Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of Anatomical Education Using Augmented Reality: An Empirical Study of Body Painting

Students in undergraduate premedical anatomy courses may experience suboptimal and superficial learning experiences due to large class sizes, passive lecture styles, and difficult‐to‐master concepts. This study introduces an innovative, hands‐on activity for human musculoskeletal system education with the aim of improving students’ level of engagement and knowledge retention. In this study, a collaborative learning intervention using the REFLECT (augmented reality for learning clinical anatomy) system is presented. The system uses the augmented reality magic mirror paradigm to superimpose anatomical visualizations over the user’s body in a large display, creating the impression that she sees the relevant anatomic illustrations inside her own body. The efficacy of this proposed system was evaluated in a large‐scale controlled study, using a team‐based muscle painting activity among undergraduate premedical students (n = 288) at the Johns Hopkins University. The baseline knowledge and post‐intervention knowledge of the students were measured before and after the painting activity according to their assigned groups in the study. The results from knowledge tests and additional collected data demonstrate that the proposed interactive system enhanced learning of the musculoskeletal system with improved knowledge retention (F(10,133) = 3.14, P < 0.001), increased time on task (F(1,275) = 5.70, P < 0.01), and a high level of engagement (F(9,273) = 8.28, P < 0.0001). The proposed REFLECT system will be of benefit as a complementary anatomy learning tool for students.
Rs4676410 and Rs2531875 are Associated with the Risk of Ankylosing Spondylitis in the Han Chinese Population

Objectives: Although the exact cause of ankylosing spondylitis (AS) is unknown, genetics play a key role in AS. A recent genome-wide association study identified new immune-related susceptibility loci for AS in East Asians, and these need to be validated in the Chinese population. Methods: We enrolled 848 patients who met the modified New York criteria for AS and 1123 healthy normal controls in the present study. High-resolution melting analysis accompanied with sequencing was carried out to genotype five polymorphisms: rs12615545, rs4676410, rs1250550, rs2531875, and rs7282490. Distributions of genotypes and alleles were compared between AS patients and healthy controls, and among AS patients stratified by clinical parameters, age, and gender. Results: rs4676410 (p=0.0237; odds ratio (OR): 1.109; 95% confidence interval (CI): 1.014–1.213) and rs2531875 (p=0.0308; OR: 1.117; 95% CI: 1.01–1.234) were both associated with the risk of AS. However, no association was found between the studied polymorphisms and AS severity. An association between the rs4676410T allele and iridocyclitis was observed (p=0.0142; OR: 1.403; 95% CI: 1.11–1.774). Conclusion: rs4676410 and rs2531875 are associated with AS susceptibility in the Han Chinese population. The rs4676410T allele might be correlated with iridocyclitis.
High prevalence of enteric viruses associated with acute gastroenteritis in pediatric patients in a low‐income area in Vitória, Southeastern Brazil

Acute gastroenteritis (AGE) is a significant cause of child mortality worldwide. In Brazil, despite the reduction in infant mortality achieved in recent years, many children still die because of undiagnosed AGE. The prevalence, viral load, and circulating genotypes of rotavirus A (RVA), human adenovirus (HAdV), and norovirus GII (NoV GII) were investigated in children with AGE during 12 months in Vitoria, Espírito Santo, Southeastern Brazil. Enteric viruses were detected in stool samples, quantified by quantitative polymerase chain reaction, sequenced, and compared phylogenetically. The overall prevalence was 93.3% (125/134). Cases of single infection (41.8%) and mixed infection (51.5%) were observed; in 21.6% of cases, all the three viruses were detected. RVA had the highest number of copies in all infections. Phylogenetic analysis revealed predominantly the presence of RVA genotype G3, followed by G2 and G9. HAdV clustered within subgroup C, but some samples harbored subgroups A, D, or F. All sequenced NoV‐positive samples clustered within the prevalent genotype GII.4. The high prevalence of RVA, HAdV, and NoV in diarrheal feces clarifies the etiology of AGE in this population, and the presence of RVA in vaccinated children reinforces the importance of monitoring programs to identify the causes of gastroenteritis and contribute to the reliability of diagnosis.
Social Competence in Parents Increases Children’s Educational Attainment: Replicable Genetically-Mediated Effects of Parenting Revealed by Non-Transmitted DNA

Abstract We recently reported an association of offspring educational attainment with polygenic risk scores (PRS) computed on parent’s non-transmitted alleles for educational attainment using the second GWAS meta-analysis article on educational attainment published by the Social Science Genetic Association Consortium. Here we test the replication of these findings using a more powerful PRS from the third GWAS meta-analysis article by the Consortium. Each of the key findings of our previous paper is replicated using this improved PRS (N = 2335 adolescent twins and their genotyped parents). The association of children’s attainment with their own PRS increased substantially with the standardized effect size, moving from β = 0.134, 95% CI = 0.079, 0.188 for EA2, to β = 0.223, 95% CI = 0.169, 0.278, p < . 001, for EA3. Parent’s PRS again predicted the socioeconomic status (SES) they provided to their offspring and increased from β = 0.201, 95% CI = 0.147, 0.256 to β = 0.286, 95% CI = 0.239, 0.333. Importantly, the PRS for alleles not transmitted to their offspring — therefore acting via the parenting environment — was increased in effect size from β = 0.058, 95% CI = 0.003, 0.114 to β = 0.067, 95% CI = 0.012, 0.122, p = . 016. As previously found, this non-transmitted genetic effect was fully accounted for by parental SES. The findings reinforce the conclusion that genetic effects of parenting are substantial, explain approximately one-third the magnitude of an individual’s own genetic inheritance and are mediated by parental socioeconomic competence.
hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data

Heavy methyl Stable Isotope Labeling with Amino acids in Cell culture (hmSILAC) is a metabolic labeling strategy employed in proteomics to increase the confidence of global identification of methylated peptides by MS. However, to this day, the automatic and robust identification of heavy and light peak doublets from MS‐raw data of hmSILAC experiments is a challenging task, for which the choice of computational methods is very limited. Here, hmSEEKER, a software designed to work downstream of a MaxQuant analysis for in‐depth search of MS peak pairs that correspond to light and heavy methyl‐peptide within MaxQuant‐generated tables is described with good sensitivity and specificity. The software is written in Perl, and its code and user manual are freely available at Bitbucket (https://bit.ly/2scCT9u).
Adverse events reported by anxious school refusing adolescents receiving cognitive behavioral therapy with and without fluoxetine

Background: Investigating adverse events associated with antidepressant treatments in adolescents is important given the concerns about increased risk of suicidal ideation and behavior in this age group. The aim of this study is to investigate adverse and serious adverse events associated with the treatment of anxiety (cognitive behavioral therapy (CBT)-only, CBT-plus-placebo, and CBT-plus-fluoxetine) in anxious school-refusing adolescents. Methods: A side-effect symptom checklist was completed by participants prior to commencing treatment and during treatment (weekly/fortnightly). Results: CBT-plus-fluoxetine was well tolerated and not associated with higher levels of adverse events than the other treatments. Adverse events in all groups decreased over time, and the only adverse event distinct to fluoxetine was nausea. Baseline anxiety predicted higher levels of adverse events. There was one suicide attempt in the CBT-plus-placebo group but no statistically significant difference in suicide attempts between groups. Participants with a comorbid depressive disorder were more likely to report self-injury ideation but not suicidal ideation compared with those who did not have comorbid depressive disorder. Frequency of suicidal ideation and non-suicidal self-injury was significantly lower in the CBT-plus-fluoxetine group compared with the CBT-only group. Frequency of self-injury ideation was significantly lower in the CBT-plus-fluoxetine group compared with both other groups. Conclusions: Overall, the treatments were well tolerated and fluoxetine plus CBT appeared to be protective against suicidal ideation, non-suicidal self-injury, and self-injury ideation in this sample.
Characterization and identification of long non-coding RNAs based on feature relationship

The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.
Associations between nutritional status, physical performance, and disability among older Americans

ii Acknowledgments iv List of Tables vii List of Figures x List of Abbreviations xi Chapter 1 General Introduction 1 Chapter 2 Literature Review 4 2.1 Functional status in older adults 4 2.2 Diet quality and functional status 19 2.3 Food insecurity and functional status 48 Chapter 3 Association between Overall Diet Quality and Physical Performance: Results from National Health and Nutritional Examination Survey (NHANES) 1999-2002 65 3.1 Abstract 65 3.2 Introduction 67 3.3 Methods 69 3.4 Results 74 3.5 Discussion 76 Chapter 4 Association between Overall Diet Quality and Self-reported Disability among Older Americans: Results from National Health and Nutritional Examination Survey (NHANES) 1999-2004 90 vi 4.1 Abstract 90 4.2 Introduction 92 4.3 Methods 93 4.4 Results 98 4.5 Discussion 101 Chapter 5 Smoking Modifies the Association between Food Insecurity and Physical Performance: Results from National Health and Nutritional Examination Survey (NHANES) 1999-2002 123 5.1 Abstract 123 5.2 Introduction 125 5.3 Methods 126 5.4 Results 131 5.5 Discussion 134 Chapter 6 Overall Conclusions 152 6.1 Goal 152 6.2 Significance of research 154 6.3 Advantages and limitations 155 6.4 Directions for future research 157 References 159 Appendix 183
Different temporal windows for CB1 receptor involvement in contextual fear memory destabilisation in the amygdala and hippocampus

Reconsolidation is a process in which re-exposure to a reminder causes a previously acquired memory to undergo a process of destabilisation followed by subsequent restabilisation. Different molecular mechanisms have been postulated for destabilisation in the amygdala and hippocampus, including CB1 receptor activation, protein degradation and AMPA receptor exchange; however, most of the amygdala studies have used pre-reexposure interventions, while those in the hippocampus have usually performed them after reexposure. To test whether the temporal window for destabilisation is similar across both structures, we trained Lister Hooded rats in a contextual fear conditioning task, and 1 day later performed memory reexposure followed by injection of either the NMDA antagonist MK-801 (0.1 mg/kg) or saline in order to block reconsolidation. In parallel, we also performed local injections of either the CB1 antagonist SR141716A or its vehicle in the hippocampus or in the amygdala, either immediately before or immediately after reactivation. Infusion of SR141716A in the hippocampus prevented the reconsolidation-blocking effect of MK-801 when performed after reexposure, but not before it. In the amygdala, meanwhile, pre-reexposure infusions of SR141716A impaired reconsolidation blockade by MK-801, although the time-dependency of this effect was not as clear as in the hippocampus. Our results suggest the temporal windows for CB1-receptor-mediated memory destabilisation during reconsolidation vary between brain structures. Whether this reflects different time windows for engagement of these structures or different roles played by CB1 receptors in destabilisation across structures remains an open question for future studies.
Anthocyanin Consumption and Risk of Colorectal Cancer: A Meta-Analysis of Observational Studies

Abstract This meta-analysis aimed to summarize the association between anthocyanin consumption and the risk of colorectal cancer. All relative articles were located on online databases, including PubMed, Embase, and the Cochrane Library as of June 11, 2018. Risk ratios (RRs) or odds ratio and their 95% confidence intervals (CIs) were calculated through the STATA 12.0 software package. A total of seven studies were included in the meta-analysis. A significant inverse association was found between total anthocyanin consumption and colorectal cancer risk (RR = 0.78; 95% CI, 0.64–0.95). Likewise, there was significant evidence of a relationship between anthocyanin intake and colorectal cancer in the colon site (RR = 0.81; 95% CI, 0.71–0.92); men (RR = 0.88; 95% CI, 0.81–0.95), and case-control studies (RR = 0.69; 95% CI, 0.60–0.78). A dose–response relationship was not found in this meta-analysis. The Grades of Recommendations Assessment, Development, and Evaluation quality in our study was very low. This meta-analysis indicates that anthocyanin consumption is inversely associated with the risk of colorectal cancer. Anthocyanins may play an active role in the prevention of colorectal cancer. Key teaching points: Some epidemiological studies found an inverse correlation between the high consumption of anthocyanins and low risk of colorectal cancer. Because of this structure, anthocyanins/anthocyanidins have a powerful capability of donating electrons, which can be characterized as antioxidant properties. Anthocyanins can also inhibit colon cancer by interfering in the cell cycle and inducing the effect of anti-proliferation and apoptosis. The formation of cytoplasmic vacuoles in cells also indicates that anthocyanins may induce autophagy. From the findings of nonrandomized controlled trials, anthocyanins may play an active role in the prevention of colorectal cancer.
Absence of TGFβ signaling in retinal microglia induces retinal degeneration and exacerbates choroidal neovascularization

Constitutive TGFβ signaling is important in maintaining retinal neurons and blood vessels and is a factor contributing to the risk for age-related macular degeneration (AMD), a retinal disease involving neurodegeneration and microglial activation. How TGFβ signaling to microglia influences pathological retinal neuroinflammation is unclear. We discovered that ablation of the TGFβ receptor, TGFBR2, in retinal microglia of adult mice induced abnormal microglial numbers, distribution, morphology, and activation status, and promoted a pathological microglial gene expression profile. TGFBR2-deficient retinal microglia induced secondary gliotic changes in Müller cells, neuronal apoptosis, and decreased light-evoked retinal function reflecting abnormal synaptic transmission. While retinal vasculature was unaffected, TGFBR2-deficient microglia demonstrated exaggerated responses to laser-induced injury that was associated with increased choroidal neovascularization, a hallmark of advanced exudative AMD. These findings demonstrate that deficiencies in TGFβ-mediated microglial regulation can drive neuroinflammatory contributions to AMD-related neurodegeneration and neovascularization, highlighting TGFβ signaling as a potential therapeutic target.
Carotid Flow Augmentation, Arterial Aging, and Cerebral White Matter Hyperintensities: Comparison With Pressure Augmentation

Objective— Aortic stiffness and pressure wave reflection are associated with age-related cerebral microvascular disease, but the underlying mechanism remains obscure. We hypothesized that cerebral (carotid) flow alterations potentially mediate these associations. Approach and Results— Doppler waveforms were recorded in 286 patients with hypertension to measure the carotid flow augmentation index (FAIx) as the late/early-systolic velocity amplitude ratio. Tonometric waveforms were recorded to estimate the aortic pressure AIx (PAIx), aortic compliance, and carotid-femoral and carotid-radial pulse wave velocities. Additionally, white matter hyperintensities on brain magnetic resonance imaging were evaluated using the Fazekas scale. With increasing age, the carotid late systolic velocity increased, whereas the early systolic velocity decreased, although the aortic augmented pressure increased in parallel with the incident wave height (P<0.001). Both FAIx and PAIx increased with age, but the age-dependent curves were upwardly concave and convex, respectively. FAIx increased exponentially with increasing PAIx (r=0.71). Compared with PAIx, FAIx was more closely (P⩽0.001) correlated with the aortic pulse wave velocity, aortic compliance, and elastic/muscular pulse wave velocity ratio. FAIx was associated with white matter hyperintensities scores independently of confounders including age, sex, diabetes mellitus, hypercholesterolemia, and aortic pulse wave velocity (P=0.01), and was more predictive of white matter hyperintensities presence than PAIx. Conclusions— Carotid FAIx had closer associations with age, aortic stiffness, and cerebral white matter hyperintensities than aortic PAIx. These results indicate that carotid flow augmentation (enhanced by aortic stiffening and pressure wave reflection from the lower body) causes microcerebrovascular injury potentially through increasing cerebral flow pulsations, but this detrimental effect is greater than that estimated from PAIx.
LINC00261 and the Adjacent Gene FOXA2 Are Epithelial Markers and Are Suppressed during Lung Cancer Tumorigenesis and Progression

Lung cancer continues to be the leading cause of cancer-related deaths worldwide, with little improvement in patient survival rates in the past decade. Long non-coding RNAs (lncRNAs) are gaining importance as possible biomarkers with prognostic potential. By large-scale data mining, we identified LINC00261 as a lncRNA which was significantly downregulated in lung cancer. Low expression of LINC00261 was associated with recurrence and poor patient survival in lung adenocarcinoma. Moreover, the gene pair of LINC00261 and its neighbor FOXA2 were significantly co-regulated. LINC00261 as well as FOXA2 negatively correlated with markers for epithelial-to-mesenchymal transition (EMT) and were suppressed by the EMT inducer TGFβ. Hierarchical clustering of gene expression data from lung cancer cell lines could further verify the association of high LINC00261/FOXA2 expression to an epithelial gene signature. Furthermore, higher expression of the LINC00261/FOXA2 locus was associated with lung cancer cell lines with lower migratory capacity. All these data establish LINC00261 and FOXA2 as an epithelial-specific marker pair, downregulated during EMT and lung cancer progression, and associated with lower cell migration potential in lung cancer cells.
The role of stimulation protocol, number of oocytes retrieved with respect to follicular fluid oxidative stress and IVF outcome

Abstract The study was conducted on a population of 203 women attending the IVF clinic, Ahmedabad, India, to explore the role of stimulation protocol and the number of oocytes retrieved on oxidative stress in follicular fluid and IVF outcome. Follicular fluid was collected during ovum pick-up to determine the oxidative stress markers: superoxide dismutase (SOD), malondialdehyde (MDA), glutathione (GSH), total thiols (TT), l-ascorbic acid (AA), total protein, glutathione S-transferase (GST) and glutathione reductase (GRD). The average number of oocytes retrieved was significantly higher in the women receiving a long GnRH agonist protocol compared to GnRH antagonist protocol while the percentage of women with positive IVF outcome was lower in the long agonist protocol. The level of total thiols was significantly lower in the group of women administered a short agonist protocol. The proportion of ETs carried out and positive IVF outcome were higher following retrieval of an intermediate number of oocytes (6–10 oocytes) compared to a lower (0–5 oocytes) and higher (>10 oocytes) number. Mean glutathione reductase (GRD) activity in follicular fluid was significantly elevated in the intermediate (6–10) and higher (>10) oocyte retrieval groups compared to the lower oocyte retrieval group. Positive IVF outcomes were highest when oocyte retrieval was in the range of 6–10 oocytes, and the level of MDA was lower (1.76 ± 0.13 nmol/ml) as compared to 0–5 and >10 oocytes retrieved groups.
Is there an asymmetry of the condylar and coronoid processes of the mandible in individuals with unilateral crossbite?

OBJECTIVES To evaluate if there is a true skeletal asymmetry of the condylar and coronoid processes of the mandible in growing individuals with unilateral posterior crossbite (UPC) either functional or not. MATERIALS AND METHODS This cross-sectional study screened a total of 1120 cone beam computed tomography (CBCT) scans based on inclusion and exclusion criteria. The final sample comprised 20 CBCT images of individuals with UPC and 19 CBCT images of individuals without transverse malocclusion. The lengths of the condylar and coronoid processes were measured to evaluate asymmetry, as well as the magnitude of the mandibular lateral deviation in the UPC group. RESULTS There was a significant difference between the lengths of the affected and nonaffected sides of the coronoid processes in the UPC group (P < .01). The same was not observed in the condyle in the UPC group (P > .05). There were no significant differences between the groups (P > .05). CONCLUSIONS Although no differences in the condyle were observed, the coronoid process was asymmetric in individuals with UPC. However, this asymmetry was not considered to be clinically significant.