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https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#1
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#2
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938088/small-molecule-inhibitors-targeting-dna-repair-and-dna-repair-deficiency-in-research-and-cancer-therapy
#3
REVIEW
Sarah R Hengel, M Ashley Spies, Maria Spies
To maintain stable genomes and to avoid cancer and aging, cells need to repair a multitude of deleterious DNA lesions, which arise constantly in every cell. Processes that support genome integrity in normal cells, however, allow cancer cells to develop resistance to radiation and DNA-damaging chemotherapeutics. Chemical inhibition of the key DNA repair proteins and pharmacologically induced synthetic lethality have become instrumental in both dissecting the complex DNA repair networks and as promising anticancer agents...
September 21, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28938009/altering-neuronal-excitability-to-preserve-network-connectivity-in-a-computational-model-of-alzheimer-s-disease
#4
Willem de Haan, Elisabeth C W van Straaten, Alida A Gouw, Cornelis J Stam
Neuronal hyperactivity and hyperexcitability of the cerebral cortex and hippocampal region is an increasingly observed phenomenon in preclinical Alzheimer's disease (AD). In later stages, oscillatory slowing and loss of functional connectivity are ubiquitous. Recent evidence suggests that neuronal dynamics have a prominent role in AD pathophysiology, making it a potentially interesting therapeutic target. However, although neuronal activity can be manipulated by various (non-)pharmacological means, intervening in a highly integrated system that depends on complex dynamics can produce counterintuitive and adverse effects...
September 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28937978/a-new-discrete-dynamic-model-of-aba-induced-stomatal-closure-predicts-key-feedback-loops
#5
Réka Albert, Biswa R Acharya, Byeong Wook Jeon, Jorge G T Zañudo, Mengmeng Zhu, Karim Osman, Sarah M Assmann
Stomata, microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur, are closed in response to drought by the phytohormone abscisic acid (ABA). This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades. Although a core signaling chain has been elucidated consisting of ABA binding to receptors, which alleviates negative regulation by protein phosphatases 2C (PP2Cs) of the protein kinase OPEN STOMATA 1 (OST1) and ultimately results in activation of anion channels, osmotic water loss, and stomatal closure, over 70 additional components have been identified, yet their relationships with each other and the core components are poorly elucidated...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#6
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
September 22, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28937906/protein-activation-in-periapical-reaction-to-iodoform-containing-root-canal-sealer
#7
Nili Tickotsky, Moti Moskovitz
OBJECTIVES: An association between root canal sealers and periapical lesions in primary dentition has been suggested, yet the chemical-protein interactions that may be involved in it have not been studied. The present study explored root sealer components' effect on periapical tissue proteins using bioinformatics tools. STUDY DESIGN: For each chemical component of Endoflas F.S. root sealing material we identified the known and predicted target proteins, using STITCH (search tool for interactions of chemicals http://stitch...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28937832/aberrant-plasticity-in-the-hippocampus-after-neonatal-seizures
#8
Xiaoqian Zhang, Huiling Qu, Ying Wang, Shanshan Zhao, Ting Xiao, Chuansheng Zhao, Weiyu Teng
Neonatal seizures are the most frequent type of neurological disorder and those newborn babies that experience seizures carry an increased risk of epileptogenesis and other long-term morbidities. The newly generated dentate granule cells (DGCs) integrate functionally into the mature hippocampal network by continuously forming connections with their targets but this process of adult neurogenesis can be influenced by seizures. When compared to adult seizures, neonatal seizures may exert different effects on neurogenesis due to the high resistance of the newborn's neurons to cell death combined with the inherent high sensitivity to seizures in the immature brain...
September 22, 2017: International Journal of Neuroscience
https://www.readbyqxmd.com/read/28937628/integrative-pathway-analysis-of-genes-and-metabolites-reveals-metabolism-abnormal-subpathway-regions-and-modules-in-esophageal-squamous-cell-carcinoma
#9
Chunquan Li, Qiuyu Wang, Jiquan Ma, Shengshu Shi, Xin Chen, Haixiu Yang, Junwei Han
Aberrant metabolism is one of the main driving forces in the initiation and development of ESCC. Both genes and metabolites play important roles in metabolic pathways. Integrative pathway analysis of both genes and metabolites will thus help to interpret the underlying biological phenomena. Here, we performed integrative pathway analysis of gene and metabolite profiles by analyzing six gene expression profiles and seven metabolite profiles of ESCC. Multiple known and novel subpathways associated with ESCC, such as 'beta-Alanine metabolism', were identified via the cooperative use of differential genes, differential metabolites, and their positional importance information in pathways...
September 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28937603/proteome-stability-as-a-key-factor-of-genome-integrity
#10
REVIEW
Sentiljana Gumeni, Zoi Evangelakou, Vassilis G Gorgoulis, Ioannis P Trougakos
DNA damage is constantly produced by both endogenous and exogenous factors; DNA lesions then trigger the so-called DNA damaged response (DDR). This is a highly synchronized pathway that involves recognition, signaling and repair of the damage. Failure to eliminate DNA lesions is associated with genome instability, a driving force in tumorigenesis. Proteins carry out the vast majority of cellular functions and thus proteome quality control (PQC) is critical for the maintenance of cellular functionality. PQC is assured by the proteostasis network (PN), which under conditions of proteome instability address the triage decision of protein fold, hold, or degrade...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28937340/research-domain-criteria-as-psychiatric-nosology
#11
Faisal Akram, James Giordano
Diagnostic classification systems in psychiatry have continued to rely on clinical phenomenology, despite limitations inherent in that approach. In view of these limitations and recent progress in neuroscience, the National Institute of Mental Health (NIMH) has initiated the Research Domain Criteria (RDoC) project to develop a more neuroscientifically based system of characterizing and classifying psychiatric disorders. The RDoC initiative aims to transform psychiatry into an integrative science of psychopathology in which mental illnesses will be defined as involving putative dysfunctions in neural nodes and networks...
October 2017: Cambridge Quarterly of Healthcare Ethics: CQ: the International Journal of Healthcare Ethics Committees
https://www.readbyqxmd.com/read/28937333/provider-prioritized-domains-of-quality-in-pediatric-home-based-hospice-and-palliative-care-a-study-of-the-ohio-pediatric-palliative-care-and-end-of-life-network
#12
Rachel Thienprayoon, Melissa San Julian Mark, Daniel Grossoehme
BACKGROUND: Children receiving hospice and palliative care (HPC) differ from adults in important ways. Children are more likely to have rare diagnoses, less likely to have cancer, have longer lengths of stay on hospice, and are more likely to be technology dependent than adults. The National Consensus Project (NCP) in Palliative Care established domains of quality for HPC, but these domains have not been evaluated for applicability in children. OBJECTIVES: This study aims to establish consensus stakeholder-prioritized domains of high-quality pediatric home-based hospice and palliative care (HBHPC)...
September 22, 2017: Journal of Palliative Medicine
https://www.readbyqxmd.com/read/28936969/systematic-integration-of-biomedical-knowledge-prioritizes-drugs-for-repurposing
#13
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms...
September 22, 2017: ELife
https://www.readbyqxmd.com/read/28936867/anisotropic-dye-adsorption-and-anhydrous-proton-conductivity-in-smectic-liquid-crystal-networks-the-role-of-cross-link-density-order-and-orientation
#14
Ting Liang, Huub P C van Kuringen, Dirk J Mulder, Shuai Tan, Yong Wu, Zandrie Borneman, Kitty Nijmeijer, Albertus P H J Schenning
In this work the decisive role of rigidity, orientation and order in the smectic liquid crystalline network on the anisotropic proton and adsorbent properties is reported. The rigidity in the hydrogen-bonded polymer network has been altered by changing the cross-link density, the order by using different mesophases (smectic, nematic and isotropic phases) while the orientation of the mesogens was controlled by alignment layers. Adding more cross-linker improved the integrity of the polymer films. For the proton conduction, an optimum was found in the amount of cross-linker and the smectic organization results in the highest anhydrous proton conduction...
September 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28936831/-real-world-analysis-to-explore-xiyanping-injection-combined-with-other-drugs-for-hand-foot-mouth-disease
#15
Zhi-Fei Wang, Hai-Wei Fan, Yan-Ming Xie
Integrated network analysis was used in this paper to analyze Xiyanping injection combined therapy for hand-foot-mouth disease based on the registered research data of 3 204 cases. It was found that the drug combination therapy was almost consistent with the guidelines for the diagnosis and treatment of hand foot mouth disease, but there were some problems to be noticed: there were too many applications of antibiotics, more than the need in preventing secondary infection; and ribavirin was not necessary for use...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28936744/cardiac-telocyte-derived-exosomes-and-their-possible-implications-in-cardiovascular-pathophysiology
#16
Mirca Marini, Lidia Ibba-Manneschi, Mirko Manetti
Among cardiac interstitial cells, the recently described telocytes (TCs) display the unique ability to build a supportive three-dimensional network formed by their very long and thin prolongations named telopodes. Cardiac TCs are increasingly regarded as pivotal regulators in intercellular signaling with multiple cell types, such as cardiomyocytes, stem/progenitor cells, microvessels, nerve endings, fibroblasts and immune cells, thus converting the cardiac stromal compartment into an integrated system that may drive either heart development or maintenance of cardiac homeostasis in post-natal life...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28936215/omics-approaches-for-understanding-grapevine-berry-development-regulatory-networks-associated-with-endogenous-processes-and-environmental-responses
#17
REVIEW
Alejandra Serrano, Carmen Espinoza, Grace Armijo, Claudio Inostroza-Blancheteau, Evelyn Poblete, Carlos Meyer-Regueiro, Anibal Arce, Francisca Parada, Claudia Santibáñez, Patricio Arce-Johnson
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28936173/combining-spect-and-quantitative-eeg-analysis-for-the-automated-differential-diagnosis-of-disorders-with-amnestic-symptoms
#18
Yvonne Höller, Arne C Bathke, Andreas Uhl, Nicolas Strobl, Adelheid Lang, Jürgen Bergmann, Raffaele Nardone, Fabio Rossini, Harald Zauner, Margarita Kirschner, Amirhossein Jahanbekam, Eugen Trinka, Wolfgang Staffen
Single photon emission computed tomography (SPECT) and Electroencephalography (EEG) have become established tools in routine diagnostics of dementia. We aimed to increase the diagnostic power by combining quantitative markers from SPECT and EEG for differential diagnosis of disorders with amnestic symptoms. We hypothesize that the combination of SPECT with measures of interaction (connectivity) in the EEG yields higher diagnostic accuracy than the single modalities. We examined 39 patients with Alzheimer's dementia (AD), 69 patients with depressive cognitive impairment (DCI), 71 patients with amnestic mild cognitive impairment (aMCI), and 41 patients with amnestic subjective cognitive complaints (aSCC)...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28936168/mining-time-resolved-functional-brain-graphs-to-an-eeg-based-chronnectomic-brain-aged-index-cbai
#19
Stavros I Dimitriadis, Christos I Salis
The brain at rest consists of spatially and temporal distributed but functionally connected regions that called intrinsic connectivity networks (ICNs). Resting state electroencephalography (rs-EEG) is a way to characterize brain networks without confounds associated with task EEG such as task difficulty and performance. A novel framework of how to study dynamic functional connectivity under the notion of functional connectivity microstates (FCμstates) and symbolic dynamics is further discussed. Furthermore, we introduced a way to construct a single integrated dynamic functional connectivity graph (IDFCG) that preserves both the strength of the connections between every pair of sensors but also the type of dominant intrinsic coupling modes (DICM)...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28935924/multipurpose-silicon-photonics-signal-processor-core
#20
Daniel Pérez, Ivana Gasulla, Lee Crudgington, David J Thomson, Ali Z Khokhar, Ke Li, Wei Cao, Goran Z Mashanovich, José Capmany
Integrated photonics changes the scaling laws of information and communication systems offering architectural choices that combine photonics with electronics to optimize performance, power, footprint, and cost. Application-specific photonic integrated circuits, where particular circuits/chips are designed to optimally perform particular functionalities, require a considerable number of design and fabrication iterations leading to long development times. A different approach inspired by electronic Field Programmable Gate Arrays is the programmable photonic processor, where a common hardware implemented by a two-dimensional photonic waveguide mesh realizes different functionalities through programming...
September 21, 2017: Nature Communications
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