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https://www.readbyqxmd.com/read/28530547/application-of-machine-learning-approaches-for-protein-protein-interactions-prediction
#1
Mengying Zhang, Qiang Su, Yi Lu, Manman Zhao, Bing Niu
BACKGROUND: Proteomics endeavors to study the structures, functions and interactions of proteins. Information of the protein-protein interactions (PPIs) helps to improve our knowledge of the functions and the 3D structures of proteins. Thus determining the PPIs is essential for the study of the proteomics. OBJECTIVE: In this review, in order to study the application of machine learning in predicting PPI, some machine learning approaches such as support vector machine (SVM), artificial neural networks (ANNs) and random forest (RF) were selected, and the examples of its applications in PPIs were listed...
May 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28528705/complications-of-proton-pump-inhibitor-therapy
#2
REVIEW
Michael F Vaezi, Yu-Xiao Yang, Colin W Howden
Safety issues associated with proton pump inhibitors (PPIs) have recently attracted widespread media and lay attention. Gastroenterologists are frequently asked about the appropriateness of PPI therapy for specific patients. Furthermore, some patients may have had PPI therapy discontinued abruptly or inappropriately due to safety concerns. Faced with such a wide variety of potentially serious adverse consequences, prescribers need to evaluate the evidence objectively to discern the likelihood that any reported association might actually be causal...
May 18, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28524201/a-computational-framework-for-distinguishing-direct-versus-indirect-interactions-in-human-functional-protein-protein-interaction-networks
#3
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28514401/-differentiation-therapy-for-non-acidic-gastroesophageal-reflux-disease
#4
N B Lishchuk, V I Simanenkov, S V Tikhonov
AIM: To investigate the clinical and pathogenetic features of the non-acidic types of gastroesophageal reflux disease (GERD) and to evaluate the impact of combined therapy versus monotherapy on the course of this disease. SUBJECTS AND METHODS: The investigation enrolled 62 patients with non-acidic GERD. The follow-up period was 6 weeks. The patients were divided into 2 groups: 1) weakly acidic gastroesophageal refluxes (GER); 2) weakly alkaline GER. Then each group was distributed, thus making up 4 groups: 1) 19 patients with weakly acidic GER who received monotherapy with rabeprazole 20 mg/day; 2) 21 patients with weakly acidic GER had combined therapy with rabeprazole 20 mg and itopride; 3) 8 patients with weakly alkaline GER who received ursodeoxycholic acid (UDCA) monotherapy; and 4) 14 patients with weakly alkaline GER who had combined therapy with UDCA and itopride, The clinical symptoms of the disease, the endoscopic pattern of the upper gastrointestinal tract (GIT) mucosa, histological changes in the esophageal and gastric mucosa, and the results of 24-hour impedance pH monitoring were assessed over time...
2017: Terapevticheskiĭ Arkhiv
https://www.readbyqxmd.com/read/28514151/deepppi-boosting-prediction-of-protein-protein-interactions-with-deep-neural-networks
#5
Xiuquan Du, Shiwei Sun, Changlin Hu, Yu Yao, Yuanting Yan, Yanping Zhang
The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example, protein-protein interactions (PPIs). In this study, we address this challenge using a recent machine learning advance-deep neural networks (DNNs). We aim at improving the performance of PPIs prediction and propose a method called DeepPPI (Deep neural networks for Protein-Protein Interactions prediction), which employs deep neural networks to effectively learn the representations of proteins from common protein descriptors...
May 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28512114/associations-of-acid-suppressive-therapy-with-cardiac-mortality-in-heart-failure-patients
#6
Akiomi Yoshihisa, Mai Takiguchi, Yuki Kanno, Akihiko Sato, Tetsuro Yokokawa, Shunsuke Miura, Satoshi Abe, Tomofumi Misaka, Takamasa Sato, Satoshi Suzuki, Masayoshi Oikawa, Atsushi Kobayashi, Takayoshi Yamaki, Hiroyuki Kunii, Kazuhiko Nakazato, Hitoshi Suzuki, Shu-Ichi Saitoh, Yasuchika Takeishi
BACKGROUND: It has been recently reported that histamine H2 receptor antagonists (H2RAs) are associated with impairment of ventricular remodeling and incident heart failure. In addition, favorable pleiotropic effects and adverse effects of proton pump inhibitors (PPIs) on cardiovascular disease have also been reported. We examined the associations of acid suppressive therapy using H2RAs or PPIs with cardiac mortality in patients with heart failure. METHODS AND RESULTS: In total, 1191 consecutive heart failure patients were divided into 3 groups: a non-acid suppressive therapy group (n=363), an H2RA group (n=164), and a PPI group (n=664)...
May 16, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28512024/repurposing-of-proton-pump-inhibitors-as-first-identified-small-molecule-inhibitors-of-endo-%C3%AE-n-acetylglucosaminidase-engase-for-the-treatment-of-ngly1-deficiency-a-rare-genetic-disease
#7
Yiling Bi, Matthew Might, Hariprasad Vankayalapati, Balagurunathan Kuberan
N-Glycanase deficiency, or NGLY1 deficiency, is an extremely rare human genetic disease. N-Glycanase, encoded by the gene NGLY1, is an important enzyme involved in protein deglycosylation of misfolded proteins. Deglycosylation of misfolded proteins precedes the endoplasmic reticulum (ER)-associated degradation (ERAD) process. NGLY1 patients produce little or no N-glycanase (Ngly1), and the symptoms include global developmental delay, frequent seizures, complex hyperkinetic movement disorder, difficulty in swallowing/aspiration, liver dysfunction, and a lack of tears...
May 5, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28508234/surgical-treatment-of-extraesophageal-manifestations-of-gastroesophageal-reflux-disease
#8
REVIEW
Feroze Sidwa, Alessandra L Moore, Elaine Alligood, P Marco Fisichella
OBJECTIVE: To review the current literature on the role of antireflux surgery (ARS) for the treatment of extraesophageal manifestations of GERD. The extraesophageal manifestations of gastroesophageal reflux disease (GERD) include chronic cough, laryngopharyngeal reflux, and asthma. They are responsible for significant morbidity in affected patients and a high economic burden on healthcare resources. We recently published a larger review on the symptoms, diagnosis, medical, and surgical treatment of the extraesophageal manifestations of GERD...
May 15, 2017: World Journal of Surgery
https://www.readbyqxmd.com/read/28507948/characterizing-the-hot-spots-involved-in-ron-msp%C3%AE-complex-formation-using-in-silico-alanine-scanning-mutagenesis-and-molecular-dynamics-simulation
#9
Omid Zarei, Maryam Hamzeh-Mivehroud, Silvia Benvenuti, Fulya Ustun-Alkan, Siavoush Dastmalchi
Purpose: Implication of protein-protein interactions (PPIs) in development of many diseases such as cancer makes them attractive for therapeutic intervention and rational drug design. RON (Recepteur d'Origine Nantais) tyrosine kinase receptor has gained considerable attention as promising target in cancer therapy. The activation of RON via its ligand, macrophage stimulation protein (MSP) is the most common mechanism of activation for this receptor. The aim of the current study was to perform in silico alanine scanning mutagenesis and to calculate binding energy for prediction of hot spots in protein-protein interface between RON and MSPβ chain (MSPβ)...
April 2017: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28507597/low-adherence-to-national-guidelines-for-proton-pump-inhibitor-prescription-in-patients-receiving-combination-aspirin-and-anticoagulation
#10
Rajani Sharma, Abhik Roy, Christopher Ramos, Richard Rosenberg, Reuben Garcia-Carrasquillo, Benjamin Lebwohl
BACKGROUND: Aspirin, when used with concurrent anticoagulation, increases the risk of gastrointestinal bleeding (GIB). Therefore, multisociety guidelines recommend prophylactic proton-pump inhibitors (PPIs) for patients receiving aspirin and anticoagulation. We aimed to determine rates and predictors of adherence to these recommendations. METHODS: All adult inpatients discharged from the hospital on aspirin and anticoagulation from July 2009 to June 2014 were retrospectively evaluated for PPI prescription on discharge instructions...
May 2017: Therapeutic Advances in Gastroenterology
https://www.readbyqxmd.com/read/28507564/management-of-the-hormonal-syndrome-of-neuroendocrine-tumors
#11
Paweł Gut, Joanna Waligórska-Stachura, Agata Czarnywojtek, Nadia Sawicka-Gutaj, Maciej Bączyk, Katarzyna Ziemnicka, Jakub Fischbach, Kosma Woliński, Jarosław Kaznowski, Elżbieta Wrotkowska, Marek Ruchała
Gastroenteropancreatic neuroendocrine tumors (GEP/NET) are unusual and rare neoplasms that present many clinical challenges. They characteristically synthesize store and secrete a variety of peptides and neuroamines which can lead to the development of distinct clinical syndrome, however many are clinically silent until late presentation with mass effects. Management strategies include surgery cure and cytoreduction with the use of somatostatin analogues. Somatostatin have a broad range of biological actions that include inhibition of exocrine and endocrine secretions, gut motility, cell proliferation, cell survival and angiogenesis...
April 1, 2017: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/28506028/comparison-of-the-hospital-acquired-clostridium-difficile-infection-risk-of-using-proton-pump-inhibitors-versus-histamine-2-receptor-antagonists-for-prophylaxis-and-treatment-of-stress-ulcers-a-systematic-review-and-meta-analysis
#12
Mohamed Azab, Loomee Doo, Daniel H Doo, Yousif Elmofti, Muazer Ahmed, John Jay Cadavona, Xibei B Liu, Amaan Shafi, Moon Kyung Joo, Ji Won Yoo
Background/Aims: Although proton pump inhibitors (PPIs) have been widely used for the prevention and treatment of stress gastric ulcers in hospital settings, there are concerns that PPIs increase the risk of Clostridium difficile infection (CDI). However, little is known about the risk of CDI following PPI and histamine-2 receptor antagonist (H2RA) use. We evaluated the comparative hospital-acquired CDI occurrence risk associated with the concurrent use of PPIs versus H2RAs. Methods: A systematic search of PubMed, MEDLINE/ Ovid, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, and Google Scholar through August 19, 2016, identified 12 studies that reported the hospital-acquired CDI occurrence following H2RA and PPI use for the prevention and treatment of stress gastric ulcers...
May 17, 2017: Gut and Liver
https://www.readbyqxmd.com/read/28501868/factors-associated-with-potassium-competitive-acid-blocker-non-response-in-patients-with-proton-pump-inhibitor-refractory-gastroesophageal-reflux-disease
#13
Masatsugu Okuyama, Kenichi Nakahara, Narika Iwakura, Tomoki Hasegawa, Maizumi Oyama, Ayumi Inoue, Hirotaka Ishizu, Hiroshi Satoh, Yasuhiro Fujiwara
BACKGROUND/AIMS: Approximately 20-40% of patients with gastroesophageal reflux disease (GERD) are refractory to proton pump inhibitor (PPI) treatment. The acid-inhibitory effect of vonoprazan, a novel potassium-competitive acid blocker (P-CAB), is significantly greater when compared to the effect of PPIs. We investigated the efficacy of vonoprazan treatment for PPI-refractory GERD and factors associated with P-CAB non-response. METHODS: We enrolled 277 GERD patients receiving continuous PPI therapy...
May 13, 2017: Digestion
https://www.readbyqxmd.com/read/28500192/deprescribing-proton-pump-inhibitors-evidence-based-clinical-practice-guideline
#14
Barbara Farrell, Kevin Pottie, Wade Thompson, Taline Boghossian, Lisa Pizzola, Farah Joy Rashid, Carlos Rojas-Fernandez, Kate Walsh, Vivian Welch, Paul Moayyedi
OBJECTIVE: To develop an evidence-based guideline to help clinicians make decisions about when and how to safely taper or stop proton pump inhibitors (PPIs); to focus on the highest level of evidence available and seek input from primary care professionals in the guideline development, review, and endorsement processes. METHODS: Five health professionals (1 family physician, 3 pharmacists, and 1 gastroenterologist) and 5 nonvoting members comprised the overall team; members disclosed conflicts of interest...
May 2017: Canadian Family Physician Médecin de Famille Canadien
https://www.readbyqxmd.com/read/28497645/peptic-ulcer-bleeding-patients-with-rockall-scores-%C3%A2-6-are-at-risk-of-long-term-ulcer-rebleeding-a-3-5-year-prospective-longitudinal-study
#15
Er-Hsiang Yang, Hsiu-Chi Cheng, Chung-Tai Wu, Wei-Ying Chen, Meng-Ying Lin, Bor-Shyang Sheu
BACKGROUND: Patients with high Rockall scores have increased risk of rebleeding and mortality within 30 days after peptic ulcer bleeding, but long-term outcomes deserve follow-up after cessation of proton-pump inhibitors (PPIs). AIM: To validate whether patients with high Rockall scores have more recurrent ulcer bleeding in a 3.5-year longitudinal cohort. METHODS: Between August, 2011 and July, 2014, 368 patients with peptic ulcer bleeding were prospectively enrolled after endoscopic hemostasis to receive PPIs for at least 8 to 16 weeks...
May 11, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28492483/pcvmzm-using-the-probabilistic-classification-vector-machines-model-combined-with-a-zernike-moments-descriptor-to-predict-protein-protein-interactions-from-protein-sequences
#16
Yanbin Wang, Zhuhong You, Xiao Li, Xing Chen, Tonghai Jiang, Jingting Zhang
Protein-protein interactions (PPIs) are essential for most living organisms' process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate...
May 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28489837/-validation-of-the-rapid-urease-test-for-the-detection-of-helicobacter-pylori-in-a-peruvian-hospital
#17
Vladimir Espinoza Ildefonso, Harold Tabori Peinado, Claudia Meza Borja, Alejandra Bussalleu Cavero, Luis Vásquez Elera, Víctor Aguilar Sánchez, José Luis Pinto Valdivia, Jaime Cok, Alejandro Bussalleu Rivera
OBJECTIVE: To validate a rapid urease test (RUT) in Cayetano Heredia Hospital (HCH) in Lima, Peru. MATERIALS AND METHODS: This is a prospective observational study that included 181 patients over 18 years old with dyspeptic symptoms. All of them underwent upper gastrointestinal endoscopy at the Department of Gastroenterology at HCH. They had not received, during the last four weeks, proton pump inhibitors (PPIs), bismuth or antibiotics. Two biopsies of antrum were taken, one to perform the TRU (Sensibacter pylori test®) and the other one for pathology, in order to determine by both methods the presence of H...
January 2017: Revista de Gastroenterología del Perú: órgano Oficial de la Sociedad de Gastroenterología del Perú
https://www.readbyqxmd.com/read/28489008/-do-opioids-sedatives-and-proton-pump-inhibitors-increase-the-risk-of-fractures
#18
Gudlaug Thorsdottir, Elisabet Benedikz, Sigridur A Thorgeirsdottir, Magnus Johannsson
INTRODUCTION: A pharmacoepidemiological study was conducted to analyse the relationship between bone fracture and the use of certain drugs. MATERIAL/METHODS: The study includes patients 40 years and older, diagnosed with bone fractures in the Emergency Department of Landspitali University Hospital in Reykjavik, Iceland, during a 10-year period (2002-2011). Also were included those who picked up from a pharmacy 90 DDD or more per year of the drugs included in the study in the capital region of Iceland during same period...
May 2017: Læknablađiđ
https://www.readbyqxmd.com/read/28487939/identification-of-novel-genes-associated-with-fracture-healing-in-osteoporosis-induced-by-krm2-overexpression-or-lrp5-deficiency
#19
Feng Gao, Feng Xu, Dankai Wu, Jieping Cheng, Peng Xia
The aim of the present study was to screen potential key genes associated with osteoporotic fracture healing. The microarray data from the Gene Expression Omnibus database accession number GSE51686, were downloaded and used to identify differentially expressed genes (DEGs) in fracture callus tissue samples obtained from the femora of type I collagen (Col1a1)‑kringle containing transmembrane protein 2 (Krm2) mice and low density lipoprotein receptor‑related protein 5‑/‑ (Lrp5‑/‑) transgenic mice of osteoporosis compared with those in wild‑type (WT) mice...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28483454/exploration-of-pyrrole-derivatives-to-find-an-effective-potassium-competitive-acid-blocker-with-moderately-long-lasting-suppression-of-gastric-acid-secretion
#20
Haruyuki Nishida, Ikuo Fujimori, Yasuyoshi Arikawa, Keizo Hirase, Koji Ono, Kazuo Nakai, Nobuhiro Inatomi, Yasunobu Hori, Jun Matsukawa, Yasushi Fujioka, Akio Imanishi, Hideo Fukui, Fumio Itoh
With the aim to discover a novel excellent potassium-competitive acid blocker (P-CAB) that could perfectly overcome the limitations of proton pump inhibitors (PPIs), we tested various approaches based on pyrrole derivative 1 as a lead compound. As part of a comprehensive approach to identify a new effective drug, we tried to optimize the duration of action of the pyrrole derivative. Among the compounds synthesized, fluoropyrrole derivative 20j, which has a 2-F-3-Py group at position 5, fluorine atom at position 4, and a 4-Me-2-Py sulfonyl group at the first position of the pyrrole ring, showed potent gastric acid-suppressive action and moderate duration of action in animal models...
April 27, 2017: Bioorganic & Medicinal Chemistry
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