Miracle-dz/UniFAR-FTUs huggingface dataset:
A fully coupled framework for in silico investigation of in-stent restenosis

Abstract Finite element analysis (FEA) can be implemented along with Agent-based model (ABM) to investigate the biomechanical and mechanobiological mechanisms of pathophysiological processes. However, traditional ABM-FEA approaches are often partially coupled and lack the feedback responses from biological analysis. To overcome this problem, a fully coupled ABM-FEA framework is developed in this paper by linking the macro-scale and cell-scale modules bi-directionally. Numerical studies of the in-stent restenosis process are conducted using the proposed approach and comparisons are made between the two types of frameworks. A reduction in lumen loss rate, which is possibly caused by the time-varying stresses, is observed in the fully coupled simulations. The re-endothelialisation process is also simulated under different frameworks and the simulation results show strong inhibition of endothelial cells to vascular restenosis. The proposed method is proved to be effective to explain the biomechanical-mechanobiological coupling characteristics of the restenosis problem and can be utilized for stent design and optimization.
IL-37 gene variant (rs3811047): A marker of disease activity in rheumatoid arthritis: A pilot study

Abstract Background: Rheumatoid arthritis (RA) is a joint destructive disorder with great morbidity. Unraveling genetic determinants causing the disease would pave the road towards early detection and precise medicine. Interleukin 37 (IL-37), a natural inhibitor of innate immunity, was shown to be a key modulator in RA. Plasma levels were deregulated and correlated with disease activity. Therefore, we hypothesized the IL-37 gene variants could influence the clinical characteristics of RA patients. Objective: This is a pilot study to assess the association of rs3811047 variant of IL-37 gene with RA development and disease activity in an Egyptian population. Methods: A total of 100 individuals (50 RA patients and 50 healthy individuals) were enrolled in the study. Disease activity score of 28 joints (DAS28) was estimated for RA patients. Genotyping was performed using Real-Time PCR technology. Results: There was no statistically significant association between genotype frequencies of rs3811047 and RA risk. However, there was a significant relationship between the studied single nucleotide polymorphism (SNP) and disease activity. Patients carrying the GG genotype had higher DAS28 score than patients with AA or AG genotypes (p = .041). Conclusion: IL-37 gene rs3811047 SNP was associated with more severe RA disease activity in the current population. Larger epidemiological study is warranted to validate our results.
Aesthetic perception, acceptability and satisfaction in the treatment of caries lesions with silver diamine fluoride: A scoping review.

BACKGROUND Silver diamine fluoride (SDF) causes dental black staining after its application. AIM Evaluate the aesthetic perception, acceptability, and/or satisfaction of patients, parents, and professionals to the treatment of caries lesions with SDF through a scoping review. DESIGN A search was performed in seven databases and two key journals with no language or date restrictions. Studies that evaluated the aesthetic perception, satisfaction, and/or acceptability of patients, parents, and professionals to the treatment of carious lesions with SDF were considered eligible. RESULTS From a total of 1177 articles, 10 studies were full text assessed for eligibility, with nine included in this scoping review. In general, the studies varied by population, study design, and methodologic evaluation. The type of tooth (anterior or posterior), family income, parental schooling, ethnicity, and need for advanced behaviour control methods were factors that influenced the results. The acceptability level increased as the child required more advanced methods of behaviour guidance. In general, the pigmentation caused by SDF did not interfere with the parents' acceptability of the treatment; however, professionals believe that this could have influence. Regarding satisfaction, pigmentation did not influence parental satisfaction. CONCLUSION Parents were satisfied with and found SDF acceptable, whereas professionals did not.
Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar

Plants have evolved a sophisticated system to respond to various stresses. Fungal attack or infection is one of the most important biotic stresses for most plants. During the defense response to fungal infection, the plant hormones jasmonic acid (JA) and salicylic acid (SA) play critical roles. Here, gene expression data on JA/SA treatments and Melampsora larici-populina (MLP) infection were generated. Integrated transcriptome analyses of these data were performed, and 943 genes in total were identified as common responsive genes (CRG). Gene ontology (GO) term analysis revealed that the genes from CRG are generally involved in the processes of stress responses, metabolism, and growth and development. The further cluster analysis of the CRG identified a set of core genes that are involved in the JA/SA-mediated response to fungal defense with distinct gene expression profiles upon JA/SA treatment, which highlighted the different effects of these two hormones on plant fungal defenses. The modifications of several pathways relative to metabolism, biotic stress, and plant hormone signal pathways suggest the possible roles of JA/SA on the regulation of growth and defense responses. Co-expression modules (CMs) were also constructed using the poplar expression data on JA, SA, M. larici-populina, Septoria musiva, and Marssonina brunnea treatment or infection. A total of 23 CMs were constructed, and different CMs clearly exhibited distinct biological functions, which conformably regulated the concerted processes in response to fungal defense. Furthermore, the GO term analysis of different CMs confirmed the roles of JA and SA in regulating growth and defense responses, and their expression profiles suggested that the growth ability was reduced when poplar deployed defense responses. Several transcription factors (TFs) among the CRG in the co-expression network were proposed as hub genes in regulating these processes. According to this study, our data finely uncovered the possible roles of JA/SA in regulating the balance between growth and defense responses by integrating multiple hormone signaling pathways. We were also able to provide more knowledge on how the plant hormones JA/SA are involved in the regulation of the balance between growth and plant defense.
Three-dimensional modelling of the femur and humerus in adult male guinea pigs (guinea pig) with computed tomography and some biometric measurement values.

BACKGROUND Guinea pig is a species belonging to the Caviidae family of the Rodentia order and is frequently used in experimental studies. Biomedical imaging methods are used in the diagnosis and treatment of many diseases in medicine. Among these methods, computed tomography (CT) is one of the most important imaging methods. In this study, it was aimed to perform the three-dimensional modelling of the CT images, obtained from the humerus and femur in the guinea pigs, via the MIMICS programme and to make some biometric measurements regarding the bones over these models. MATERIALS AND METHODS In the present study, 12 male adult guinea pigs were used. The soft tissue on humerus and femur bones of the guinea pigs was removed. After this procedure, CT images at a 0.5 mm-thickness were obtained from the animals. The images were recorded in DICOM format. Then, the reconstruction process was performed from the images by using the three-dimensional modelling programme MIMICS® 13.1. On the 3D model of the humerus and femur (right-left), volumes, surface areas and lengths as well as other biometric parameters were measured separately, and the values were recorded. In addition, measurements of the bones were made by the help of a digital calliper. RESULTS Among the parameters obtained from 3D models, a statistical difference is observed between the right and left cortex thicknesses of the femur from the measurements of calliper and the right and left humerus volumes (p<0.05); whereas, no statistical difference was found in other parameters of both measurements (p>0.05). CONCLUSIONS It can be stated that CT and 3D modelling can be used for the measurement of some parameters in the long bones of the guinea pigs.
Technology Use Patterns Among Patients Enrolled in Inpatient Detoxification Treatment.

BACKGROUND Technology-based interventions offer a practical, low-cost, and scalable approach to optimize the treatment of substance use disorders (SUDs) and related comorbidities (HIV, hepatitis C infection). This study assessed technology use patterns (mobile phones, desktop computers, internet, social media) among adults enrolled in inpatient detoxification treatment. METHODS A 49-item, quantitative and qualitative semi-structured survey assessed for demographic characteristics, technology use patterns (ie, mobile phone, text messaging [TM], smart phone applications, desktop computer, internet, and social media use), privacy concerns, and barriers to technology use. We used multivariate logistic regression models to assess the association between respondent demographic and clinical characteristics and their routine use of technologies. RESULTS Two hundred and six participants completed the survey. Nearly all participants reported mobile phone ownership (86%). Popular mobile phone features included TM (96%), web-browsers (81%), and accessing social media (61%). There was high mobile phone (3.3 ± 2.98) and phone number (2.6 ± 2.36) turnover in the preceding 12 months. Nearly half described daily or weekly access to desktop computers (48%) and most reported internet access (67%). Increased smartphone ownership was associated with higher education status (P = 0.022) and homeless respondents were less likely to report mobile phone ownership (P = 0.010) compared to participants with any housing status (ie, own apartment, residing with friends, family, or in a halfway house). Internet search engines were used by some participants (39.4%, 71/180) to locate 12 step support group meetings (37%), inpatient detoxification programs (35%), short- or long-term rehabilitation programs (32%), and outpatient treatment programs (4%). CONCLUSIONS Technology use patterns among this hard-to-reach sample of inpatient detoxification respondents suggest high rates of mobile phone ownership, TM use, and moderate use of technology to facilitate linkage to addiction treatment services.
Differential clinical significance of pre-, interim-, and post-treatment plasma Epstein–Barr virus DNA load in NK/T-cell lymphoma treated with P-GEMOX protocol

Abstract Circulating EBV-DNA is an accurate biomarker of tumor load in extranodal natural killer (NK)/T cell lymphoma (ENKTL); however, its role in patients treated with P-GEMOX has not been evaluated. In this study, we examined plasma EBV-DNA of 99 patients at different time points by real-time quantitative polymerase chain reaction. Multivariate analysis revealed that ECOG PS score, response rate, and post-treatment EBV-DNA level were independent predictors of progression-free survival (PFS) and overall survival (OS). Positive post-treatment plasma EBV-DNA was associated with poor OS in ENKTL patients. The 3-year OS for patients with positive pre-, interim-, post-treatment EBV-DNA was significantly lower than that for patients with negative EBV-DNA; the values were 70.2% vs. 93.9% (p = .022), 53.8% vs. 99.1% (p < .001), and 40.6% vs. 91.8% (p < .001), respectively. We conclude that monitoring dynamic changes in plasma EBV-DNA in ENKTL patients treated with P-GEMOX could predict important outcomes such as OS.
Daily Caffeine Consumption Does Not Influence Acupuncture Analgesia in Healthy Individuals: A Preliminary Study

Animal studies suggest that caffeine may interfere with acupuncture analgesia. This study investigated the modulation effect of daily caffeine intake on acupuncture analgesia in 27 healthy subjects using a crossover design. We found that real acupuncture increased pain thresholds compared to sham acupuncture. Further, there was no association between caffeine intake measurements of daily caffeine use, duration of caffeine consumption, or their interaction and preacupuncture and postacupuncture pain threshold changes. Our findings suggest that daily caffeine intake may not influence acupuncture analgesia in the cohort of healthy subjects who participated in study.
Alzheimer’s disease and the processing of uncertainty during choice task performance: Executive dysfunction within the Hick–Hyman law

ABSTRACT The Hick–Hyman law states that choice response time (RT) increases linearly with increasing information uncertainty. Neuroimaging studies suggest that the representation of uncertainty in support of response generation is mediated by the cognitive control network (CCN), which is disrupted in Alzheimer’s disease (AD). Thus, we predicted that patients with AD would be sensitive to increased uncertainty particularly under conditions that place demands on the internal representation of uncertainty, and that choice RT performance under these conditions would be associated with performance on tests of executive function. Cognitively normal older adults (CN) and patients with AD completed card-sorting tasks that separately manipulated either externally cued uncertainty (i.e., number of sorting piles with a fixed probability of each stimulus type) or more internally driven uncertainty (i.e., the probability of each stimulus type with a fixed number of sorting piles). Consistent with our predictions, AD patients were impaired relative to CN particularly on the internally driven uncertainty task, and RT in this task was associated with performance on neuropsychological measures of executive functioning but not episodic memory. We suggest that this pattern of findings is consistent with presumed disruptions to the CCN in AD and provides neuropsychological evidence in support of the role of the CCN in the representation of uncertainty.
Differential Changes in the Number and Morphology of the New Neurons after Chronic Infusion of Wnt7a, Wnt5a, and Dkk‐1 in the Adult Hippocampus In Vivo

In the adult hippocampus of many mammals, a particular microenvironment in the neurogenic niche regulates the proliferation, self‐renewal, and differentiation of neuronal stem cells. In this proliferative niche, a variety of molecules provide a finely regulated molecular signaling that controls stem cell properties. During development, Wnt signaling has been implicated in cell fate determination and proliferation, in the establishment of cell polarity, as well as a cue for axonal growth and dendrite orientation. In the adult brain, this pathway also participates in the stem cell self‐renewal and neuronal differentiation. However, the effects of the chronic Wnt signaling modulation in the adult hippocampus, through the infusion of Wnt7a, Wnt5a, and Dkk‐1, on the rate of neurogenesis and on the induction of neurite arborization have not been studied. In this study, we show that Wnt7a and Wn5a further increased the rate of newly generated neurons. However, Wnt5a exerted additional effects by promoting neurite growth and neurite misorientation in the dentate gyrus of adult rats. The chronic exposure to Dkk‐1 also generated aberrant location of growing neurites. These results suggest that the interplay of canonical and non‐canonical Wnt ligands participates in neuronal stem cell proliferation and in the establishment of proper neurite maturation. Anat Rec, 302:1647–1657, 2019. © 2019 American Association for Anatomy
PI3K‐PKB‐mTOR hyperactivation in relation to nasopharyngeal carcinoma progression and prognosis

Nasopharyngeal carcinoma (NPC) has a unique and complex etiology, which is not completely understood. The aim of this study is to investigate the expression patterns of phosphatidylinositol 3‐kinase (PI3K), protein kinase B (PKB), and mammalian target of rapamycin (mTOR) proteins in patients with NPC and their relationship with NPC progression and prognosis. Between January 2008 and March 2010, PI3K, PKB, and mTOR protein expressions were detected using immunohistochemistry among 119 patients with NPC and 30 healthy people. A 5‐year follow‐up was conducted for all patients. Correlations of PI3K, PKB, and mTOR proteins with the clinicopathological features and prognosis of NPC were evaluated using Spearman's rank correlation coefficient and Kaplan‐Meier curve. Cox's regression analysis was performed to analyze the risk factors for the prognosis of NPC. First, PI3K, PKB, and mTOR were highly expressed in patients with NPC. The expressions of PI3K, PKB, and mTOR proteins were associated with T stage, N stage, clinical stage, relapse, and distant metastasis. Meanwhile, PI3K is positively correlated with PKB and PKB is positively correlated with mTOR in NPC. Higher PI3K, PKB, and mTOR protein expressions were related to a shorter survival time and a lower survival rate in NPC. Cox regression analysis revealed that age, T stage, N stage, PI3K, PKB, and mTOR were independent risk factors for NPC patient survival. Altogether, our data suggest that overexpression of PI3K, PKB, and mTOR proteins is an important indicator of poor survival in NPC. In addition, inhibition of PI3K‐PKB‐mTOR signaling may also contribute to the development of new therapeutic strategies for NPC.
IL‐23‐ and Imiquimod‐Induced Models of Experimental Psoriasis in Mice

Genome‐wide association studies have found that polymorphisms in genes for IL‐23 and its receptor are important in psoriasis, and blocking IL‐23 is an effective therapy in the disease. The use of Aldara™, a cream that contains the TLR7 and TLR8 agonist imiquimod (IMQ), was found to exacerbate psoriasis in some patients with pre‐existing disease. Intradermal injections of IL‐23 and topical application of Aldara/IMQ induce skin inflammation in mice with features similar to psoriasis—including epidermal hyperplasia and accumulation of inflammatory cells in epidermis and dermis—which is mediated by IL‐17A, IL‐22, and other factors implicated in the human disease. Consequently, these models can be used in preclinical studies to investigate the molecular and cellular pathogenesis of psoriasis, as well as in the evaluation of potential therapies. This article provides detailed methodologies for creating and evaluating the IL‐23‐ and Aldara/IMQ‐induced mouse models of psoriasis. The article also provides a protocol for analyzing skin leukocytes by flow cytometry. © 2019 by John Wiley & Sons, Inc.
One-year visual outcomes after laser for Type 1 prethreshold retinopathy of prematurity among very low birth weight neonates at a tertiary center in western India – A prospective cohort study

Abstract Objective: To evaluate the visual outcomes after laser treatment for retinopathy of prematurity (ROP) among very-low-birth-weight neonates at 1-year corrected age in population of western India. Methods: In this prospective cohort study, 35 neonates received laser treatment for type 1 prethreshold ROP. Structural and refractive status were assessed at 1-year corrected age in these neonates. Results: Total 32 neonates (64 eyes) were followed-up at the age of 1 year. The mean gestational age and birth weight were 27.6 weeks and 900 g, respectively. All 64 eyes reported favorable structural outcome. The mean refractive error was −1.82 D (range: −11 to +4 D). Prevalence of myopia was 62.5% [43.8% low myopia; 18.8% high myopia]. Eight eyes (12.5%) had insignificant hyperopia. Conclusion: We concluded that timely and adequate screening of eyes of preterm neonates followed by early and appropriate laser treatment improves the later visual outcomes. High refractive error is common and may be the cause of visual impairment.
Understanding the Barriers to Introducing Early Palliative Care for Patients with Advanced Cancer: A Qualitative Study.

Background: Palliative care is often underutilized or initiated late in the course of life-threatening illness. Randomized clinical Early Palliative Care (EPC) trials provide an opportunity for changing oncologists' perceptions of palliative care and their attitudes to referring patients to palliative care services. Aim: To describe French oncologists' perceptions of EPC and their effects on referral practices before a clinical EPC trial was launched. Design: A qualitative study involving semistructured face-to-face interviews. The data were analyzed using the Grounded Theory coding method. Setting/Participants: Thirteen oncologists and 19 palliative care specialists (PCSs) working at 10 hospitals all over France were interviewed. Most of them were involved in clinical EPC trials. Results: The findings suggest that referral to PCSs shortly after the diagnosis of advanced cancer increases the terminological barriers, induces avoidance patterns, and makes early disclosure of poor prognosis harder for oncologists. This situation is attributable to the widespread idea that palliative care means terminal care. In addition, the fact that the EPC concept is poorly understood increases the confusion between EPC and supportive care. Conclusion: Defining the EPC concept more clearly and explaining to health professionals and patients what EPC consists of and what role it is intended to play, and the potential benefits of palliative care services could help to overcome the wording barriers rooted in the traditional picture of palliative care. In addition, training French oncologists how to disclose "bad news" could help them cope with the emotional issues involved in referring patients to specialized palliative care.
Reduced Natural Killer Cell Subsets in Perinatally Acquired Long-Term Non-Progressor Human Immunodeficiency Virus-Infected Children.

Lymphocyte subsets of long-term non-progressor (LPNT) HIV-infected children is a less studied aspect of HIV infection. Evaluation of different lymphocyte subsets was done in HIV-infected children ≥8 years of age. Subjects were divided in two groups-group 1 (LTNP), treatment-naive with CD4 ≥ 500 cells/μL (n = 20); group 2, non-long-term non-progressor (nLTNPs) receiving antiretroviral therapy (ART) with CD4 count ≤500 on at least one occasion (n = 21). Group 3 comprised age-, sex-matched healthy controls (HCs, n = 20). Lymphocyte subsets were acquired with a flow cytometer (Navios; Beckman Coulter), and data were analyzed using Kaluza flow analysis software. The mean ages were 12.1 (±2.4 SD) and 12.5 (±2.7) years with mean duration of follow-up of 6.8 (±3.4) and 5.6 (±1.95) years in LTNP and nLTNP subjects, respectively. The mean duration of ART was 5.17 years for group 2. Absolute count and percentage of CD4+ T cells was lower in nLTNPs than in LTNPs. Cytotoxic T cells were high in both HIV-infected groups compared with HCs. Natural killer (NK) cells were found to be significantly lower in LTNP and nLTNP groups compared with HCs (p ≤ .000003 and p ≤ .00003, respectively). Naïve B cells were more in HIV-infected individuals than in HCs. NK cells were significantly lower in LTNP and nLTNP groups. Immune reconstitution was comparable in children initiated with ART early versus long-term HIV-infected children receiving no ART.
Nuclear FGFR2 regulates musculoskeletal integration within the developing limb

Bent bone dysplasia syndrome (BBDS), a congenital skeletal disorder caused by dominant mutations in fibroblast growth factor receptor 2 (FGFR2), is characterized by bowed long bones within the limbs. We previously showed that the FGFR2 mutations in BBDS enhance nuclear and nucleolar localization of the receptor; however, exactly how shifts in subcellular distribution of FGFR2 affect limb development remained unknown.