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https://www.readbyqxmd.com/read/28549153/chippi-a-novel-method-for-mapping-chimeric-protein-protein-interactions-uncovers-selection-principles-of-protein-fusion-events-in-cancer
#1
Milana Frenkel-Morgenstern, Alessandro Gorohovski, Somnath Tagore, Vaishnovi Sekar, Miguel Vazquez, Alfonso Valencia
Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28547854/nucleus-accumbens-functional-connectivity-at-age-20-is-associated-with-trajectory-of-adolescent-cannabis-use-and-predicts-psychosocial-functioning-in-young-adulthood
#2
Sarah D Lichenstein, Samuel Musselman, Daniel S Shaw, Stephanie Sitnick, Erika E Forbes
AIMS: To identify trajectories of cannabis use across adolescence, 2) to measure the influence of cannabis use characteristics on functional connectivity of the nucleus accumbens (NAcc), and 3) to assess whether patterns of functional connectivity related to cannabis use are associated with psychosocial functioning 2 years later. DESIGN: The Pitt Mother & Child Project (PMCP) is a prospective, longitudinal study of male youth at high risk for psychopathology based on family income and gender...
May 26, 2017: Addiction
https://www.readbyqxmd.com/read/28545612/drug-repositioning-based-on-triangularly-balanced-structure-for-tissue-specific-diseases-in-incomplete-interactome
#3
Liang Yu, Jin Zhao, Lin Gao
Finding new uses for existing drugs has become a new strategy for decades to treat more patients. Few traditional approaches consider the tissue specificities of diseases. Moreover, disease genes, drug targets and protein interaction (PPI) networks remain largely incomplete and the relationships between drugs and diseases conform to the triangularly balanced structure. Therefore, based on tissue specificities of diseases, we apply the triangularly balanced theory and the module distance defined for incomplete interaction networks to build drug-disease associations...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28545462/sequence-based-prediction-of-protein-protein-interaction-using-a-deep-learning-algorithm
#4
Tanlin Sun, Bo Zhou, Luhua Lai, Jianfeng Pei
BACKGROUND: Protein-protein interactions (PPIs) are critical for many biological processes. It is therefore important to develop accurate high-throughput methods for identifying PPI to better understand protein function, disease occurrence, and therapy design. Though various computational methods for predicting PPI have been developed, their robustness for prediction with external datasets is unknown. Deep-learning algorithms have achieved successful results in diverse areas, but their effectiveness for PPI prediction has not been tested...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28544767/a-poly-propyleneimine-dendrimer-based-polyplex-system-for-single-chain-antibody-mediated-targeted-delivery-and-cellular-uptake-of-sirna
#5
Stefanie Tietze, Isabell Schau, Susanne Michen, Franka Ennen, Andreas Janke, Gabriele Schackert, Achim Aigner, Dietmar Appelhans, Achim Temme
Therapeutics based on small interfering RNAs (siRNAs) offer a great potential to treat so far incurable diseases or metastatic cancer. However, the broad application of siRNAs using various nonviral carrier systems is hampered by unspecific toxic side effects, poor pharmacokinetics due to unwanted delivery of siRNA-loaded nanoparticles into nontarget organs, or rapid renal excretion. In order to overcome these obstacles, several targeting strategies using chemically linked antibodies and ligands have emerged...
May 22, 2017: Small
https://www.readbyqxmd.com/read/28544091/a-new-predictive-model-for-acute-gastrointestinal-bleeding-in-patients-taking-oral-anticoagulants-a-cohort-study
#6
Akira Shimomura, Naoyoshi Nagata, Takuro Shimbo, Toshiyuki Sakurai, Shiori Moriyasu, Hidetaka Okubo, Kazuhiro Watanabe, Chizu Yokoi, Junichi Akiyama, Naomi Uemura
BACKGROUND: We developed a predictive model of long-term gastrointestinal (GI) bleeding risk in patients receiving oral anticoagulants and compared it with the HAS-BLED score. METHODS: We periodically followed a cohort of 508 patients taking oral anticoagulants (66 direct oral anticoagulants users and 442 warfarin users). Absence of GI bleeding at an initial examination, and any subsequent GI bleeding, were confirmed endoscopically. The bleeding model was developed by multivariate survival analysis and evaluated by Harrell's c-index...
May 19, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28543861/postreflux-swallow-induced-peristaltic-wave-index-and-nocturnal-baseline-impedance-can-link-ppi-responsive-heartburn-to-reflux-better-than-acid-exposure-time
#7
L Frazzoni, M Frazzoni, N de Bortoli, S Tolone, M Furnari, I Martinucci, H Bertani, S Marchi, R Conigliaro, L Fuccio, V Savarino, E Savarino
BACKGROUND: Acid exposure time (AET) is considered the most useful parameter to predict response of reflux-related heartburn to medical or surgical treatment. However, recent studies showed high rates of heartburn response to proton pump inhibitor (PPI) therapy in patients with normal AET. We aimed to compare the efficacy of postreflux swallow-induced peristaltic wave (PSPW) index and mean nocturnal baseline impedance (MNBI) with AET in linking PPI-responsive heartburn to reflux. METHODS: Off-therapy impedance-pH tracings from 425 patients, 317 with PPI-responsive and 108 with PPI-refractory heartburn were blindly re-analyzed...
May 25, 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/28542290/new-paradigm-for-auditory-paired-pulse-suppression
#8
Nobuyuki Takeuchi, Shunsuke Sugiyama, Koji Inui, Kousuke Kanemoto, Makoto Nishihara
Sensory gating is a mechanism of sensory processing used to prevent an overflow of irrelevant information, with some indexes, such as prepulse inhibition (PPI) and P50 suppression, often utilized for its evaluation. In addition, those are clinically important for diseases such as schizophrenia. In the present study, we investigated long-latency paired-pulse suppression of change-related cortical responses using magnetoencephalography. The test change-related response was evoked by an abrupt increase in sound pressure by 15 dB in a continuous sound composed of a train of 25-ms pure tones at 65 dB...
2017: PloS One
https://www.readbyqxmd.com/read/28541665/identification-of-small-molecule-translesion-synthesis-inhibitors-that-target-the-rev1-ct-rir-protein-protein-interaction
#9
Vibhavari Sail, Alessandro A Rizzo, Nimrat Chatterjee, Radha Charan Dash, Zuleyha Ozen, Graham C Walker, Dmitry M Korzhnev, M Kyle Hadden
Translesion synthesis (TLS) is an important mechanism through which proliferating cells tolerate DNA damage during replication. The mutagenic Rev1/Polζ-dependent branch of TLS helps cancer cells survive first-line genotoxic chemotherapy and introduces mutations that can contribute to the acquired resistance so often observed with standard anti-cancer regimens. As such, inhibition of Rev1/Polζ-dependent TLS has recently emerged as a strategy to enhance the efficacy of first-line chemotherapy and reduce the acquisition of chemoresistance by decreasing tumor mutation rate...
May 25, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28541284/a-scalable-double-barcode-sequencing-platform-for-characterization-of-dynamic-protein-protein-interactions
#10
Ulrich Schlecht, Zhimin Liu, Jamie R Blundell, Robert P St Onge, Sasha F Levy
Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28541215/balanceali-multiple-ppi-network-alignment-with-balanced-high-coverage-and-consistency
#11
Jianliang Gao, Bo Song, Weimao Ke, Xiaohua Hu
Coverage and consistency are two most considered metrics to evaluate the effectiveness of network alignment. But they are a pair of contradictory evaluation metrics in PPI network alignment. It is difficult, if not impossible, to achieve high coverage and consistency simultaneously. Furthermore, existing methods of multiple PPI network alignment mostly ignore k-coverage or k-consistency, where k indicates the number of aligned species. In this paper, we propose BalanceAli, a novel approach for global alignment of multiple PPI networks that achieves high k-coverage and k-consistency simultaneously...
May 18, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28536974/neonatal-immune-challenge-with-lipopolysaccharide-triggers-long-lasting-sex-and-age-related-behavioral-and-immune-neurotrophic-alterations-in-mice-relevance-to-autism-spectrum-disorders
#12
Charllyany Sabino Custódio, Bruna Stefânia Ferreira Mello, Adriano José Maia Chaves Filho, Camila Nayane de Carvalho Lima, Rafaela Carneiro Cordeiro, Fábio Miyajima, Gislaine Z Réus, Silvânia Maria Mendes Vasconcelos, Tatiana Barichello, João Quevedo, Antônio Carlos de Oliveira, David Freitas de Lucena, Danielle S Macedo
Early-life challenges, particularly infections and stress, are related to neuropsychiatric disorders such as autism and schizophrenia. Here, we conducted a wide range of behavioral tests in periadolescent (postnatal day (PN) 35) and adult (PN70) Swiss mice neonatally challenged with LPS on PN5 and -7, to unveil behavioral alterations triggered by LPS exposure. Immune and neurotrophic (brain-derived neurotrophic factor-BDNF) alterations were determined in the prefrontal cortex (PFC), hippocampus (HC), and hypothalamus (HT)...
May 23, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28536638/abcc6-knockdown-in-hepg2-cells-induces-a-senescent-like-cell-phenotype
#13
Rocchina Miglionico, Angela Ostuni, Maria Francesca Armentano, Luigi Milella, Elvira Crescenzi, Monica Carmosino, Faustino Bisaccia
BACKGROUND: Pseudoxanthoma elasticum (PXE) is characterized by progressive ectopic mineralization of elastic fibers in dermal, ocular and vascular tissues. No effective treatment exists. It is caused by inactivating mutations in the gene encoding for the ATP-binding cassette, sub-family C member 6 transporter (ABCC6), which is mainly expressed in the liver. The ABCC6 substrate (s) and the PXE pathomechanism remain unknown. Recent studies have shown that overexpression of ABCC6 in HEK293 cells results in efflux of ATP, which is rapidly converted into nucleoside monophosphates and pyrophosphate (PPi)...
2017: Cellular & Molecular Biology Letters
https://www.readbyqxmd.com/read/28536485/management-of-refractory-eosinophilic-oesophagitis
#14
REVIEW
Evan S Dellon
The goal of this Review is to discuss the clinical approach to patients who do not respond to treatment for eosinophilic oesophagitis (EoE). Refractory EoE is challenging to manage as there are limited data to guide decision-making. In this Review, refractory EoE is defined as persistent eosinophilia in the setting of incomplete resolution of the primary presenting symptoms and incomplete resolution of endoscopic findings following a PPI trial, and after treatment with either topical steroids or dietary elimination...
May 24, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28534782/reinforce-an-ensemble-approach-for-inferring-ppi-network-from-ap-ms-data
#15
Bo Tian, Qiong Duan, Can Zhao, Ben Teng, Zengyou He
Affinity Purification-Mass Spectrometry (AP-MS) is one of the most important technologies for constructing protein-protein interaction (PPI) networks. In this paper, we propose an ensemble method, Reinforce, for inferring PPI network from AP-MS data set. The new algorithm named Reinforce is based on rank aggregation and false discovery rate control. Under the null hypothesis that the interaction scores from different scoring methods are randomly generated, Reinforce follows three steps to integrate multiple ranking results from different algorithms or different data sets...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28533674/impact-of-gastroesophageal-reflux-control-through-tailored-proton-pump-inhibition-therapy-or-fundoplication-in-patients-with-barrett-s-esophagus
#16
Francisco Baldaque-Silva, Michael Vieth, Mumen Debel, Bengt Håkanson, Anders Thorell, Nuno Lunet, Huan Song, Miguel Mascarenhas-Saraiva, Gisela Pereira, Lars Lundell, Hanns-Ulrich Marschall
AIM: To determine the impact of upwards titration of proton pump inhibition (PPI) on acid reflux, symptom scores and histology, compared to clinically successful fundoplication. METHODS: Two cohorts of long-segment Barrett's esophagus (BE) patients were studied. In group 1 (n = 24), increasing doses of PPI were administered in 8-wk intervals until acid reflux normalization. At each assessment, ambulatory 24 h pH recording, endoscopy with biopsies and symptom scoring (by a gastroesophageal reflux disease health related quality of life questionnaire, GERD/HRLQ) were performed...
May 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28530547/application-of-machine-learning-approaches-for-protein-protein-interactions-prediction
#17
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/28530108/twelve-day-quintuple-regime-containing-four-antibiotics-as-a-rescue-therapy-for-helicobacter-pylori-eradication-in-the-central-region-of-portugal
#18
Diogo Branquinho, Nuno Miguel Peres de Almeida, Carlos Gregório, Adriano Casela, Maria Manuel Donato, Luís Tomé
BACKGROUND: Helicobacter pylori eradication rates with standard triple therapy in many countries are clinically unacceptable. Fluoroquinolone resistance is increasing and jeopardizing second-line regimens. There is a growing need for an effective strategy in patients who failed previous therapies. METHODS: This is a single-center, non-randomized clinical study conducted in the central region of Portugal. Sixty-four patients were included with a positive 13C-urea breath test (UBT) or histology for H...
May 22, 2017: Revista Española de Enfermedades Digestivas
https://www.readbyqxmd.com/read/28529870/symptom-specific-amygdala-hyperactivity-modulates-motor-control-network-in-conversion-disorder
#19
Thomas Hassa, Alexandra Sebastian, Joachim Liepert, Cornelius Weiller, Roger Schmidt, Oliver Tüscher
Initial historical accounts as well as recent data suggest that emotion processing is dysfunctional in conversion disorder patients and that this alteration may be the pathomechanistic neurocognitive basis for symptoms in conversion disorder. However, to date evidence of direct interaction of altered negative emotion processing with motor control networks in conversion disorder is still lacking. To specifically study the neural correlates of emotion processing interacting with motor networks we used a task combining emotional and sensorimotor stimuli both separately as well as simultaneously during functional magnetic resonance imaging in a well characterized group of 13 conversion disorder patients with functional hemiparesis and 19 demographically matched healthy controls...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28528705/complications-of-proton-pump-inhibitor-therapy
#20
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
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