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Complex Network

Lucia Russo, Paola Russo, Constantinos I Siettos
Based on complex network theory, we propose a computational methodology which addresses the spatial distribution of fuel breaks for the inhibition of the spread of wildland fires on heterogeneous landscapes. This is a two-level approach where the dynamics of fire spread are modeled as a random Markov field process on a directed network whose edge weights are determined by a Cellular Automata model that integrates detailed GIS, landscape and meteorological data. Within this framework, the spatial distribution of fuel breaks is reduced to the problem of finding network nodes (small land patches) which favour fire propagation...
2016: PloS One
Shi-Peng Chen, Chih-Hsien Kuo, Hsueh-Han Lu, Hui-Shan Lo, Kai-Wun Yeh
IbNAC1 is known to activate the defense system by reprogramming a genetic network against herbivory in sweet potato. This regulatory activity elevates plant defense potential but relatively weakens plants by IbNAC1-mediated JA response. The mechanism controlling IbNAC1 expression to balance plant vitality and survival remains unclear. In this study, a wound-responsive G-box cis-element in the IbNAC1 promoter from -1484 to -1479 bp was identified. From a screen of wound-activated transcriptomic data, one transcriptional activator, IbbHLH3, and one repressor, IbbHLH4, were selected that bind to and activate or repress, respectively, the G-box motif in the IbNAC1 promoter to modulate the IbNAC1-mediated response...
October 2016: PLoS Genetics
Tian Tian, Linying Guo, Jing Xu, Shun Zhang, Jingjing Shi, Chengxia Liu, Yuanyuan Qin, Wenzhen Zhu
Peripheral nerve damage does not fully explain the pathogenesis of trigeminal neuralgia (TN). Central nervous system changes can follow trigeminal nerve dysfunction. We hypothesized that brain white matter and functional connectivity changes in TN patients were involved in pain perception, modulation, the cognitive-affective system, and motor function; moreover, changes in functional reorganization were correlated with white matter alterations. Twenty left TN patients and twenty-two healthy controls were studied...
October 25, 2016: Scientific Reports
M Viprey, R Jeannin, V Piriou, P Chevalier, C Michel, G Aulagner, J Berthiller, X Armoiry
WHAT IS KNOWN AND OBJECTIVE: The complex dose regimens of the direct-acting oral anticoagulants (DOAC) make their appropriate prescribing highly challenging. Inappropriate prescribing of the DOAC remains poorly addressed. We studied the patterns of DOAC prescription and estimated the prevalence of drug-related problems (DRPs) associated with their use. METHODS: A cross-sectional study was conducted using data from medical records system of the Lyon teaching hospitals...
October 24, 2016: Journal of Clinical Pharmacy and Therapeutics
Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He, Lin Gui
The recognition of disease and chemical named entities in scientific articles is a very important subtask in information extraction in the biomedical domain. Due to the diversity and complexity of disease names, the recognition of named entities of diseases is rather tougher than those of chemical names. Although there are some remarkable chemical named entity recognition systems available online such as ChemSpot and tmChem, the publicly available recognition systems of disease named entities are rare. This article presents a system for disease named entity recognition (DNER) and normalization...
2016: Database: the Journal of Biological Databases and Curation
Zhong-Hua Chen, Guang Chen, Fei Dai, Yizhou Wang, Adrian Hills, Yong-Ling Ruan, Guoping Zhang, Peter J Franks, Eviatar Nevo, Michael R Blatt
Grasses began to diversify in the late Cretaceous Period and now dominate more than one third of global land area, including three-quarters of agricultural land. We hypothesize that their success is likely attributed to the evolution of highly responsive stomata capable of maximizing productivity in rapidly changing environments. Grass stomata harness the active turgor control mechanisms present in stomata of more ancient plant lineages, maximizing several morphological and developmental features to ensure rapid responses to environmental inputs...
October 21, 2016: Trends in Plant Science
S K Sanyal, S Rao, L K Mishra, M Sharma, G K Pandey
At any given time and location, plants encounter a flood of environmental stimuli. Diverse signal transduction pathways sense these stimuli and generate a diverse array of responses. Calcium (Ca(2+)) is generated as a second messenger due to these stimuli and is responsible for transducing the signals downstream in the pathway. A large number of Ca(2+) sensor-responder components are responsible for Ca(2+) signaling in plants. The sensor-responder complexes calcineurin B-like protein (CBL) and CBL-interacting protein kinases (CIPKs) are pivotal players in Ca(2+)-mediated signaling...
2016: Enzymes
Chiara Baldo, Lorena Casareto, Alessandra Renieri, Giuseppe Merla, Barbara Garavaglia, Stefano Goldwurm, Elena Pegoraro, Maurizio Moggio, Marina Mora, Luisa Politano, Luca Sangiorgi, Raffaella Mazzotti, Valeria Viotti, Ilaria Meloni, Maria Teresa Pellico, Chiara Barzaghi, Chiuhui Mary Wang, Lucia Monaco, Mirella Filocamo
BACKGROUND: Rare diseases (RDs) are often neglected because they affect a small percentage of the population (6-8 %), which makes research and development of new therapies challenging processes. Easy access to high-quality samples and associated clinical data is therefore a key prerequisite for biomedical research. In this context, Genetic Biobanks are critical to developing basic, translational and clinical research on RDs. The Telethon Network of Genetic Biobanks (TNGB) is aware of the importance of biobanking as a service for patients and has started a dialogue with RD-Patient Organisations via promotion of dedicated meetings and round-tables, as well as by including their representatives on the TNGB Advisory Board...
October 24, 2016: Orphanet Journal of Rare Diseases
Chrysoula Konstantinidou, Stavros Taraviras, Vassilis Pachnis
BACKGROUND: In vertebrate organisms, the neural crest (NC) gives rise to multipotential and highly migratory progenitors which are distributed throughout the embryo and generate, among other structures, the peripheral nervous system, including the intrinsic neuroglial networks of the gut, i.e. the enteric nervous system (ENS). The majority of enteric neurons and glia originate from vagal NC-derived progenitors which invade the foregut mesenchyme and migrate rostro-caudally to colonise the entire length of the gut...
October 24, 2016: BMC Biology
Nelly Rahkonen, Aki Stubb, Maia Malonzo, Sanna Edelman, Maheswara Reddy Emani, Elisa Närvä, Harri Lähdesmäki, Hannele Ruohola-Baker, Riitta Lahesmaa, Riikka Lund
MicroRNAs (miRNA) are central regulators of diverse biological processes and are important in the regulation of stem cell self-renewal. One of the widely studied miRNA-protein regulators is the Lin28-Let-7 pair. In this study, we demonstrate that contrary to the well-established models of mouse ES cells (mESC) and transformed human cancer cells, the pluripotent state of human ES cells (hESC) involves expression of mature Let-7 family miRNAs with concurrent expression of all LIN28 proteins. We show that mature Let-7 miRNAs are regulated during hESC differentiation and have opposite expression profile with LIN28B...
September 24, 2016: Stem Cell Research
Money Gupta, Rashi Chauhan, Yamuna Prasad, Gulshan Wadhwa, Chakresh Kumar Jain
The lack of complete treatments and appearance of multiple drug-resistance strains of Burkholderia cepacia complex (Bcc) are causing an increased risk of lung infections in cystic fibrosis patients. Bcc infection is a big risk to human health and demands an urgent need to identify new therapeutics against these bacteria. Network biology has emerged as one of the prospective hope in identifying novel drug targets and hits. We have applied protein-protein interaction methodology to identify new drug-target candidates (orthologs) in Burkhloderia cepacia GG4, which is an important strain for studying the quorum-sensing phenomena...
October 8, 2016: Computational Biology and Chemistry
Anna Hojka-Osinska, Lucyna Budzko, Agnieszka Zmienko, Agnieszka Rybarczyk, Patrick Maillard, Agata Budkowska, Marek Figlerowicz, Paulina Jackowiak
Hepatitis C virus (HCV) infection is one of the major causes of chronic liver diseases. Unfortunately, the mechanisms of HCV infection-induced liver injury and host-virus interactions are still not well recognized. To better understand these processes we determined the changes in the host gene expression that occur during HCV infection of Huh-7.5 cells. As a result, we identified genes that may contribute to the immune and metabolic cellular responses to infection. Pathway enrichment analysis indicated that HCV induced an increased expression of genes involved in mitogen-activated protein kinases signaling, adipocytokine signaling, cell cycle and nitrogen metabolism...
October 25, 2016: Acta Biochimica Polonica
Doyeon Kim, You Me Sung, Jinman Park, Sukjun Kim, Jongkyu Kim, Junhee Park, Haeok Ha, Jung Yoon Bae, SoHui Kim, Daehyun Baek
The functional rules for microRNA (miRNA) targeting remain controversial despite their biological importance because only a small fraction of distinct interactions, called site types, have been examined among an astronomical number of site types that can occur between miRNAs and their target mRNAs. To systematically discover functional site types and to evaluate the contradicting rules reported previously, we used large-scale transcriptome data and statistically examined whether each of approximately 2 billion site types is enriched in differentially downregulated mRNAs responding to overexpressed miRNAs...
October 24, 2016: Nature Genetics
Yuchen Gao, Xin Xiong, Spencer Wong, Emeric J Charles, Wendell A Lim, Lei S Qi
The ability to dynamically manipulate the transcriptome is important for studying how gene networks direct cellular functions and how network perturbations cause disease. Nuclease-dead CRISPR-dCas9 transcriptional regulators, while offering an approach for controlling individual gene expression, remain incapable of dynamically coordinating complex transcriptional events. Here, we describe a flexible dCas9-based platform for chemical-inducible complex gene regulation. From a screen of chemical- and light-inducible dimerization systems, we identified two potent chemical inducers that mediate efficient gene activation and repression in mammalian cells...
October 24, 2016: Nature Methods
Verónica Jornet-Mollá, Yan Duan, Carlos Giménez-Saiz, João C Waerenborgh, Francisco M Romero
The paper reports the syntheses, crystal structures, thermal and (photo)magnetic properties of spin crossover salts of formula [Fe(bpp)2](C6H8O4)·4H2O (1·4H2O), [Fe(bpp)2](C8H4O4)·2CH3OH·H2O (2·2MeOH·H2O) and [Fe(bpp)2](C8H4O4)·5H2O (2·5H2O) (bpp = 2,6-bis(pyrazol-3yl)pyridine; C6H8O4 = adipate dianion; C8H4O4 = terephthalate dianion). The salts exhibit an intricate network of hydrogen bonds between low-spin iron(ii) complexes and carboxylate dianions, with solvent molecules sitting in the voids. Desolvation is accompanied by a low-spin (LS) to high-spin (HS) transformation in the materials...
October 24, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Xiaozhe Xiong, Tatyana Panchenko, Shuang Yang, Shuai Zhao, Peiqiang Yan, Wenhao Zhang, Wei Xie, Yuanyuan Li, Yingming Zhao, C David Allis, Haitao Li
Recognition of histone covalent modifications by 'reader' modules constitutes a major mechanism for epigenetic regulation. A recent upsurge of newly discovered histone lysine acylations, such as crotonylation (Kcr), butyrylation (Kbu), and propionylation (Kpr), greatly expands the coding potential of histone lysine modifications. Here we demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylations with the strongest preference for Kcr...
October 24, 2016: Nature Chemical Biology
Kelly D Moynihan, Cary F Opel, Gregory L Szeto, Alice Tzeng, Eric F Zhu, Jesse M Engreitz, Robert T Williams, Kavya Rakhra, Michael H Zhang, Adrienne M Rothschilds, Sudha Kumari, Ryan L Kelly, Byron H Kwan, Wuhbet Abraham, Kevin Hu, Naveen K Mehta, Monique J Kauke, Heikyung Suh, Jennifer R Cochran, Douglas A Lauffenburger, K Dane Wittrup, Darrell J Irvine
Checkpoint blockade with antibodies specific for cytotoxic T lymphocyte-associated protein (CTLA)-4 or programmed cell death 1 (PDCD1; also known as PD-1) elicits durable tumor regression in metastatic cancer, but these dramatic responses are confined to a minority of patients. This suboptimal outcome is probably due in part to the complex network of immunosuppressive pathways present in advanced tumors, which are unlikely to be overcome by intervention at a single signaling checkpoint. Here we describe a combination immunotherapy that recruits a variety of innate and adaptive immune cells to eliminate large tumor burdens in syngeneic tumor models and a genetically engineered mouse model of melanoma; to our knowledge tumors of this size have not previously been curable by treatments relying on endogenous immunity...
October 24, 2016: Nature Medicine
Alexander Leithner, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, David J J de Gorter, Florian Schur, Jonathan Bayerl, Ingrid de Vries, Stefan Wieser, Robert Hauschild, Frank P L Lai, Markus Moser, Dontscho Kerjaschki, Klemens Rottner, J Victor Small, Theresia E B Stradal, Michael Sixt
Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation...
October 24, 2016: Nature Cell Biology
Encheng Xin, Yong Ju, Haiwen Yuan
A space charge density wireless measurement system based on the idea of distributed measurement is proposed for collecting and monitoring the space charge density in an ultra-high-voltage direct-current (UHVDC) environment. The proposed system architecture is composed of a number of wireless nodes connected with space charge density sensors and a base station. The space charge density sensor based on atmospheric ion counter method is elaborated and developed, and the ARM microprocessor and Zigbee radio frequency module are applied...
October 20, 2016: Sensors
Cristian Axenie, Christoph Richter, Jörg Conradt
Biological and technical systems operate in a rich multimodal environment. Due to the diversity of incoming sensory streams a system perceives and the variety of motor capabilities a system exhibits there is no single representation and no singular unambiguous interpretation of such a complex scene. In this work we propose a novel sensory processing architecture, inspired by the distributed macro-architecture of the mammalian cortex. The underlying computation is performed by a network of computational maps, each representing a different sensory quantity...
October 20, 2016: Sensors
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