Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals

Background Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics. Objective The aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis. Methods The domain and scope of the ontology were defined using competency questions. The concepts constituting the ontology and terminology were collected from clinical practice guidelines, the literature, and social media postings on adolescent depression. Class concepts, their hierarchy, and the relationships among class concepts were defined. An internal structure of the ontology was designed using the entity-attribute-value (EAV) triplet data model, and superclasses of the ontology were aligned with the upper ontology. Description logics between classes were evaluated by mapping concepts extracted from the answers to frequently asked questions (FAQs) onto the ontology concepts derived from description logic queries. The applicability of the ontology was validated by examining the representability of 1358 sentiment phrases using the ontology EAV model and conducting sentiment analyses of social media data using ontology class concepts. Results We developed an adolescent depression ontology that comprised 443 classes and 60 relationships among the classes; the terminology comprised 1682 synonyms of the 443 classes. In the description logics test, no error in relationships between classes was found, and about 89% (55/62) of the concepts cited in the answers to FAQs mapped onto the ontology class. Regarding applicability, the EAV triplet models of the ontology class represented about 91.4% of the sentiment phrases included in the sentiment dictionary. In the sentiment analyses, “academic stresses” and “suicide” contributed negatively to the sentiment of adolescent depression. Conclusions The ontology and terminology developed in this study provide a semantic foundation for analyzing social media data on adolescent depression. To be useful in social media data analysis, the ontology, especially the terminology, needs to be updated constantly to reflect rapidly changing terms used by adolescents in social media postings. In addition, more attributes and value sets reflecting depression-related sentiments should be added to the ontology.
Lysine 27 Ubiquitination of the Mitochondrial Transport Protein Miro Is Dependent on Serine 65 of the Parkin Ubiquitin Ligase*

Background: Miro is a mitochondrial protein involved in mitochondrial trafficking. Results: Mitochondrial damage drives rapid Miro ubiquitination in a manner dependent on Ser-65 in Parkin; however, Miro degradation is delayed. Conclusion: Ubiquitination of Miro, rather than its degradation, could act as a signal for mitochondrial arrest and clearance. Significance: Disruption of the mitochondrial transport machinery could be implicated in Parkinson disease. Mitochondrial transport plays an important role in matching mitochondrial distribution to localized energy production and calcium buffering requirements. Here, we demonstrate that Miro1, an outer mitochondrial membrane (OMM) protein crucial for the regulation of mitochondrial trafficking and distribution, is a substrate of the PINK1/Parkin mitochondrial quality control system in human dopaminergic neuroblastoma cells. Moreover, Miro1 turnover on damaged mitochondria is altered in Parkinson disease (PD) patient-derived fibroblasts containing a pathogenic mutation in the PARK2 gene (encoding Parkin). By analyzing the kinetics of Miro1 ubiquitination, we further demonstrate that mitochondrial damage triggers rapid (within minutes) and persistent Lys-27-type ubiquitination of Miro1 on the OMM, dependent on PINK1 and Parkin. Proteasomal degradation of Miro1 is then seen on a slower time scale, within 2–3 h of the onset of ubiquitination. We find Miro ubiquitination in dopaminergic neuroblastoma cells is independent of Miro1 phosphorylation at Ser-156 but is dependent on the recently identified Ser-65 residue within Parkin that is phosphorylated by PINK1. Interestingly, we find that Miro1 can stabilize phospho-mutant versions of Parkin on the OMM, suggesting that Miro is also part of a Parkin receptor complex. Moreover, we demonstrate that Ser-65 in Parkin is critical for regulating Miro levels upon mitochondrial damage in rodent cortical neurons. Our results provide new insights into the ubiquitination-dependent regulation of the Miro-mediated mitochondrial transport machinery by PINK1/Parkin and also suggest that disruption of this regulation may be implicated in Parkinson disease pathogenesis.
Periodontal disease, edentulism, and pancreatic cancer: a meta-analysis

Background Periodontal disease (PD), now our commonest infectious disorder leads to tooth loss, and has been linked to various systemic diseases, including various types of cancer. The aim of this study is to provide a systematic review and a meta-analysis of the relationship between PD, edentulism, and pancreatic cancer (PC). Patients and methods From an initial review of 327 references we selected eight studies concerning periodontitis or edentulism with sufficient quantitative information to allow us to examine the risk of PC. We used relative risks (RRs), hazard ratios, or odds ratios to measure the association between periodontitis, edentulism, and PC. We employed random effects models to obtain summary risks, and we also provide measures of study differences and possible biases. Results The summary RR for periodontitis and PC was 1.74 [95% confidence interval (CI) 1.41-2.15] and 1.54 for edentulism (95% CI 1.16-2.05). There was no evidence of heterogeneity for either variable, and no evidence of publication bias. The studies included reports from three continents, suggesting that the association is generalizable. Most of the studies were adjusted for variables thought to be associated with PC, such as gender, smoking, BMI, diabetes, and alcohol. Conclusions Using meta-analysis, both periodontitis and edentulism appear to be associated with PC, even after adjusting for common risk factors. As yet, the mechanisms linking oral disease and PC are uncertain, but could be related to changes in the oral microbiome-an area of current research.
Differential Transcriptional Activation of Genes Encoding Soluble Methane Monooxygenase in a Facultative Versus an Obligate Methanotroph

Methanotrophs are a specialized group of bacteria that can utilize methane (CH4) as a sole energy source. A key enzyme responsible for methane oxidation is methane monooxygenase (MMO), of either a soluble, cytoplasmic type (sMMO), or a particulate, membrane-bound type (pMMO). Methylocella silvestris BL2 and Methyloferula stellata AR4 are closely related methanotroph species that oxidize methane via sMMO only. However, Methyloferula stellata is an obligate methanotroph, while Methylocella silvestris is a facultative methanotroph able to grow on several multicarbon substrates in addition to methane. We constructed transcriptional fusions of the mmo promoters of Methyloferula stellata and Methylocella silvestris to a promoterless gfp in order to compare their transcriptional regulation in response to different growth substrates, in the genetic background of both organisms. The following patterns were observed: (1) The mmo promoter of the facultative methanotroph Methylocella silvestris was either transcriptionally downregulated or repressed by any growth substrate other than methane in the genetic background of Methylocella silvetris; (2) Growth on methane alone upregulated the mmo promoter of Methylocella silvetris in its native background but not in the obligate methanotroph Methyloferula stellata; (3) The mmo promoter of Methyloferula stellata was constitutive in both organisms regardless of the growth substrate, but with much lower promoter activity than the mmo promoter of Methylocella silvetris. These results support a conclusion that a different mode of transcriptional regulation of sMMO contributes to the facultative lifestyle of Methylocella silvetris compared to the obligate methanotroph Methyloferula stellata.
Branes on generalized calibrated submanifolds

We extend previous results on generalized calibrations to describe supersymmetric branes in supergravity backgrounds with diverse fields turned on, and provide several new classes of examples. As an important application, we show that supersymmetric D-branes in compactifications with field strength fluxes, and on SU(3)-structure spaces, wrap generalized calibrated submanifolds, defined by simple conditions in terms of the underlying globally defined, but non-closed, 2- and 3-forms. We provide examples where the geometric moduli of D-branes (for instance D7-branes in 3-form flux configurations) are lifted by the generalized calibration condition. In addition, we describe supersymmetric D6-branes on generalized calibrated 3-submanifolds of half-flat manifolds, which provide the mirror of B-type D-branes in IIB CY compactifications with 3-form fluxes. Supersymmetric sets of such D-branes carrying no homology charges are mirror to supersymmetric sets of D-branes which are homologically non-trivial, but trivial in K-theory. As an additional application, we describe models with chiral gauge sectors, realized in terms of generalized calibrated brane box configurations of NS- and D5-branes, which are supersymmetric but carry no charges, so that no orientifold planes are required in the compactification.
ALT flares during nucleotide analogue therapy are associated with HBsAg loss in genotype A HBeAg‐positive chronic hepatitis B

Alanine aminotransferase (ALT) flares during NA therapy are uncommon but occur. Evaluation of ALT flares during nucleos(t)ide analogue (NA) therapy is important as new immunomodulatory therapies for hepatitis B virus (HBV) are developed. We evaluated the association between ALT flares and HBsAg loss during long‐term therapy for genotype A CHB.
TGFβ regulates persistent neuroinflammation by controlling Th1 polarization and ROS production via monocyte‐derived dendritic cells

Intracerebral levels of Transforming Growth Factor beta (TGFβ) rise rapidly during the onset of experimental autoimmune encephalomyelitis (EAE), a mouse model of Multiple Sclerosis (MS). We addressed the role of TGFβ responsiveness in EAE by targeting the TGFβ receptor in myeloid cells, determining that Tgfbr2 was specifically targeted in monocyte‐derived dendritic cells (moDCs) but not in CNS resident microglia by using bone‐marrow chimeric mice. TGFβ responsiveness in moDCs was necessary for the remission phase since LysMCreTgfbr2fl/fl mice developed a chronic form of EAE characterized by severe demyelination and extensive infiltration of activated moDCs in the CNS. Tgfbr2 deficiency resulted in increased moDC IL‐12 secretion that skewed T cells to produce IFN‐γ, which in turn enhanced the production of moDC‐derived reactive oxygen species that promote oxidative damage and demyelination. We identified SNPs in the human NOX2 (CYBB) gene that associated with the severity of MS, and significantly increased CYBB expression was recorded in PBMCs from both MS patients and from MS severity risk allele rs72619425‐A carrying individuals. We thus identify a novel myeloid cell‐T cell activation loop active in the CNS during chronic disease that could be therapeutically targeted. GLIA 2016;64:1925–1937
Decreased Prostaglandin D2 Levels in Major Depressive Disorder Are Associated with Depression-Like Behaviors

Abstract Background Prostaglandin (PG) D2 is the most abundant prostaglandin in the mammalian brain. The physiological and pharmacological actions of PGD2 in the central nervous system seem to be associated with some of the symptoms exhibited by patients with major depressive disorder. Previous studies have found that PGD2 synthase was decreased in the cerebrospinal fluid of major depressive disorder patients. We speculated that there may be a dysregulation of PGD2 levels in major depressive disorder. Methods Ultra-performance liquid chromatography-tandem mass spectrometry coupled with a stable isotopic-labeled internal standard was used to determine PGD2 levels in the plasma of major depressive disorder patients and in the brains of depressive mice. A total of 32 drug-free major depressive disorder patients and 30 healthy controls were recruited. An animal model of depression was constructed by exposing mice to 5 weeks of chronic unpredictable mild stress. To explore the role of PGD2 in major depressive disorder, selenium tetrachloride was administered to simulate the change in PGD2 levels in mice. Results Mice exposed to chronic unpredictable mild stress exhibited depression-like behaviors, as indicated by reduced sucrose preference and increased immobility time in the forced swimming test. PGD2 levels in the plasma of major depressive disorder patients and in the brains of depressive mice were both decreased compared with their corresponding controls. Further inhibiting PGD2 production in mice resulted in an increased immobility time in the forced swimming test that could be reversed by imipramine. Conclusion Decreased PGD2 levels in major depressive disorder are associated with depression-like behaviors.
Trends in Pediatric Complicated Pneumonia in an Ontario Local Health Integration Network

Following the introduction of 7-valent pneumococcal vaccine (PCV7), while overall rates of invasive pneumococcal disease and pneumococcal pneumonia in children declined, rates of empyema increased. We examined changes in the incidence of hospitalization for pediatric complicated pneumonia (PCOMP) in Eastern Ontario, Canada, particularly since the introduction of the 13-valent vaccine (PCV13). A retrospective chart review was carried out evaluating previously healthy children admitted with PCOMP, which included empyema, parapneumonic effusion, necrotizing pneumonia, and lung abscess between 2002 and 2015. Three-hundred seventy-one children were included. Subjects had a median age of four years, and 188/370 (50.8%) required a chest tube. Admission rates changed markedly during this time period. The number of admissions per year rose most sharply between 2009 and 2012, corresponding to the period following introduction of PCV7 and then the occurrence of pandemic influenza A (H1N1). In children who likely received PCV13, the incidence of PCOMP returned to approximately pre-PCV7 levels. In contrast, rates of PCOMP in older children (who would not have received PCV13) remained elevated during the post-PCV13 time period. While rates of PCOMP, particularly in older children, remain elevated following the introduction of PCV13, this might be expected to resolve with more widespread vaccine coverage with PCV13 and herd immunity.
Randomized, Double-Blind, Placebo-Controlled Trial of N-Acetylcysteine Augmentation for Treatment-Resistant Obsessive-Compulsive Disorder.

OBJECTIVE To evaluate the efficacy of serotonin reuptake inhibitor (SRI) augmentation with N-acetylcysteine (NAC), a glutamate modulator and antioxidant medication, for treatment-resistant obsessive-compulsive disorder (OCD). METHODS We conducted a randomized, double-blind, placebo-controlled, 16-week trial of NAC (3,000 mg daily) in adults (aged 18-65 years) with treatment-resistant OCD, established according to DSM-IV criteria. Forty subjects were recruited at an OCD-specialized outpatient clinic at a tertiary hospital (May 2012-October 2014). The primary outcome measure was the Yale-Brown Obsessive Compulsive Scale (Y-BOCS) scores. To evaluate the variables group, time, and interaction effects for Y-BOCS scores at all time points, we used nonparametric analysis of variance with repeated measures. Secondary outcomes were the severity scores for anxiety, depression, specific OCD symptom dimensions, and insight. RESULTS Both groups showed a significant reduction of baseline Y-BOCS scores at week 16: the NAC group had a reduction of 4.3 points (25.6 to 21.3), compared with 3.0 points (24.8 to 21.8) for the placebo group. However, there were no significant differences between groups (P = .92). Adding NAC was superior to placebo in reducing anxiety symptoms (P = .02), but not depression severity or specific OCD symptom dimensions. In general, NAC was well tolerated, despite abdominal pain being more frequently reported in the NAC group (n [%]: NAC = 9 [60.0], placebo = 2 [13.3]; P < .01). CONCLUSIONS Our trial did not demonstrate a significant benefit of NAC in reducing OCD severity in treatment-resistant OCD adults. Secondary analysis suggested that NAC might have some benefit in reducing anxiety symptoms in treatment-resistant OCD patients. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT01555970.
A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries

Clinical Natural Language Processing (NLP) systems extract clinical information from narrative clinical texts in many settings. Previous research mentions the challenges of handling abbreviations in clinical texts, but provides little insight into how well current NLP systems correctly recognize and interpret abbreviations. In this paper, we compared performance of three existing clinical NLP systems in handling abbreviations: MetaMap, MedLEE, and cTAKES. The evaluation used an expert-annotated gold standard set of clinical documents (derived from from 32 de-identified patient discharge summaries) containing 1,112 abbreviations. The existing NLP systems achieved suboptimal performance in abbreviation identification, with F-scores ranging from 0.165 to 0.601. MedLEE achieved the best F-score of 0.601 for all abbreviations and 0.705 for clinically relevant abbreviations. This study suggested that accurate identification of clinical abbreviations is a challenging task and that more advanced abbreviation recognition modules might improve existing clinical NLP systems.
Evaluation of efforts in untrained Wistar rats following exercise on forced running wheel at maximal lactate steady state

[Purpose] We aimed to examine the effect of running speed on metabolic responses associated with maximal lactate steady state (MLSS) in rats during forced running wheel (FRW) exercise. [Methods] Forty male adult Wistar rats were divided into seven groups. The blood lactate threshold and peak running speed were determined for an incremental power test group. Five groups participated in constant power tests at intensities 10, 13, 14.5, 16, and 17.5 m/min to determine MLSS and a non-exercise group was chosen as the control. Animals were euthanized immediately after constant power tests and their corticosterone, non-esterified fatty acid (NEFA), blood glucose, and creatine kinase (CK) levels analyzed. The differences among groups were identified by one-way analysis of variance (p < 0.05). [Results] Blood lactate threshold corresponded a running intensity of 15 m/min, while MLSS was determined to be 16 m/min. Serum corticosterone concentrations were significantly higher in 14.5, 16, and 17.5 m/min groups (298.8±62, 338.3±65, and 354±26 nM, respectively) as compared to that in the control group (210.6±16 nM). Concentrations of NEFA observed in groups 13, 14.5, 16, and 17.5 m/min (662.8±24, 702.35±69, 718.4±34, and 752.8±77 μM, respectively) were significantly higher than those in 10 m/min and control groups (511.1±53 and 412.1±56 μM, respectively). The serum CK concentration recorded for group 17.5 m/min (372.4±56 U/L) was higher than those recorded for other groups. [Conclusion] The speed above 16 m/min on FRW resulted in increased physiological demands and muscle damage in untrained healthy Wistar rats.
Imbalance between cognitive systems in alcohol-dependence and Korsakoff syndrome: An exploration using the Alcohol Flanker Task

ABSTRACT Background: Alcohol-dependent individuals (ALC) simultaneously present decreased inhibitory control and increased attention towards alcohol-related cues. The dual-process models have proposed that these symptoms reflect an imbalance between prefrontal/reflective and limbic/automatic systems, respectively leading to cognitive dysfunctions in executive processes and to alcohol-related bias. However, most previous research has focused on a separate exploration of these systems among ALC, and the direct measure of their interactions remains to be conducted. Moreover, no study has explored the evolution of this imbalance across the successive stages of alcohol-related disorders, and particularly in Korsakoff syndrome (KS), the most frequent neurological complication of alcohol-dependence. Method: Ten KS, 14 ALC, and 14 matched control participants performed a modified Flanker task, the “Alcohol Flanker Task,” based on congruent, incongruent, and neutral conditions with alcohol-related stimuli. This task required inhibitory processing on alcohol-related stimuli and evaluated, through a behavioral approach, the interaction between reflective and automatic systems, as well as its evolution between ALC and KS. Results: ALC and KS both presented high reactivity towards alcohol-related stimuli, confirming the presence of alcohol-related bias. KS showed increased omission rates (related to distractor interference) while ALC showed higher false-alarm rates (related to prepotent response inhibition). These results suggest that different inhibitory subcomponents might be altered at the successive stages of the pathology, and experimentally confirms the crucial role of the interaction between reflective and automatic processes in alcohol-use disorders. Conclusion: The present results reinforce the proposal that alcohol-related cues significantly impact inhibitory control in alcohol-related disorders. However, ALC and KS present different patterns of deficits depending on task complexity (i.e., executive load), thus suggesting a dissociation in inhibitory functions when processing alcohol-related cues.
Male-to-female aggression in cage-housed common pheasants (Phasianus colchicus) during the breeding season was not related to male plasma testosterone level

ABSTRACT 1. The aim of this study was to investigate if male-to-female aggression of common pheasants in the course of the breeding season was related to the concentration of plasma testosterone and/or other biochemical plasma indicators in male pheasants housed in breeding cages. The influence of season on the concentration of testosterone and biochemical indicators was also investigated. 2. Males were divided into non-aggressive and aggressive groups during the breeding season based on ethological evaluation. At the beginning, in the middle and at the end of the breeding season, a blood sample was taken from all males on the same day and the concentration of selected biochemical indicators and the total circulating testosterone in the plasma were determined. 3. Male-to-female aggression during the breeding season of pheasants was not influenced by the total plasma testosterone of males. 4. The concentration of total plasma testosterone in males decreased gradually during the breeding season. 5. Male-to-female aggression of pheasants did not have a significant effect on any of the assessed biochemical indicators. 6. The influence of the breeding season affected the activities of alanine aminotransferase and aspartate aminotransferase as well as the concentrations of glucose, magnesium, potassium and chloride in the blood plasma of cage-housed male pheasants.