Gene-specific machine learning for pathogenicity prediction of rare BRCA1 and BRCA2 missense variants.

Machine learning-based pathogenicity prediction helps interpret rare missense variants of BRCA1 and BRCA2, which are associated with hereditary cancers. Recent studies have shown that classifiers trained using variants of a specific gene or a set of genes related to a particular disease perform better than those trained using all variants, due to their higher specificity, despite the smaller training dataset size. In this study, we further investigated the advantages of "gene-specific" machine learning compared to "disease-specific" machine learning. We used 1068 rare (gnomAD minor allele frequency (MAF) < 0.005) missense variants of 28 genes associated with hereditary cancers for our investigation. Popular machine learning classifiers were employed: regularized logistic regression, extreme gradient boosting, random forests, support vector machines, and deep neural networks. As features, we used MAFs from multiple populations, functional prediction and conservation scores, and positions of variants. The disease-specific training dataset included the gene-specific training dataset and was > 7 × larger. However, we observed that gene-specific training variants were sufficient to produce the optimal pathogenicity predictor if a suitable machine learning classifier was employed. Therefore, we recommend gene-specific over disease-specific machine learning as an efficient and effective method for predicting the pathogenicity of rare BRCA1 and BRCA2 missense variants.

Effect of High-Versus Low-Frequency of Abdominopelvic Computed Tomography Follow-Up Testing on Overall Survival in Patients With Stage II Or III Colon Cancer.

BACKGROUND: Intensive surveillance of colon cancer by using the abdominopelvic computed tomography (AP-CT) is common in real world practice; however, it is still unclear whether high-frequency surveillance using AP-CT in patients with these risk factors is superior to that in the low-frequency surveillance. PATIENTS AND METHODS: We retrospectively reviewed 1803 patients with stage II-III colon cancer receiving curative surgery between January 1, 2005 to December 31, 2015. We evaluated the average scan-to-scan intervals of postoperative AP-CT testing and assigned patients with an interval of 5 to 8 and 9 to 13 months to the high-frequency (HF) and low-frequency (LF) groups, respectively. The cutoff value of preoperative and postoperative CEA levels was 5 ng/mL. We also applied propensity score matching (PSM) and inverse probability of treatment weighting to adjust clinicopathologic differences between the 2 groups. RESULTS: We matched 1:1 for each surveillance group yielding a cohort of 776 matched patients. After PSM, Baseline demographics were overall well balanced between 2 groups. Stage III (OR, 2.00; 95% Confidence interval [CI], 1.21-3.30) and postoperative CEA elevation (OR, 2.30; 95% CI, 1.08-4.92) were independent risk factors of recurrence in multivariate analyses. Patient in the HF group had more surgery plus chemo- or radiotherapy as postrecurrence treatment than patient in the LF group (46.2% vs. 23.1%, P = .017). This trend was retained after PSM, although it is not significant (44.4% vs. 23.1%, P = .060). However, survival outcomes of high-frequency AP-CT surveillance were not superior to those of low-frequency surveillance in all subgroups, including stage III (HR 0.99, 95% CI 0.40-2.47) and postoperative CEA elevation (HR 1.36, 95% CI 0.45-4.11). CONCLUSION: High-frequency AP-CT testing is associated with a higher proportion of surgery plus chemo- or radiotherapy as postrecurrence treatment, without improvement in 5-year overall survival.

Hydrogen peroxide attenuates rhinovirus-induced anti-viral interferon secretion in sinonasal epithelial cells.

Background: Altered innate defense mechanisms, including an imbalance between oxidants and antioxidants release, have been implicated in the pathogenesis of chronic rhinosinusitis (CRS). The aim of this study is to investigate whether oxidative stress may attenuate the secretion of anti-viral interferons in human sinonasal mucosa. Methods: The levels of H2O2 in nasal secretion were increased in patients with CRS with nasal polyps, compared with that of CRS patients without nasal polyps and control subjects. Normal sinonasal epithelial cells derived from healthy subjects were cultured under an air-liquid interface. The cultured cells were infected with rhinovirus 16 (RV 16) or treated with poly (I: C), TLR3 agonist, after being pretreated with an oxidative stressor, H2O2 or antioxidant, N-acetylcysteine (NAC). Thereafter, the expression levels of type I (IFN-ß) and type III (IFN-λ1 and λ2) interferons and interferon-stimulated genes (ISGs) were evaluated with RT-qPCR, ELISA, and western blot. Results: The data showed that the production of type I (IFN-ß) and type III (IFN-λ1 and λ2) interferons and ISGs was upregulated in cells infected with RV 16 or treated with poly (I: C). However, their up-regulated expression was attenuated in cells pretreated with H2O2, but not inhibited in cells pretreated with NAC. In line with these data, the up-regulated expression of TLR3, RIG-1, MDA5, and IRF3 was reduced in cells pretreated with H2O2, but not attenuated in cells treated with NAC. Furthermore, cells transfected with Nrf2 siRNA showed decreased secretion of anti-viral interferons whereas sulforaphane treatment enhanced the secretory capacity of antiviral interferons. Conclusions: These results suggest that the production of RV16-induced antiviral interferons may be attenuated by oxidative stress.

Rhinovirus-induced anti-viral interferon secretion is not deficient and not delayed in sinonasal epithelial cells of patients with chronic rhinosinusitis with nasal polyp.

Dysregulated innate and adaptive immune response to rhinoviral infection plays an important role in the exacerbation or progressive course of chronic rhinosinusitis (CRS). However, few studies have evaluated whether rhinovirus-induced production of anti-viral interferon is deficient or delayed in inflammatory epithelial cells of patients with CRS with nasal polyps. The aim of the present study is to investigate the replication rates of rhinovirus 16 (RV 16), RV16-induced antiviral interferon secretion, and the expression levels of pattern recognition receptors after RV 16 infection or TLR3 stimulation with poly (I: C) in normal and inflammatory epithelial cells. Inflammatory epithelial cells were obtained from CRS patients with nasal polyps and normal epithelial cells were derived from ethmoid sinus mucosa during endoscopic reduction of blowout fracture or uncinate process mucosa of patients with septal deviation. Cultured cells were infected with RV 16 or treated with poly (I: C) for 24, 48, and 72 h. Cells and media were harvested at each time point and used to evaluate RV16 replication rates, the secretion of IFN-ß, -λ1, -λ2, viperin, Mx, and OAS, and the expression levels of TRL3, RIG-I, MDA5, phospho-NFκB, and phospho-IRF3. RV replication rates reached peak levels 48 h after inoculation in both normal and inflammatory epithelial cells and showed no difference between both groups of epithelial cells at any time point. The release of IFN-ß, -λ1, and -λ2 in normal and inflammatory epithelial cells was also strongly induced 48 h after RV16 inoculation but reached peak levels 24 h after poly (I: C) treatment. The expression levels of viperin, Mx, OAS, TLR3, RIG-I, MDA5, phospho-NFκB, and phospho-IRF3 showed similar patterns in both groups of epithelial cells. These results suggest that the production of RV16-induced antiviral interferons is not deficient or delayed in inflammatory epithelial cells from CRS patients with nasal polyps.

Hypoglycemic and Hypolipogenic Action of Acetic Acid and Monascus-Fermented Grain Vinegar: A Comparative Study.

Acetic acid has been proposed to improve lifestyle-related diseases, including hyperlipidemia and hyperglycemia. This study compared the hypoglycemic and hypolipogenic effects of acetic acid vinegar (AV, contains only 4% acetic acid) and Monascus-fermented grain vinegar (MV) containing various bioactive compounds in 3T3L1 cells and C57BL/KsJ-db/db mice (DB). The DB were divided randomly into three treatment groups containing nine mice each; DB-, AV-, and MV-groups were orally administered 1 mL/kg/day of distilled water, acetic acid vinegar, and Monascus vinegar, respectively, for 8 weeks. Exposure to AV and MV inhibited the adipogenic differentiation of 3T3L1 preadipocytes and lipid accumulation during differentiation. Oral administration of AV or MV to the mice resulted in a marked reduction in the body weight, liver weight, and hepatic triglyceride content compared to the control DB-group. Moreover, treatment with AV and MV clearly increased the expression of cyclic adenosine monophosphate (cAMP) and AMP-activated protein kinase (AMPK) and suppressed the expression of fatty acid synthetase in liver tissues of DB. Significantly, lower levels of fasting blood glucose, insulin, leptin, and the glycosylated hemoglobin (HbA1c) as well as higher levels of the skeletal muscle GLUT4 expression were obtained in the AV- or MV-groups than levels determined in the control DB-group (P < .05). Although MV has the potential to be a natural alternative treatment for obesity-associated type 2 diabetes, this study suggests that acetic acid is the central ingredient in MV responsible for the hypoglycemic and hypolipogenic effects in the DB mice.

Radiographic outcome of root canal treatment in dogs: 281 teeth in 204 dogs (2001-2018).

OBJECTIVE: To evaluate the radiographic outcome of root canal treatment (RCT) in dogs and compare outcomes with those reported for a previous study performed at the same institution in 2002. ANIMALS: 204 dogs representing 281 teeth that underwent RCT. PROCEDURES: The medical record database of a veterinary teaching hospital was searched to identify dogs that underwent RCT between 2001 and 2018. Only dogs that had undergone at least 1 radiographic recheck appointment a minimum of 50 days after RCT were included in the study. Dental radiographs were reviewed. Treatment was considered successful if the periapical periodontal ligament space was within reference limits and preexisting external inflammatory root resorption (EIRR), if present, had stabilized. Treatment was considered to show no evidence of failure (NEF) if preoperative EIRR had stabilized and any preoperative periapical lucency (PAL) remained the same or had decreased in size but had not completely resolved. Treatment was considered to have failed if EIRR or a PAL developed after RCT, if a preoperative PAL increased in size, or if preexisting EIRR progressed. RESULTS: Follow-up time ranged from 52 to 3,245 days (mean, 437 days). RCT was classified as successful for 199 (71%) teeth, NEF for 71 (25%) teeth, and failed for 11 (4%) teeth. CONCLUSIONS AND CLINICAL RELEVANCE: Results showed that almost 2 decades after RCT outcome in dogs was first evaluated, during which time numerous advances in dental materials and techniques had been made, the success rate of RCT was virtually unchanged.

Intergranular Corrosion and Microstructural Evolution in a Newly Designed Al-6Mg Alloy.

In this work, the microstructure and corrosion behavior of a novel Al-6Mg alloy were investigated. The alloy was prepared by casting from pure Al and Mg+Al2Ca master alloy. The ingots were homogenized at 420 °C for 8 h, hot-extruded and cold-rolled with 20% reduction (CR20 alloy) and 50% reduction (CR50 alloy). The CR50 alloy exhibited a higher value of intergranular misorientation due to a higher cold rolling reduction ratio. The average grain sizes were 19 ± 7 µm and 17 ± 9 µm for the CR20 and CR50 alloys, respectively. An intergranular corrosion (IGC) behavior was investigated after sensitization by a nitric acid mass-loss test (ASTM G67). The mass losses of both the CR20 and CR50 alloys were similar at early periods of sensitization, however, the CR20 alloy became more susceptible to IGC as the sensitization time increased. Grain size and ß phase precipitation were two critical factors influencing the IGC behavior of this alloy system.

Survival time of juvenile dogs with oral squamous cell carcinoma treated with surgery alone: A Veterinary Society of Surgical Oncology retrospective study.

OBJECTIVE: To report the signalment, staging, surgical treatment, and survival time of juvenile dogs treated surgically for oral squamous cell carcinoma (OSCC). STUDY DESIGN: Retrospective study. ANIMALS OR SAMPLE POPULATION: Twenty-five dogs, <2 years of age with OSCC treated with surgery. METHODS: Cases were solicited from the Veterinary Society of Surgical Oncology. Data retrieved included sex, breed, age, weight, clinical signs, tumor location, preoperative diagnostics and staging, histopathological diagnosis with margin evaluation, disease-free interval, and date and cause of death. A minimum follow-up time of 3 months was required for inclusion. RESULTS: Eighteen dogs were <12 months of age, and seven were <24 months. Various breeds were represented, with a mean body weight of 22.3 ± 14.4 kg. No dogs had evidence of metastatic disease prior to surgery. All dogs underwent partial maxillectomy or mandibulectomy. Histological margins were complete in 24 dogs and incomplete in one. No dogs had evidence of metastatic disease or tumor recurrence. The median follow-up time was 1556 days (92 to 4234 days). All dogs were alive at the last follow-up except for one documented death, due to dilated cardiomyopathy. Median disease-specific survival time was not reached. CONCLUSION: The prognosis after wide surgical excision of OSCC in juvenile dogs was excellent. CLINICAL SIGNIFICANCE: OSCC in juvenile dogs can be effectively treated with surgery alone.

The Expression of ephrinA1/ephA2 Receptor Increases in Chronic Rhinosinusitis and ephrinA1/ephA2 Signaling Affects Rhinovirus-Induced Innate Immunity in Human Sinonasal Epithelial Cells.

EphA2 receptor and its ephrin ligands are involved in virus infection, epithelial permeability, and chemokine secretion. We hypothesized that ephrinA1/ephA2 signaling participates in rhinovirus (RV)-induced antiviral immune response in sinonasal mucosa of patients with chronic rhinosinusitis (CRS). Therefore, we investigated the expression of ephrinA1/ephA2 in normal and inflamed sinonasal mucosa and evaluated whether they regulate chemokine secretion and the production of antiviral immune mediators including interferons (IFNs) in RV-infected human primary sinonasal epithelial cells. For this purpose, the expression and distribution of ephrinA1/ephA2 in sinonasal mucosa were evaluated with RT-qPCR, immunofluorescence, and western blot. Their roles in chemokine secretion and the production of antiviral immune mediators such as type I and III IFNs, and interferon stimulated genes were evaluated by stimulating ephA2 with ephrinA1 and inactivating ephA2 with ephA2 siRNA or inhibitor in cells exposed to RV and poly(I:C). We found that ephrinA1/ephA2 were expressed in normal mucosa and their levels increased in inflamed sinonasal mucosa of CRS patients. RV infection or poly(I:C) treatment induced chemokine secretion which were attenuated by blocking the action of ephA2 with ephA2 siRNA or inhibitor. The production of antiviral immune mediators enhanced by rhinovirus or poly (I:C) is increased by blocking ephA2 compared with that of cells stimulated by either rhinovirus or poly(I:C) alone. In addition, blocking ephA2 attenuated RV replication in cultured cells. Taken together, these results describe a novel role of ephrinA1/ephA2 signaling in antiviral innate immune response in sinonasal epithelium, suggesting their participation in RV-induced development and exacerbations of CRS.

Management of Severe Periodontal Disease and Gingival Enlargement in a Dwarf Mongoose (Helogale parvula).

Development of gingival enlargement and periodontitis is described in a young dwarf mongoose. Repeated treatments resulted in gingival resection and histologic evaluation however gingival enlargement was ultimately responsive to extraction of associated teeth. In cases such as these, surgical extraction of teeth associated with severe recurrent gingival enlargement should be considered to avoid the stress and risk of repeated immobilizations.