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Felipe Donoso, Helene Engstrand Lilja
Background Since 2005, infants with esophageal atresia (EA) in our unit are given prophylactic proton pump inhibitors (PPI) after repair until 1 year of age. The aims of this study were to identify risk factors for anastomotic strictures (AS) and to assess the efficacy of postoperative PPI prophylaxis in reducing the incidence of AS compared with symptomatic PPI. Methods Patients who underwent EA repair from 1994 to 2013 in our unit were included in this retrospective observational study approved by the local ethics review board...
October 21, 2016: European Journal of Pediatric Surgery
Navadon Khunlertgit, Byung-Jun Yoon
BACKGROUND: Discovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathways or a protein-protein interaction (PPI) network, we can find better biomarkers that lead to more accurate and reproducible prognostic predictions. In fact, recent studies have shown that, "modular markers," that integrate multiple genes with potential interactions can improve disease classification and also provide better understanding of the disease mechanisms...
October 6, 2016: BMC Bioinformatics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
Izabela Jatczak-Pawlik, Michal Gorzkiewicz, Maciej Studzian, Dietmar Appelhans, Brigitte Voit, Lukasz Pulaski, Barbara Klajnert-Maculewicz
PURPOSE: Fourth-generation poly(propylene imine) dendrimers fully surface-modified by maltose (dense shell, PPI-m DS) were shown to be biocompatible in cellular models, which is important for their application in drug delivery. We decided to verify also their inherent bioactivity, including immunomodulatory activity, for potential clinical applications. We tested their effects on the THP-1 monocytic cell line model of innate immunity effectors. METHODS: To estimate the cytotoxicity of dendrimers the reasazurin assay was performed...
October 20, 2016: Pharmaceutical Research
Lingzhi Zhao, Liu Zhao, Yanqing Miao, Chunye Liu, Chenxiao Zhang
The detection of pyrophosphatase (PPase) activity is of great significance in diagnosing diseases and understanding the function of PPase-related biological events. This study constructed a turn off-on-off fluorescent system for PPase activity assay based on PPase-regulated competitive coordination of Cu(2+) between a water-soluble fluorescent probe 6,7-dihydroxycoumarin (DHC) and pyrophosphate (PPi). The probe DHC can coordinate with Cu(2+) and consequently display on-off type fluorescence response. Furthermore, the in situ formed nonfluorescent Cu(2+)-DHC complex can act as an effective off-on type fluorescent probe for sensing PPi due to the higher coordination reactivity between Cu(2+) and PPi than that between Cu(2+) and DHC...
2016: Journal of Analytical Methods in Chemistry
Yushu Yin, Georgia Papavasiliou, Olga Y Zaborina, John C Alverdy, Fouad Teymour
The human gastrointestinal tract is the primary site of colonization of multidrug resistant pathogens and the major source of life-threatening complications in critically ill and immunocompromised patients. Eradication measures using antibiotics carry further risk of antibiotic resistance. Furthermore, antibiotic treatment can adversely shift the intestinal microbiome toward domination by resistant pathogens. Therefore, approaches directed to prevent replacement of health promoting microbiota with resistant pathogens should be developed...
October 19, 2016: Annals of Biomedical Engineering
Janghyun Yoo, Tae-Sun Lee, Byungsan Choi, Min Ju Shon, Tae-Young Yoon
Extremely weak protein-protein interactions (PPIs), signified by micromolar or even millimolar dissociation constants, are one of the keys to understanding the rapid responses of cellular systems. Although single-molecule methods are particularly useful in determining kinetics of biological processes, their application is largely limited to rather strong interactions because of the diffraction-limited observation volume. In this study, we report a single-molecule method that allows the characterization of PPIs using a prey concentration four orders of magnitude lower than the dissociation constant...
October 19, 2016: Journal of the American Chemical Society
Zhanzhan Xu, Yu Zhou, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Ovarian cancer is the first leading cause of mortality in gynecological malignancies. To identify key genes and microRNAs in ovarian cancer, mRNA microarray dataset GSE36668, GSE18520, GSE14407 and microRNA dataset GSE47841 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and microRNAs (DEMs) were obtained using GEO2R. Functional and pathway enrichment analysis were performed for DEGs using DAVID database. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape...
November 2016: Medical Oncology
Rita I Jabr, Fiona S Hatch, Samantha C Salvage, Alejandro Orlowski, Paul D Lampe, Christopher H Fry
Cardiac arrhythmias are associated with raised intracellular [Ca(2+)] and slowed action potential conduction caused by reduced gap junction (GJ) electrical conductance (Gj). Ventricular GJs are composed of connexin proteins (Cx43), with Gj determined by Cx43 phosphorylation status. Connexin phosphorylation is an interplay between protein kinases and phosphatases but the precise pathways are unknown. We aimed to identify key Ca(2+)-dependent phosphorylation sites on Cx43 that regulate cardiac gap junction conductance and action potential conduction velocity...
October 19, 2016: Pflügers Archiv: European Journal of Physiology
Florentina Sophie Ferstl, Alice Miriam Kitay, Rebecca Marion Trattnig, Abrar Alsaihati, John Peter Geibel
Prolonged exposure to gastric acid is a leading cause of gastroesophageal reflux disease (GERD) and esophagitis. With the ever increasing number of patients showing insensitivity to proton-pump-inhibitor (PPI) therapy with recurrence of symptoms over time, alternative treatment options remain an important issue. Previous studies from our laboratory have shown that a zinc sulfate salt can inhibit HCl generation at the cellular level of the parietal cell. In this paper, we examine the difference between two hydration forms of ZnSO4 (monohydrate H2O and heptahydrate 7H2O) in their entry characteristics into the parietal cell under several physiological conditions associated with acid secretion...
October 19, 2016: Pflügers Archiv: European Journal of Physiology
Zhi Chen, Hao Wu, Guohua Wang, Ye Feng
BACKGROUND: This study was aimed to explore the molecular mechanisms of hypertensive nephropathy (HTN). METHODS: Gene expression profile of GSE37460, which based on 27 healthy living donor samples (HTN group) and 15 hypertensive nephropathy samples (control group), were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between two groups were identified. STRING database was used to reveal protein-protein interaction (PPI) network of DEGs, followed by the functional enrichment analysis of the PPI network...
October 18, 2016: BMC Nephrology
J Mesquita-Guimarães, M A Leite, J C M Souza, B Henriques, F S Silva, D Hotza, A R Boccaccini, M C Fredel
In this work, TiO2 ceramic scaffolds were fabricated by the replica method using polyurethane (PU) sponges. Suspensions with high solid content were used to achieve scaffolds with improved mechanical behavior. TiO2 ceramic suspensions were optimized by rheological studies using different additives. It was found that the composition with 0.5 wt% Darvan enhanced the covering of the sponge struts. PU sponges of 45 to 80 ppi (pore per inch) were well coated without clogging pores. A thermal treatment with varying holding times, temperatures and heating rates was adjusted...
October 17, 2016: Journal of Biomedical Materials Research. Part A
Bin Zhang, Shijia Li, Chuanjun Zhuo, Meng Li, Adam Safron, Axel Genz, Wen Qin, Chunshui Yu, Martin Walter
BACKGROUND: Major depressive disorder (MDD) is a highly prevalent psychiatric condition in which patients often have difficulties regulating their emotions. Prior studies have shown that attention bias towards negative emotion is linked to activation in regions of the default mode network (DMN) in MDD individuals. Furthermore, MDD patients showed increased resting-state functional connectivity (FC) between the medial prefrontal cortex and other DMN structures. METHODS: Twenty-one MDD patients that currently experiencing depressive episodes and twenty-five healthy control participants performed the current emotional expectancy paradigm in a gradient-echo SENSE-SPIRAL fMRI...
October 7, 2016: Journal of Affective Disorders
Zaheer Nabi, D Nageshwar Reddy
Gastroesophageal reflux disease (GERD) is defined by the presence of troublesome symptoms resulting from the reflux of gastric contents. The prevalence of GERD is increasing globally. An incompetent lower esophageal sphincter underlies the pathogenesis of GERD. Proton pump inhibitors (PPIs) form the core of GERD management. However, a substantial number of patients do not respond well to PPIs. The next option is anti-reflux surgery, which is efficacious, but it has its own limitations, such as gas bloating, inability to belch or vomit, and dysphagia...
September 2016: Clinical Endoscopy
Blaz Skrlj, Tanja Kunej
BACKGROUND: Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly...
October 4, 2016: Computers in Biology and Medicine
Renu Vyas, Sanket Bapat, Esha Jain, Muthukumarasamy Karthikeyan, Sanjeev Tambe, Bhaskar D Kulkarni
In order to understand the molecular mechanism underlying any disease, knowledge about the interacting proteins in the disease pathway is essential. The number of revealed protein-protein interactions (PPI) is still very limited compared to the available protein sequences of different organisms. Experiment based high-throughput technologies though provide some data about these interactions, those are often fairly noisy. Computational techniques for predicting protein-protein interactions therefore assume significance...
September 30, 2016: Computational Biology and Chemistry
Nicole A Huijgen, Maria A J de Ridder, Katia M Verhamme, Gert R Dohle, Ann M Vanrolleghem, Miriam C J M Sturkenboom, Joop S E Laven, Régine P M Steegers-Theunissen
OBJECTIVE: To determine associations between proton-pump inhibitor (PPI) use and semen parameters in young men of couples who are planning pregnancy. DESIGN: Case-control study of a population-based registry. SETTING: Not applicable. PATIENT(S): General practitioner patients comprising 2,473 men from couples planning pregnancy with a recorded semen analysis: 241 with a low total motile sperm count (TMSC ≤1) and 714 with TMSC >1 as matched controls...
October 12, 2016: Fertility and Sterility
Ying You, Quanwei Song, Le Wang, Caixia Niu, Na Na, Jin Ouyang
Plasmon-enhanced fluorescence (PEF)-based anisotropic nanostructures are considered extremely promising tools for improving the inherent problems of traditional fluorophores and for detecting important biomolecules with high sensitivity. Herein, a novel triangular gold nanoprism (AuNPR)-based fluorescence probe, AuNPR@SiO2@12,17-tetramethyl-3-dihydro-(2s-trans)-thyl-7(Ce6), was developed for PEF by virtue of multiple "hot spots" of AuNPRs. Fluorescence enhancement of fluorophores can be realized owing to the larger and stronger electromagnetic fields located at the sharp tips of AuNPRs than those on spherical particles and nanorods...
October 14, 2016: Nanoscale
Michael P Chu, J Randolph Hecht, Dennis Slamon, Zev A Wainberg, Yung-Jue Bang, Paulo M Hoff, Alberto Sobrero, Shukui Qin, Karen Afenjar, Vincent Houe, Karen King, Sheryl Koski, Karen Mulder, Julie Price Hiller, Andrew Scarfe, Jennifer Spratlin, Yingjie J Huang, Saba Khan-Wasti, Neil Chua, Michael B Sawyer
Importance: Capecitabine is an oral cytotoxic chemotherapeutic commonly used across cancer subtypes. As with other oral medications though, it may suffer from drug interactions that could impair its absorption. Objective: To determine if gastric acid suppressants such as proton pump inhibitors (PPIs) may impair capecitabine efficacy. Design, Setting, and Participants: This secondary analysis of TRIO-013, a phase III randomized trial, compares capecitabine and oxaliplatin (CapeOx) with or without lapatinib in 545 patients with ERBB2/HER2-positive metastatic gastroesophageal cancer (GEC); patients were randomized 1:1 between CapeOx with or without lapatinib...
October 13, 2016: JAMA Oncology
Caixia Niu, Quanwei Song, Gen He, Na Na, Jin Ouyang
Optical antennas with anisotropic metal nanostructures are widely used in the field of fluorescence enhancement based on localized surface plasmons (LSPs). They overcome the intrinsic defects of low brightness of near-infrared (NIR) dyes and can be used to develop sensitive NIR sensors for bioapplications. Here, we demonstrate a novel NIR plasmon-enhanced fluorescence (PEF) system consisting of elongated gold nanobipyramids (Au NBPs) antennas, silica, and NIR dyes. Silica was chosen as the rigid spacer to regulate the distance between the metal nanostructures and dyes...
October 13, 2016: Analytical Chemistry
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