Miracle-dz/UniFAR-FTUs huggingface dataset:
Amelogenin Exon4 Forms a Novel miRNA That Directs Ameloblast and Osteoblast Differentiation

Amelogenins constitute the major portion of secretory enamel matrix proteins and are known to be highly alternative spliced. Of all the alternatively spliced forms of amelogenins, exon4 is most commonly spliced out. Our analyses of the exon4 sequence led us to hypothesize that when spliced out, exon4 may generate a novel mature miRNA. To explore this possibility, we used in vivo mouse models (wild-type and Amel knockout mice) and in vitro cell culture to investigate the presence and function of a mature miRNA derived from exon4 (miR-exon4). When ameloblast-like cells (LS8) were transfected with an amelogenin minigene to increase amelogenin synthesis, the transfected cells synthesized miR-exon4. Introduction of a mutation in the conserved CNNC sequence required for primary miRNA recognition, downstream of the mature miR-exon4 sequence, resulted in a significantly reduced production of miR-exon4 in the transfected cells. In vivo, miR-exon4 was most highly amplified from wild-type mouse enamel organs at the secretory stage. In Amel knockout mice, an in vivo model for reduced amelogenin synthesis, we found reduced miR-exon4, with no changes in expression of enamel matrix–related genes. However, expression of Runx2 and its downstream genes Odam and Amtn were significantly downregulated. Transfection of miR-exon4 mimic to the LS8 cells also significantly upregulated Runx2. The mature miR-exon4 as well as Runx2 was also present in mouse osteoblasts with no apparent change in expression level between wild-type and Amel knockout mice. However, transfecting miR-exon4 inhibitor to the MC3T3-E1 osteoblastic cells resulted in a significant downregulation of Runx2 expression. These data indicate that when exon4 is spliced out, as occurs most of the time during alternative splicing of amelogenin pre-mRNA, a novel mature miRNA is generated from exon4. This miR-exon4 may contribute to the differentiation of ameloblasts and osteoblasts through regulation of Runx2 expression.
Mast Cells Contribute to Porphyromonas gingivalis–induced Bone Loss

Periodontitis is a chronic inflammatory and bone-destructive disease. Development of periodontitis is associated with dysbiosis of the microbial community, which may be caused by periodontal bacteria, such as Porphyromonas gingivalis. Mast cells are sentinels at mucosal surfaces and are a potent source of inflammatory mediators, including tumor necrosis factors (TNF), although their role in the pathogenesis of periodontitis remains to be elucidated. This study sought to determine the contribution of mast cells to local bone destruction following oral infection with P. gingivalis. Mast cell–deficient mice (KitW-sh/W-sh) were protected from P. gingivalis–induced alveolar bone loss, with a reduction in anti–P. gingivalis serum antibody titers compared with wild-type infected controls. Furthermore, mast cell–deficient mice had reduced expression of Tnf, Il6, and Il1b mRNA in gingival tissues compared with wild-type mice. Mast cell–engrafted KitW-sh/W-sh mice infected with P. gingivalis demonstrated alveolar bone loss and serum anti–P. gingivalis antibody titers equivalent to wild-type infected mice. The expression of Tnf mRNA in gingival tissues of KitW-sh/W-sh mice was elevated following the engraftment of mast cells, indicating that mast cells contributed to the Tnf transcript in gingival tissues. In vitro, mast cells degranulated and released significant TNF in response to oral bacteria, and neutralizing TNF in vivo abrogated alveolar bone loss following P. gingivalis infection. These data indicate that mast cells and TNF contribute to the immunopathogenesis of periodontitis and may offer therapeutic targets.
A framework to detect unqualified restaurant reviews

Nowadays there are numerous user-generated restaurant reviews available on the Internet, of which they are considered valuable resources for decision making to customers. In reality, not every reviews available online are helpful to users, so the need for filtering unqualified reviews is realized. There have been several studies on spam review detection that attempt to detect unqualified reviews using n-gram linguistic features. They attempted to classify reviews written in English into two categories: filtered and unfiltered reviews. In our paper, we are aware that filtered reviews can be categorized further into advertisements, complaints, and non-review opinions. Each type of filtered reviews requires different actions be taken on them. For instance, advertisements should be deleted while the others should be hidden. This paper proposes a framework for unqualified restaurant reviews detection using SVM. The data set of restaurant reviews is provided by a web portal for restaurants in Thailand. There are three main processes in our framework: (1) filtering obvious spam, (2) data pre-processing, and (3) classification using SVM. We find that the procedures in our framework can improve classification accuracy compared with standard frameworks.
Classification in medical images using adaptive metric k-NN

The performance of the k-nearest neighborhoods (k-NN) classifier is highly dependent on the distance metric used to identify the k nearest neighbors of the query points. The standard Euclidean distance is commonly used in practice. This paper investigates the performance of k-NN classifier with respect to different adaptive metrics in the context of medical imaging. We propose using adaptive metrics such that the structure of the data is better described, introducing some unsupervised learning knowledge in k-NN. We investigated four different metrics are estimated: a theoretical metric based on the assumption that images are drawn from Brownian Image Model (BIM), the normalized metric based on variance of the data, the empirical metric is based on the empirical covariance matrix of the unlabeled data, and an optimized metric obtained by minimizing the classification error. The spectral structure of the empirical covariance also leads to Principal Component Analysis (PCA) performed on it which results the subspace metrics. The metrics are evaluated on two data sets: lateral X-rays of the lumbar aortic/spine region, where we use k-NN for performing abdominal aorta calcification detection; and mammograms, where we use k-NN for breast cancer risk assessment. The results show that appropriate choice of metric can improve classification.
A Critical Role for Extracellular DNA in Dental Plaque Formation

Extracellular DNA (eDNA) has been identified in the matrix of many different monospecies biofilms in vitro, including some of those produced by oral bacteria. In many cases, eDNA stabilizes the structure of monospecies biofilms. Here, the authors aimed to determine whether eDNA is an important component of natural, mixed-species oral biofilms, such as plaque on natural teeth or dental implants. To visualize eDNA in oral biofilms, approaches for fluorescently stained eDNA with either anti-DNA antibodies or an ultrasensitive cell-impermeant dye, YOYO-1, were first developed using Enterococcus faecalis, an organism that has previously been shown to produce extensive eDNA structures within biofilms. Oral biofilms were modelled as in vitro “microcosms” on glass coverslips inoculated with the natural microbial population of human saliva and cultured statically in artificial saliva medium. Using antibodies and YOYO-1, eDNA was found to be distributed throughout microcosm biofilms, and was particularly abundant in the immediate vicinity of cells. Similar arrangements of eDNA were detected in biofilms on crowns and overdenture abutments of dental implants that had been recovered from patients during the restorative phase of treatment, and in subgingival dental plaque of periodontitis patients, indicating that eDNA is a common component of natural oral biofilms. In model oral biofilms, treatment with a DNA-degrading enzyme, NucB from Bacillus licheniformis, strongly inhibited the accumulation of biofilms. The bacterial species diversity was significantly reduced by treatment with NucB and particularly strong reductions were observed in the abundance of anaerobic, proteolytic bacteria such as Peptostreptococcus, Porphyromonas and Prevotella. Preformed biofilms were not significantly reduced by NucB treatment, indicating that eDNA is more important or more exposed during the early stages of biofilm formation. Overall, these data demonstrate that dental plaque eDNA is potentially an important target for oral biofilm control.
Multi-point impedance control for redundant manipulators

This paper proposes an impedance control method called the multi-point impedance control (MPIC) for redundant manipulators. The method can not only control end-effector impedance, but also regulate impedances of several points on the links of the manipulator, which are called virtual end-point impedances, utilizing arm redundancy. Two approaches for realizing the MPIC are presented. In the first approach, controlling the end-effector impedance and the virtual end-point impedances are considered as the tasks with the same level, and the joint control law developed in this approach can realize the closest impedances of the multiple points, including the end-effector and the virtual end-points to the desired ones in the least squared sense. On the other hand, in the second approach, controlling the end-effector impedance is considered the most important task, and regulating the impedances of the virtual end-points is considered as a sub-task. Under the second approach, the desired end-effector impedance can be always realized since the joint control torque for the regulation of the virtual end-point impedances is designed in such a way that it has no effect on the end-effector motion of the manipulator. Simulation experiments are performed to confirm the validity and to show the advantages of the proposed method.
Longitudinal Stability of Common TMJ Structural Disorders

The longitudinal course of temporomandibular joint (TMJ) disc displacement (DD) and degenerative joint disease (DJD) has never been conclusively described with magnetic resonance imaging and computed tomography, respectively. This 8-y observational study’s objective was to assess the longitudinal stability of DD and DJD among 401 subjects. The Validation Project provided baseline measures; follow-up was performed in the TMJ Impact Project. With magnetic resonance imaging, 2 radiologists rendered a consensus diagnosis of normal/indeterminate, DD with reduction, or DD without reduction. Computed tomography consensus diagnoses included normal/indeterminate, grade 1 DJD, or grade 2 DJD. Radiologist reliability was assessed by kappa; a Hui-Walter model was used to estimate, after accounting for diagnostic disagreement, the frequency of diagnostic progression and reversal. Permutation tests were used to test the statistical influence of concurrent baseline diagnoses on diagnostic changes at follow-up. Of 789 baseline joint-specific soft tissue diagnoses of DD, 598 (76%) joints showed no change; 109 (14%) demonstrated progression; and 82 (10%) had reversal. Of 794 joints with baseline joint-specific hard tissue diagnoses of DJD, progression was observed in 122 (15%) joints, no change in 564 (71%), and reversal in 108 (14%). Radiologist reliability (kappa) was 0.73 (95% CI, 0.64 to 0.83) for DD and 0.76 (95% CI, 0.68 to 0.83) for DJD. After accounting for the influence of diagnostic disagreement, progression of hard tissue diagnoses in the right TMJ occurred in 15.2% of subjects (95% CI, 10.5% to 20.8%) and reversal in 8.3% (95% CI, 4.9% to 12.3%); results were similar for soft tissue diagnoses and the left TMJ. Concurrent baseline soft tissue diagnoses were associated with hard tissue diagnostic changes at follow-up (P < 0.0001). Baseline hard tissue diagnoses showed no statistical association with soft tissue changes at follow-up (P = 0.11). Longitudinally, 76% of baseline TMJ soft tissue diagnoses and 71% of the baseline hard tissue diagnoses remained stable. Diagnostic reversal and progression were confirmed for both soft and hard tissues.
Characterization of endocytic uptake of MK2‐inhibitor peptides

Cell penetrating peptides (CPP) have been widely used to increase the cellular delivery of their associated cargo. Multiple modes of uptake have been identified; however, they cannot be predicted a priori. Elucidating these mechanisms is important for understanding peptide function as well as further optimizing cellular delivery. We have developed a class of mitogen activated protein kinase activated protein kinase 2 (MK2) inhibitor peptides, named FAK and YARA that utilize CPP domains to gain cellular access. In this study, we investigate the mechanism of endocytosis of these MK2 inhibitors by examining the uptake of fluorescently labeled peptide in human monocyte (THP‐1) and mesothelial cells, and looking for colocalization with known markers of endocytosis. Our results indicate that uptake of the MK2 inhibitors was minimally enhanced by the addition of the fluorescent label, and that the type of endocytosis used by the inhibitor depends on several factors including concentration, cell type, and which CPP was used. We found that in THP‐1 cells, the uptake of YARA occurred primarily via macropinocytosis, whereas FAK entered via all three mechanisms of endocytosis examined in this study. In mesothelial cells, uptake of YARA occurred via caveolae‐mediated endocytosis, but became less specific at higher concentrations; whereas uptake of FAK occurred through clathrin‐mediated endocytosis. In all cases, the delivery resulted in active inhibition of MK2. In summary, the results support endocytic uptake of fluorescently labeled FAK and YARA in two different cell lines, with the mechanism of uptake dependent on extracellular concentration, cell type, and choice of CPP. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Induction of TNF-α Autoantibody Production by AutoVac TNF106: A Novel Therapeutic Approach for the Treatment of Allergic Diseases

Background: Cytokines play an integral role in the coordination and persistence of allergic inflammatory processes and therefore represent prime targets for novel therapies in diseases such as asthma. Multiple attempts to generate low-molecular-weight cytokine inhibitors have failed, and the main attention has focused on the development of biological agents such as neutralizing antibodies. The present work describes a simple and effective method to induce the production of therapeutic anti-cytokine autoantibodies by active immunization against a modified endogenous cytokine. Methods: Balb/c mice were subcutaneously injected with AutoVac TNF106, a recombinant murine TNF-α molecule containing a foreign immunogenic T helper epitope, and the induction of neutralizing anti-TNF-α autoantibodies was analysed. These mice were then sensitized with ovalbumin (OVA), and the effect of neutralizing anti-TNF-α autoantibodies on the allergen-induced airway inflammation was analysed. Results: AutoVac TNF106-immunized mice developed high titres of neutralizing anti-TNF-α autoantibodies, which were maintained for at least 4 weeks after the last booster injection. Mice vaccinated with AutoVac TNF106 and further immunized against OVA showed diminished TNF-α levels in the bronchoalveolar lavage (BAL) fluid after OVA challenge. Moreover, pretreatment with AutoVac TNF106 resulted in significantly reduced numbers of eosinophils and neutrophils in BAL fluid in response to single or multiple allergen exposure. Conclusion: The induction of anti-TNF-α autoantibody production by the AutoVac TNF106 technology not only confirmed the role of TNF-α in the induction of allergic inflammation but also offers a novel approach to block the activity of cytokines in order to treat allergic inflammatory conditions.
Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment

Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing (NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries. For example, the determination of complete bacterial microbiomes of oral samples rather than selected species, together with oral metatranscriptome and metabolome analyses, supports the viewpoint of dysbiosis of the supragingival biofilms. In addition, metabolome studies have been instrumental in disclosing the contributions of major pathways for central carbon and amino acid metabolisms to biofilm pH homeostasis. New, often noncultured, oral streptococci have been identified, and their phenotypic characterization has revealed candidates for probiotic therapy. Although findings from OMICS research have been greatly informative, problems related to study design, data quality, integration, and reproducibility still need to be addressed. Also, the emergence and continuous updates of these computationally demanding technologies require expertise in advanced bioinformatics for reliable interpretation of data. Despite the obstacles cited above, OMICS research is expected to encourage the discovery of novel caries biomarkers and the development of next-generation diagnostics and therapies for caries control. These observations apply equally to the study of other oral diseases.
IGF-1 Mediates EphrinB1 Activation in Regulating Tertiary Dentin Formation

Eph receptors belong to a subfamily of receptor tyrosine kinases that are activated by membrane-spanning ligands called ephrins. Previously, we demonstrated that the ephrinB1-EphB2 interaction regulates odontogenic/osteogenic differentiation from dental pulp cells (DPCs) in vitro. The goal of this study was to identify the molecular mechanisms regulated by the EphB2/ephrinB1 system that govern tertiary dentin formation in vitro and in vivo. During tooth development, ephrinB1, and EphB2 were expressed in preodontoblast and odontoblasts at postnatal day 4. EphrinB1 was continuously expressed in odontoblasts and odontoblastic processes until the completion of tooth eruption. In addition, ephrinB1 was expressed in odontoblastic processes 2 wk following tooth injury without pulp exposure, whereas EphB2 was expressed in the center of pulp niches but not odontoblasts. In a model of tooth injury with pulp exposure, ephrinB1 was strongly expressed in odontoblasts 4 wk postinjury. In vitro studies with human and mouse DPCs treated with calcium hydroxide (CH) or mineral trioxide aggregate (MTA) showed an increased expression of insulin-like growth factor 1 (IGF-1). Experiments using several inhibitors of IGF-1 receptor signaling revealed that inhibiting the Ras/Raf-1/MAPK pathway inhibited EphB2 expression, and inhibiting the PI3K/Akt/mTOR pathway specifically inhibited ephrinB1 gene expression. Tooth injury in mice with odontoblast-specific IGF-1 receptor ablation exhibited a reduced tertiary dentin volume, mineral density, and ephrinB1 expression 4 wk following injury. We conclude that the IGF-1/ephrinB1 axis plays significant roles in the early stages of tooth injury. Further research is needed to fully understand the potential of targeting ephrinB1 as a regenerative pulp therapy.
TinySDN: Enabling Multiple Controllers for Software-Defined Wireless Sensor Networks

Software-Defined Networking (SDN) has been envisioned as a way to reduce the complexity of network configuration and management, enabling innovation in production networks. While SDN started focusing on wired networks, there were proposals specifically for Wireless Sensor Networks (WSN), but all of them required a single controller to be coupled to the sink. This paper presents TinySDN, a TinyOS-based SDN framework that enables multiple controllers within the WSN. It comprises two main components: the SDN-enabled sensor node, which has an SDN switch and an SDN end device, and the SDN controller node, where the control plane is programmed. TinySDN was designed and implemented to be hardware independent. Experiments were conducted on COOJA simulator, and results concerning delay and memory footprint are presented.
Psychosocial Interventions for Women with HIV/AIDS

Objective Recent research on psychosocial interventions addressing the well-being of women with HIV/AIDS has brought new options for practitioners. This study critically reviews the treatment features, methodological quality, and efficacy of these interventions. Methods A comprehensive search between 2000 and 2011 identified 19 studies employing 10 different interventions. Results In all, 11 studies were methodologically strong and 12 reported interventions superior to other treatments. Among those with positive results, Cohen’s effect sizes ranged from small (d = 0.33) to large (d = 1.50) across well-being outcomes. The Cognitive Behavioral Stress Management/Expressive Supportive and Structural Ecosystems Therapies ranked as probably efficacious. The Teaching, Raising and Communicating with Kids and the Maternal HIV Self-Care Symptom Management programs were ranked as promising treatments.
Zen in the Art of Occupational Therapy, Part One

In recent years, rapid changes have occurred within the health care system. Economic, political, scientific and social forces are transforming our view of health and, with the awakened interest in unconventional models of treatment, it is Important to assess the new set of demands placed on occupational therapy in relation to this change. Now that a greater emphasis is being placed on integrated methods of treatment, it is appropriate that we should consider the concepts of our own profession and their application to current changes of thought. The holistic approach to occupational therapy still has a valid contribution to make in the treatment process but perhaps a fresher application of this concept, including alternative Eastern philosophies, would promote a more balanced, dynamic outlook for occupational therapy, encour aging principles of self-help and creating a more challenging and more integrated practice of treatment. The article attempts to explain the principles of Eastern philosophy with reference to the Chinese ‘Book of Changes’ — the ‘I Ching’ — and to illustrate its relevance to new technology and scientific research.
Shape from Shading: A Survey

Since the first shape-from-shading (SFS) technique was developed by Horn in the early 1970s, many different approaches have emerged. In this paper, six well-known SFS algorithms are implemented and compared. The performance of the algorithms was analyzed on synthetic images using mean and standard deviation of depth (Z) error, mean of surface gradient (p, q) error, and CPU timing. Each algorithm works well for certain images, but performs poorly for others. In general, minimization approaches are more robust, while the other approaches are faster.
Social Capital and Psychological Distress

The author proposes a conceptual model to explain the diverse roles of social capital—resources embedded in social networks—in the social production of health. Using a unique national U.S. sample, the author estimated a path analysis model to examine the direct and indirect effects of social capital on psychological distress and its intervening effects on the relationships between other structural antecedents and psychological distress. The results show that social capital is inversely associated with psychological distress, and part of that effect is indirect through subjective social status. Social capital also acts as an intervening mechanism to link seven social factors (age, gender, race-ethnicity, education, occupational prestige, annual family income, and voluntary participation) with psychological distress. This study develops the theory of social capital as network resources and demonstrates the complex functions of social capital as a distinct social determinant of health.