lipids, and genetic information able to modify the phenotype and function of the target cells. EVs carry specific markers of the cell of origin that make possible monitoring their fluctuations in the circulation as potential biomarkers inasmuch their circulating levels are increased in metabolic syndrome patients. Because of the mixed components of EVs, the content or the number of EVs derived from distinct cells of origin, the mode of cell stimulation, and the ensuing mechanisms for their production, it is difficult to attribute specific functions as drivers or biomarkers of diseases. This review reports recent data of EVs from different origins, including endothelial, smooth muscle cells, macrophages, hepatocytes, adipocytes, skeletal muscle, and finally, those from microbiota as bioeffectors of message, leading to metabolic syndrome. Depicting the complexity of the mechanisms involved in their functions reinforce the hypothesis that EVs are valid biomarkers, and they represent targets that can be harnessed for innovative therapeutic approaches.
Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse

Significance How the locus-specific histone modifications are achieved is not fully understood. One of the contributing mechanisms is that DNA binding molecules recognize specific sequences and their binding recruits or stabilizes the histone modification enzyme complexes. Comprehensive identification of such sequence patterns is the first step toward revealing possible regulatory grammar for establishing histone modifications. In this study, we have cataloged the DNA motifs tightly associated with six and eight important histone modifications in human and mouse, respectively. We show that mutating the found motifs at particular loci led to significant reduction of the histone modification levels. These histone-associated motifs, especially H3K4me3 motifs, significantly overlap with expression of quantitative trait loci SNPs in cancer patients more than known motifs, further suggesting their regulatory roles. We also found possible feedback loops mediated by these motifs, implicating their possible roles in histone modification dynamics and epigenetic priming. Histones are modified by enzymes that act in a locus, cell-type, and developmental stage-specific manner. The recruitment of enzymes to chromatin is regulated at multiple levels, including interaction with sequence-specific DNA-binding factors. However, the DNA-binding specificity of the regulatory factors that orchestrate specific histone modifications has not been broadly mapped. We have analyzed 6 histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3, K3H9me3, H3K36me3) across 121 human cell types and tissues from the NIH Roadmap Epigenomics Project as well as 8 histone marks (with addition of H3K4me2 and H3K9ac) from the mouse ENCODE Consortium. We have identified 361 and 369 DNA motifs in human and mouse, respectively, that are the most predictive of each histone mark. Interestingly, 107 human motifs are conserved between the two species. In human embryonic cell line H1, we mutated only the found DNA motifs at particular loci and the significant reduction of H3K27ac levels validated the regulatory roles of the perturbed motifs. The functionality of these motifs was also supported by the evidence that histone-associated motifs, especially H3K4me3 motifs, significantly overlap with the expression of quantitative trait loci SNPs in cancer patients more than the known and random motifs. Furthermore, we observed possible feedbacks to control chromatin dynamics as the found motifs appear in the promoters or enhancers associated with various histone modification enzymes. These results pave the way toward revealing the molecular mechanisms of epigenetic events, such as histone modification dynamics and epigenetic priming.
General Public Views, Attitudes, and Experiences toward Drug Safety in Dubai, United Arab Emirates: A Qualitative Approach

Ensuring drug safety among the patients is the main domain of pharmacovigilance activities worldwide. A pharmacovigilance system was established in the United Arab Emirates (UAE) in 2008. Research evidence reflects that the current system is lacking in active participation from patients, and also, the inadequate role of healthcare professionals is anticipated. In this context, it is pertinent to know the general public’s understandings and their patterns of safe use of medication, which are unexplored areas in Dubai, UAE. The current study aimed to explore the public views, attitudes, and experiences toward medication safety, and to explore key factors enhancing the safe use of medications among the public in Dubai. This study adopted a qualitative approach and face-to-face, 14 in-depth interviews with public individuals, selected purposively using the snowball sampling technique. The interviews were conducted in different places in Dubai recorded and transcribed verbatim and thematically analyzed for data analysis. Reporting of adverse drug reaction was not well-known among all the participants. Public views towards safe use of medicines were limited to the side effects of the consumed medicines only, and to a lesser extent to the inappropriate indication and dosage. Most of the participants mentioned that gaining knowledge about the side effects of the prescribed drug was the main reason for reading the patient information leaflet. Quite a few participants have experienced side effects while consuming their medicines and they were unsure of how to deal with the situation. The current research also reflected the lack of proper communication between pharmacists and physicians in managing drug safety issues. Conclusively, the current research revealed gaps in public views regarding medication’s safety, which consequently may impact their attitudes during the course of medication use. Efforts need to be strengthened to enhance positive views and attitudes of the public towards medication safety and ADR reporting in the UAE.
The joint effects of bilingualism, DLD and item frequency on children's lexical-retrieval performance.

BACKGROUND Bilingual children and children diagnosed with developmental language disorder (DLD) are characterized by reduced lexical-retrieval abilities. Few studies examined their joint contribution and the mechanisms underlying these effects in the lexical domain. AIMS To explore the joint effects of bilingualism and DLD by adopting a four-group comparison in which the difference between bi- and monolingual children with DLD is directly compared with that of bi- and monolingual children with typical language development (TLD). In addition, to examine the mechanisms underlying the effects of bilingualism and DLD on children's lexical-retrieval abilities, we tested how item's characteristics (frequency of use) modulate the effects of bilingualism and DLD. METHODS & PROCEDURES Fifty-eight children (aged 9-14 years) participated in the current study. They were either Hebrew monolingual or Hebrew-English bilinguals and were either diagnosed with DLD or had TLD. Children completed a Hebrew picture-naming task and verbal short-term memory tests. The influence of participants' characteristics, including bilingualism, DLD and verbal short-term memory, as well as item's characteristics (frequency of use) were tested. OUTCOMES & RESULTS Accuracy analysis revealed that bilingual children scored lower than monolingual children and that children with DLD scored lower than children with TLD. Critically, the two factors interacted such that their joint presence resulted in less-than-additive effects. Specifically, although bilingual children with DLD performed worse than all other groups, they performed better than expected under an additive model. Interestingly, monolingual children with DLD performed similarly to bilingual children with TLD. Increased verbal short-term memory was associated with better performance across the four groups. Finally, bilingualism and DLD interacted with item frequency, such that being bilingual, having DLD, or both, resulted in increased sensitivity to item frequency manifested in exceptionally lower performance on low-frequency items. CONCLUSIONS & IMPLICATIONS The findings suggest that the strength of linguistic representations contribute to the effects of bilingualism and DLD. Further, the presence of bilingualism in the context of DLD does not exaggerate the impact of DLD. Clinically, this suggests that differences between bi- and monolingual children with DLD must be considered in reference to the gap in lexical-retrieval performance observed between bi- and monolingual children with TLD. Finally, because monolingual children with DLD and bilingual children with TLD performed similarly, sensitive diagnostic tools and intervention programmes should be adopted to allow correct identification and treatment of bilingual children with DLD.