Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Dental Caries and Associated Factors in East Africa, 2000–2020: Systematic Review and Meta-Analysis

Background: Dental caries affects mastication, growth and development, and school attendance and has a long-term psychological effect on affected individuals. In developing countries, the prevalence of dental caries is increasing due to the growing consumption of sugary foods, poor tooth brushing habits, and a low level of awareness about dental caries. Even if there was a high prevalence of dental caries in sub-Saharan Africa, there is a paucity of data on the prevalence of dental caries in East Africa. Hence, this study aimed to determine the prevalence of dental caries and associated factors in East Africa. Methods: A systematic search of articles was conducted in MEDLINE, Scopus, and Google Scholar using all the synonyms of dental caries in published literature (until December 2020) in East Africa. Important data were extracted using a standardized data extraction form prepared in Excel. Stata software (version 14.0) was used to calculate the pooled prevalence of dental caries. Besides, subgroup analysis was done based on country and dentition type. Moreover, associated factors of dental caries were assessed and the overall effect was presented in the form of odds ratios. The quality of the included studies was evaluated using the Joanna Briggs Institute reviewers' manual. Results: The overall pooled prevalence of dental caries was found to be 45.7% (95% CI = 38.0–53.4). The pooled prevalence was high in Eritrea (65.2%, 95% CI = 49.2–81.1), followed by Sudan (57.8%, 95% CI = 36.0–79.7), and a low prevalence was found in Tanzania (30.7%, 95% CI = 21.5–39.9). Moreover, the subgroup analysis revealed a prevalence of 50% (95% CI = 38.4–62.1) in permanent dentition and 41.3% (95% CI = 33.5–49.2) in mixed dentition. The overall mean decayed, missed, and filled permanent (DMFT) and primary (dmft) teeth were 1.941 (95% CI = 1.561–2.322) and 2.237 (95% CI = 1.293–3.181), respectively. High DMFT scores were reported in Sudan (3.146, 95% CI = 1.050–5.242) and Uganda (2.876, 95% CI = 2.186–3.565). Being female (OR = 1.34, 95% CI = 1.24–1.46) and having poor tooth brushing habit (OR = 1.967, 95% CI = 1.67–2.33) were independent risk factors of dental caries. Conclusion: The overall prevalence of dental caries was comparatively high. Being female and poor oral health practice were independent risk factors of dental caries. The Ministry of Health of the member countries, along with dental associations of each country, ought to offer due attention to strengthen the oral health program in schools and primary health care centers and the implementation of school water fluoridation.
Systemic Screening for 22q11.2 Copy Number Variations in Hungarian Pediatric and Adult Patients With Congenital Heart Diseases Identified Rare Pathogenic Patterns in the Region

Congenital heart defects (CHD) are the most common developmental abnormalities, affecting approximately 0.9% of livebirths. Genetic factors, including copy number variations (CNVs), play an important role in their development. The most common CNVs are found on chromosome 22q11.2. The genomic instability of this region, caused by the eight low copy repeats (LCR A-H), may result in several recurrent and/or rare microdeletions and duplications, including the most common, ∼3 Mb large LCR A-D deletion (classical 22q.11.2 deletion syndrome). We aimed to screen 22q11.2 CNVs in a large Hungarian pediatric and adult CHD cohort, regardless of the type of their CHDs. All the enrolled participants were cardiologically diagnosed with non-syndromic CHDs. A combination of multiplex ligation-dependent probe amplification (MLPA), chromosomal microarray analysis and droplet digital PCR methods were used to comprehensively assess the detected 22q11.2 CNVs in 212 CHD-patients. Additionally, capillary sequencing was performed to detect variants in the TBX1 gene, a cardinal gene located in 22q11.2. Pathogenic CNVs were detected in 5.2% (11/212), VUS in 0.9% and benign CNVs in 1.8% of the overall CHD cohort. In patients with tetralogy of Fallot the rate of pathogenic CNVs was 17% (5/30). Fifty-four percent of all CNVs were typical proximal deletions (LCR A-D). However, nested (LCR A-B) and central deletions (LCR C-D), proximal (LCR A-D) and distal duplications (LCR D-E, LCR D-H, LCR E-H, LCR F-H) and rare combinations of deletions and duplications were also identified. Segregation analysis detected familial occurrence in 18% (2/11) of the pathogenic variants. Based on in-depth clinical information, a detailed phenotype–genotype comparison was performed. No pathogenic variant was identified in the TBX1 gene. Our findings confirmed the previously described large phenotypic diversity in the 22q11.2 CNVs. MLPA proved to be a highly efficient genetic screening method for our CHD-cohort. Our results highlight the necessity for large-scale genetic screening of CHD-patients and the importance of early genetic diagnosis in their clinical management.
Dietary Carbohydrate and Diverse Health Outcomes: Umbrella Review of 30 Systematic Reviews and Meta-Analyses of 281 Observational Studies

Background and Aims: The associations between dietary carbohydrate and diverse health outcomes remain controversial and confusing. To summarize the existing evidence of the association between dietary carbohydrate intake and diverse health outcomes and to evaluate the credibility of these sources of evidence. We performed this umbrella review of evidence from meta-analyses of observational studies. Methods: PubMed, Embase, Web of Science databases, and manual screening of references up to July 2020 were searched. Systematic reviews with meta-analyses of observational studies in humans investigating the association between dietary carbohydrate intake and multiple health outcomes were identified. We assessed the evidence levels by using summary effect sizes, 95% prediction intervals, between-study heterogeneity, evidence of small-study effects, and evidence of excess significance bias for each meta-analysis. Results: We included 43 meta-analyses of observational research studies with 23 health outcomes, including cancer (n = 26), mortality (n = 4), metabolic diseases (n = 4), digestive system outcomes (n = 3), and other outcomes [coronary heart disease (n = 2), stroke (n = 1), Parkinson's disease (n = 1), and bone fracture (n = 2)]. This umbrella review summarized 281 individual studies with 13,164,365 participants. Highly suggestive evidence of an association between dietary carbohydrate intake and metabolic syndrome was observed with adjusted summary odds ratio of 1.25 [95% confidence interval (CI) 1.15–1.37]. The suggestive evidences were observed in associations of carbohydrate consumption with esophageal adenocarcinoma (0.57, 95% CI = 0.42–0.78) and all-cause mortality (adjusted summary hazard ratio 1.19, 95% CI = 1.09–1.30). Conclusions: Despite the fact that numerous systematic reviews and meta-analyses have explored the relationship between carbohydrate intake and diverse health outcomes, there is no convincing evidence of a clear role of carbohydrate intake. However, there is highly suggestive evidence suggested carbohydrate intake is associated with high risk of metabolic syndrome, suggestive evidence found its association with increased risk of all-cause mortality and decreased risk of esophageal adenocarcinoma. Systematic Review Registration: CRD42020197424.
A Cross-Sectional Study Investigating the Relationship Between Alexithymia and Suicide, Violence, and Dual Harm in Male Prisoners

Background: Suicide and violence are common within male prisoners. One suggested risk factor for both behaviors is alexithymia. Alexithymia describes a deficit in identifying and describing feelings and is also related to externally oriented thinking. This study aimed to explore the relationship between alexithymia, suicide, violence and dual harm in male prisoners. Methods: Eighty male prisoners were recruited from three prisons. Participants were asked to complete a battery of questionnaires including measures of alexithymia (TAS-20), suicide ideation (ASIQ), suicide behavior, violence ideation (SIV), violence behavior, depression (BDI-II), hopelessness (BHS), impulsivity (DII) and anger (NAS-PI). Regression analyses and ANOVAS were conducted to assess the association between alexithymia (and its subcomponents) with six outcomes; suicide ideation, suicide behavior, violence ideation, violence behavior, dual harm ideation and dual harm behavior. Results: Alexithymia was a univariate predictor of suicide ideation, though was not a significant predictor when considered in a multivariate model. Alexithymia was a significant multivariate predictor of suicide behavior. Alexithymia was not a significant multivariate predictor of violence ideation or behavior. There were no significant differences in alexithymia or subscales between those with suicide ideation/behavior alone, violence ideation/behavior alone and those with dual harm ideation/behavior. Conclusion: In male prisoners, alexithymia appears an important univariate predictor of suicide and violence, though the current study suggests no significant contribution above other well-known correlates of suicide and violence.
A Proposed Hypothesis on Dementia: Inflammation, Small Vessel Disease, and Hypoperfusion Is the Sequence That Links All Harmful Lifestyles to Cognitive Impairment

There is growing consensus that certain lifestyles can contribute to cognitive impairment and dementia, but the physiological steps that link a harmful lifestyle to its negative impact are not always evident. It is also unclear whether all lifestyles that contribute to dementia do so through the same intermediary steps. This article will focus on three lifestyles known to be risk factors for dementia, namely obesity, sedentary behavior, and insufficient sleep, and offer a unifying hypothesis proposing that lifestyles that negatively impact cognition do so through the same sequence of events: inflammation, small vessel disease, decline in cerebral perfusion, and brain atrophy. The hypothesis will then be tested in a recently identified risk factor for dementia, namely hearing deficit. If further studies confirm this sequence of events leading to dementia, a significant change in our approach to this debilitating and costly condition may be necessary, possible, and beneficial.
Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological Samples: Peptides Presented by I-Ab in C57BL/6 Mouse Thymus

Antigen presentation by MHC-II proteins in the thymus is central to selection of CD4 T cells, but analysis of the full repertoire of presented peptides responsible for positive and negative selection is complicated by the low abundance of antigen presenting cells. A key challenge in analysis of limiting abundance immunopeptidomes by mass spectrometry is distinguishing true MHC-binding peptides from co-eluting non-specifically bound peptides present in the mixture eluted from immunoaffinity-purified MHC molecules. Herein we tested several approaches to minimize the impact of non-specific background peptides, including analyzing eluates from isotype-control antibody-conjugated beads, considering only peptides present in nested sets, and using predicted binding motif analysis to identify core epitopes. We evaluated these methods using well-understood human cell line samples, and then applied them to analysis of the I-Ab presented immunopeptidome of the thymus of C57BL/6 mice, comparing this to the more easily characterized splenic B cell and dendritic cell populations. We identified a total of 3473 unique peptides eluted from the various tissues, using a data dependent acquisition strategy with a false-discovery rate of <1%. The immunopeptidomes presented in thymus as compared to splenic B cells and DCs identified shared and tissue-specific epitopes. A broader length distribution was observed for peptides presented in the thymus as compared to splenic B cells or DCs. Detailed analysis of 61 differentially presented peptides indicated a wider distribution of I-Ab binding affinities in thymus as compared to splenic B cells. These results suggest different constraints on antigen processing and presentation pathways in central versus peripheral tissues.
Social-Cognitive Determinants of HIV Testing Among Tuberculosis Infected Patients in Kassala State, Sudan

Background: Use of HIV testing and counselling (HTC) services remains low among TB patients in Sudan. Identifying the social-cognitive (sub) determinants associated with HTC uptake is essential before developing interventions to promote uptake. This study aims to assess the sub-determinants of intention to use and actual behaviour of using HTC services among TB patients in Sudan and to ascertain the most relevant beliefs to inform future interventions. Methods: A cross-sectional study was carried out in five health facilities selected randomly in Kassala State. First, a small elicitation study (N = 25) was conducted to inform the Reasoned Action Approach (RAA) based questionnaire. A total of 411 TB patients completed the survey questionnaire. Confidence Interval Based Estimation of Relevance analysis (CIBER) was employed to establish the sub-determinants' relevance. Result: The studied beliefs explained 38–52% of the variance in the intention and 20–35% in the behaviour variance. The beliefs that “Using HTC services increases my fear of being tested positive for HIV” and “Using HTC services increases my fear of losing my partner if I have a positive test result” were negatively associated with intentions and use of HTC services; and both were highly relevant for intervention. The belief “If I use HTC services, I would know my HIV status” was positively associated with intentions and use of HTC services. However, it was less relevant for intervention. Perceived susceptibility to HIV infection was not associated with intention and only weakly associated with use of HTC services. Its relevance was low for intervention. Conclusions: The study showed that the social-cognitive beliefs (sub-determinants) vary in their relationship with the intention and use of HTC services among TB patients; with variable relevance for intervention. Interventions to enhance the use of HTC services should address the most relevant beliefs to maximise the effectiveness of interventions. Further studies are needed to identify other relevant sub-determinants of HTC use behaviour.
Sense of Resistance for a Cursor Moved by User’s Keystrokes

Haptic sensation of a material can be modulated by its visual appearance. A technique that utilizes this visual-haptic interaction is called as pseudo-haptic feedback. Conventional studies have investigated pseudo-haptic feedback in situations, wherein a user manipulated a virtual object using a computer mouse, a force-feedback device, etc. The present study investigated whether and how it was possible to offer pseudo-haptic feedback to a user who manipulated a virtual object using keystrokes. Participants moved a cursor toward a destination by pressing a key. While the cursor was moving, the cursor was temporarily slowed down on a square area of the screen. The participants’ task was to report, on a five-point scale, how much resistance they felt to the cursor’s movement. In addition to the basic speed of the cursor, the ratio of the basic speed to the speed within the square area was varied. In Experiment 1, we found that these two factors interacted significantly with each other, but further analysis showed that the cursor speed within the square area was the most important determinant of perceived resistance. In Experiment 2, consistent with the results of the previous experiment, it was found that the cursor movement outside of the square area was not required to generate the sense of resistance. Counterintuitively, in Experiment 3, the sense of resistance was apparent even without user’s keystrokes. We discuss how the sense of resistance for a cursor moved by keystrokes can be triggered visually, but interpreted by the brain as a haptic impression.
Comprehensive Analysis of Myeloid Signature Genes in Head and Neck Squamous Cell Carcinoma to Predict the Prognosis and Immune Infiltration

Myeloid cells are a major heterogeneous cell population in the tumor immune microenvironment (TIME). Imbalance of myeloid response remains a major obstacle to a favorable prognosis and successful immune therapy. Therefore, we aimed to construct a risk model to evaluate the myeloid contexture, which may facilitate the prediction of prognosis and immune infiltration in patients with head and neck squamous cell carcinoma (HNSCC). In our study, six myeloid signature genes (including CCL13, CCR7, CD276, IL1B, LYVE1 and VEGFC) analyzed from 52 differentially expressed myeloid signature genes were finally pooled to establish a prognostic risk model, termed as myeloid gene score (MGS) in a training cohort and validated in a test cohort and an independent external cohort. Furthermore, based on the MGS subgroups, we were able to effectively identify patients with a poor prognosis, aggressive clinical parameters, immune cell infiltration status and immunotherapy response. Thus, MGS may serve as an effective prognostic signature and predictive indicator for immunotherapy response in patients with HNSCC.
Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord

The spinal cord dorsal horn is a major station for integration and relay of somatosensory information and comprises both excitatory and inhibitory neuronal populations. The homeobox gene Tlx3 acts as a selector gene to control the development of late-born excitatory (dILB) neurons by specifying glutamatergic transmitter fate in dorsal spinal cord. However, since Tlx3 direct transcriptional targets remain largely unknown, it remains to be uncovered how Tlx3 functions to promote excitatory cell fate. Here we combined a genomics approach based on chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and expression profiling, with validation experiments in Tlx3 null embryos, to characterize the transcriptional program of Tlx3 in mouse embryonic dorsal spinal cord. We found most dILB neuron specific genes previously identified to be directly activated by Tlx3. Surprisingly, we found Tlx3 also directly represses many genes associated with the alternative inhibitory dILA neuronal fate. In both cases, direct targets include transcription factors and terminal differentiation genes, showing that Tlx3 directly controls cell identity at distinct levels. Our findings provide a molecular frame for the master regulatory role of Tlx3 in developing glutamatergic dILB neurons. In addition, they suggest a novel function for Tlx3 as direct repressor of GABAergic dILA identity, pointing to how generation of the two alternative cell fates being tightly coupled.
Does the Rural Environment Influence Symptomatology and Optimize the Effectiveness of Disease Acceptance? A Study Among Women With Fibromyalgia

The present study aims to explore whether the symptoms associated with fibromyalgia are contextually influenced by the area of residence (rural/urban). Furthermore, it is analyzed whether the effect of the acceptance of the disease on the emotional, cognitive and physical symptoms is moderated by the patients’ place of residence. Using a cross-sectional design, a total of 234 women with fibromyalgia (mean age = 56.91 years; SD = 8.94) were surveyed, of which 55.13% resided in rural areas and 44.87% in urban areas. Self-reported questionnaires were used to assess pain severity, anxiety and depression, functional limitation, physical and mental fatigue and acceptance of the disease. The results show significant differences in acceptance (p = 0.040), pain (p < 0.001), and physical and mental fatigue (p = 0.003 and p = 0.004, respectively) between patients from rural and urban areas. The rural area patients presented higher levels of acceptance and pain and lesser levels of physical and mental fatigue compared to the urban area. The moderation analysis add that, only in patients from the rural area, the variables of physical symptoms (pain, functional limitation, and physical fatigue) were significantly and negatively associated with acceptance. This study addresses for the first time the role of the place of residence in suffering from fibromyalgia, suggesting that the rural or urban environment plays a relevant role in the severity and/or management of symptoms in fibromyalgia women. Limitations and practical implications are also discussed.
Production and Characterization of High Value Prebiotics From Biorefinery-Relevant Feedstocks

Hemicellulose, a structural polysaccharide and often underutilized co-product stream of biorefineries, could be used to produce prebiotic ingredients with novel functionalities. Since hot water pre-extraction is a cost-effective strategy for integrated biorefineries to partially fractionate hemicellulose and improve feedstock quality and performance for downstream operations, the approach was applied to process switchgrass (SG), hybrid poplar (HP), and southern pine (SP) biomass at 160°C for 60 min. As a result, different hemicellulose-rich fractions were generated and the chemical characterization studies showed that they were composed of 76–91% of glucan, xylan, galactan, arabinan, and mannan oligosaccharides. The hot water extracts also contained minor concentrations of monomeric sugars (≤18%), phenolic components (≤1%), and other degradation products (≤3%), but were tested for probiotic activity without any purification. When subjected to batch fermentations by individual cultures of Lactobacillus casei, Bifidobacterium bifidum, and Bacteroides fragilis, the hemicellulosic hydrolysates elicited varied responses. SG hydrolysates induced the highest cell count in L. casei at 8.6 log10 cells/ml, whereas the highest cell counts for B. fragilis and B. bifidum were obtained with southern pine (5.8 log10 cells/ml) and HP hydrolysates (6.4 log10 cells/ml), respectively. The observed differences were attributed to the preferential consumption of mannooligosaccharides in SP hydrolysates by B. fragilis. Lactobacillus casei preferentially consumed xylooligosaccharides in the switchgrass and southern pine hydrolysates, whereas B. bifidum consumed galactose in the hybrid poplar hydrolysates. Thus, this study (1) reveals the potential to produce prebiotic ingredients from biorefinery-relevant lignocellulosic biomass, and (2) demonstrates how the chemical composition of hemicellulose-derived sources could regulate the viability and selective proliferation of probiotic microorganisms.
Systematic Evaluation of Design Choices for Deep Facial Action Coding Across Pose

The performance of automated facial expression coding is improving steadily. Advances in deep learning techniques have been key to this success. While the advantage of modern deep learning techniques is clear, the contribution of critical design choices remains largely unknown, especially for facial action unit occurrence and intensity across pose. Using the The Facial Expression Recognition and Analysis 2017 (FERA 2017) database, which provides a common protocol to evaluate robustness to pose variation, we systematically evaluated design choices in pre-training, feature alignment, model size selection, and optimizer details. Informed by the findings, we developed an architecture that exceeds state-of-the-art on FERA 2017. The architecture achieved a 3.5% increase in F1 score for occurrence detection and a 5.8% increase in Intraclass Correlation (ICC) for intensity estimation. To evaluate the generalizability of the architecture to unseen poses and new dataset domains, we performed experiments across pose in FERA 2017 and across domains in Denver Intensity of Spontaneous Facial Action (DISFA) and the UNBC Pain Archive.