Predicting missing annotations in Gene Ontology with Knowledge Graph Embeddings and True Path Rule

Gene Ontology (GO) and its Annotations (GOA) provide a controlled and evolving vocabulary for gene products and gene functions widely used in molecular biology. GO & GOA are updated and maintained both automatically from biological publications and manually by curators. These knowledge bases however are often incomplete for two reasons: 1) Research in biological domain itself is still ongoing; 2) The amount of experimental evidence might not be yet sufficient to validate annotations. In this paper, we address the gap in evidence between gene products and their annotations by making link predictions using Knowledge Graph Embedding (KGE) methods. Through the application of the True Path Rule (TPR) in the training stage of KGE, we were able to improve the performance of traditional KGE methods. We report two experimental scenarios with GO and GO Chicken Annotation datasets to show the contribution of embedding TPR to prediction accuracy

A Dilemma in Staging of Esophageal Cancer: How Should We Stage ypT0 N2 M0 Esophageal Cancer after Neoadjuvant Therapy?

Background. Since neoadjuvant treatment in esophageal cancer began to become popular, a complete pathological response at the primary tumour site has been commonly reported. An issue of conflict is whether complete response in the esophageal lumen means that the esophagus is completely tumour-free. Another important issue is whether lymph nodes that are retrieved from pathologically complete response cases are also tumour-free or not. There is a gap in the esophageal cancer staging system for ypT0 N2 M0 tumours that have received neoadjuvant therapy. Here, we will discuss the problem about staging of esophageal cancer associated with neoadjuvant therapy. Case. A female aged 40 years complaining of dysphagia was diagnosed as having locally advanced thoracic esophageal cancer. Neoadjuvant therapy decision was taken by oncology committee. Six weeks after neoadjuvant therapy, with a curative intention, minimal invasive surgery was performed. The pathology report was as follows. “There were no neoplastic cells in the suspected area of the esophageal mucosa upon examination with all staining. There was no cancer at resection margins. Four metastatic lymph nodes were infiltrated with squamous cell cancer.” Conclusion. Despite the growing use of neoadjuvant treatment in locally advanced esophageal cancer in world, we do not have a protocol for the evaluation of these patients’ pathology reports. We believe that new studies and new ideas are needed to resolve this dilemma associated with neoadjuvant therapy

Predicting missing annotations in Gene Ontology with Knowledge Graph Embeddings and True Path Rule - Presentation

Gene Ontology (GO) and its Annotations (GOA) provide an evolving and controlled vocabulary for gene functions to enhance the understanding of molecular biology. GO & GOA are maintained automatically from biological publications or manually by curators. These knowledge bases however are often incomplete for two reasons: 1) Research in biological domain itself is still ongoing; 2) The amount of experimental evidence is not yet sufficient for the validation of annotations. In this paper, we tackle this problem under link prediction with Knowledge Graph Embedding (KGE) methods between gene products and their annotations. We achieve this through the application of the True Path Rule (TPR) into the training stage of KGE. We report two experimental scenarios with GO and GO Chicken Annotation datasets to show the contribution from TPR to prediction accuracy

Tracheobronchopathia osteochondroplastica: a case report

AbstractTracheobronchopathia osteochondroplastica (TO) is a rare benign condition, characterized by the presence of multiple cartilaginous and/or osseous  submucosal nodules protruding into  of the tracheobronchial lumen. In general, tracheobronchopathia osteochondroplastic(TO) is diagnosed incidentally during bronchoscopy or autopsy and is not associated with a specific disease. it can be asymptomatic or present with non-specific respiratory symptoms. We present a case of a 62 year-old female with the dry cough  who was diagnosed with TPO by flexible bronchoscopy

Pseudoxanthoma elasticum: Case series of three siblings

Pseudoxanthoma elasticum (PXE) is a rare multisystemic genetic disease with dermatologic, cardiovascular and ocular involvement. PXE primarily affects the skin, and the ocular involvement is noted in almost 85% of patients. Cardiovascular complications caused by PXE often develop in adults. Since the prognosis of PXE is primarily dependent on extracutaneous organ involvement, early diagnosis of PXE is of prime importance for taking preventive measures. In this report, we present three siblings diagnosed with PXE

THE EFFECT OF FUCOIDAN ON THE GENTAMICIN INDUCED NEPHROTOXICITY IN RATS

WOS: 000430372900032Possible preventive or therapuetic effects of fuciodan, which has antioxidant properties and was administered together with gentamicin (GM) made up nephrotoxicity through giving GM to the rats, have been searched. The rats used in this study were randomly grouped in three: control, GM (80 mg/kg/day/i.p GM was administered for 8 days), GM+fucoidan (80 mg/kg/day/i.p GM for 8 days + fucoidan 100 mg/kg/day/ for 8 days were administered with intra-gastric gavage) groups. Blood and tissue samples were taken 24 hours after the 8 days trial period. Besides determining plasma creatinine, BUN, sodium, potassium, chloride levels in auto-analyser, whole blood glutathione, plasma MDA and AOPP levels were analyzed spectrophotometrically. The highest plasma creatinine, BUN, potassium, AOPP and MDA levels were found in the GM group. It was determined that while the levels of creatinin (p<0.01), BUN (p<0.05), potassium (p<0.05), AOPP (p<0.01), MDA (p<0.01) in GM+fucoidan group were decreasing with regard to those in GM group, chloride levels were rising (p<0.05). The study revealed the nephroprotective effect of fucoidan. These findings suggest that fucoidan administration together with GM may attenuate renal dysfunction and structural damage through the reduction of oxidative stress in the kidney.Van YYU Directory of Scientific Research Project [2012-SBE-YL003]This research was supported by the Van YYU Directory of Scientific Research Project as 2012-SBE-YL003 Project number. The study has been orally presented and published as abstract in the 8th National Veterinary Biochemistry and Clinical Biochemistry Congress 22-24 September 2016, Bursa, Turkey

Effects of jnk inhibitor on inflammation and fibrosis in the ovary tissue of a rat model of polycystic ovary syndrome.

In our study, we aimed to investigate the effects of Jun N-terminal kinase inhibitor (SP600125) on fibrosis and inflammation in rats with polycystic ovary syndrome (PCOS)

Effects of jnk inhibitor on inflammation and fibrosis in the ovary tissue of a rat model of polycystic ovary syndrome

Objective: In our study, we aimed to investigate the effects of Jun N-terminal kinase inhibitor (SP600125) on fibrosis and inflammation in rats with polycystic ovary syndrome (PCOS). Method: 50 Wistar-albino rats were divided into five groups (n=10 each): control group, sham group, PCOS group, SP600125+ PCOS group and SP600125 group. In the estradiol valerate (EV)-treated group in which PCOS was injected with a single 4 mg/kg i.p. of EV in 0.2 ml sesame oil and the rats were sacrificed on day 60. The estradiol valerate (EV)-treated + SP600125-treated group was injected with a single 4 mg/kg i.p. of EV in 0.2 ml sesame oil. As of day 60, the treatment group was additionally given 15 mg/kg i.p. of SP600125 once daily for 4 consecutive days and the rats were sacrificed on day 65. Histopathological findings (ovarian morphology, edema, inflammatory cell infiltration, vascular congestion and hyperemia) and collagen type IV immunoexpression were assessed. Results: The SP600125+ PCOS group showed a significant level of improvement in ovarian follicle morphology, edema, inflammatory infiltrate, vascular congestion and hyperemia as compared with the PCOS group. Furthermore, collagen type IV immunoexpression showed a significant reduction in staining intensity on the theca cell layer and ovary stroma as compared to the PCOS group. Conclusion: This study demonstrates the therapeutic effect of SP600125 in the prevention of PCOS in an experimental model.Yuzuncu Yil University Scientific Research Project Coordination Unit, Van, TurkeyYuzuncu Yil University [2014-HIZ-TF079]This project is supported by a Grant from Yuzuncu Yil University Scientific Research Project Coordination Unit, Van, Turkey. (2014-HIZ-TF079)