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https://www.readbyqxmd.com/read/28227130/verification-of-a-research-prototype-for-hemodynamic-analysis-of-cerebral-aneurysms
#1
Takashi Suzuki, Cosmin Ioan Nita, Saikiran Rapaka, Hiroyuki Takao, Viorel Mihalef, Soichiro Fujimura, Chihebeddine Dahmani, Puneet Sharma, Hiroya Mamori, Toshihiro Ishibashi, Thomas Redel, Makoto Yamamoto, Yuichi Murayama, Takashi Suzuki, Cosmin Ioan Nita, Saikiran Rapaka, Hiroyuki Takao, Viorel Mihalef, Soichiro Fujimura, Chihebeddine Dahmani, Puneet Sharma, Hiroya Mamori, Toshihiro Ishibashi, Thomas Redel, Makoto Yamamoto, Yuichi Murayama, Cosmin Ioan Nita, Puneet Sharma, Hiroya Mamori, Soichiro Fujimura, Thomas Redel, Saikiran Rapaka, Chihebeddine Dahmani, Toshihiro Ishibashi, Makoto Yamamoto, Viorel Mihalef, Takashi Suzuki, Hiroyuki Takao, Yuichi Murayama
Owing to its clinical importance, there has been a growing body of research on understanding the hemodynamics of cerebral aneurysms. Traditionally, this work has been performed using general-purpose, state-of-the-art commercial solvers. This has meant requiring engineering expertise for making appropriate choices on the geometric discretization, time-step selection, choice of boundary conditions etc. Recently, a CFD research prototype has been developed (Siemens Healthcare GmbH, Prototype - not for diagnostic use) for end-to-end analysis of aneurysm hemodynamics...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226262/an-urban-runoff-model-designed-to-inform-stormwater-management-decisions
#2
Nicole G Beck, Gary Conley, Lisa Kanner, Margaret Mathias
We present an urban runoff model designed for stormwater managers to quantify runoff reduction benefits of mitigation actions that has lower input data and user expertise requirements than most commonly used models. The stormwater tool to estimate load reductions (TELR) employs a semi-distributed approach, where landscape characteristics and process representation are spatially-lumped within urban catchments on the order of 100 acres (40 ha). Hydrologic computations use a set of metrics that describe a 30-year rainfall distribution, combined with well-tested algorithms for rainfall-runoff transformation and routing to generate average annual runoff estimates for each catchment...
February 19, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28226238/defense-priming-an-adaptive-part-of-induced-resistance
#3
Brigitte Mauch-Mani, Ivan Baccelli, Estrella Luna, Victor Flors
Priming is an adaptive strategy that improves the defensive capacity of plants. This phenomenon is marked by an enhanced activation of induced defense mechanisms. Stimuli from pathogens, beneficial microbes, or arthropods, as well as chemicals and abiotic cues, can trigger the establishment of priming by acting as warning signals. Upon stimulus perception, changes may occur in the plant at the physiological, transcriptional, metabolic, and epigenetic levels. This phase is called the priming phase. Upon subsequent challenge, the plant effectively mounts a faster and/or stronger defense response that defines the postchallenge primed state and results in increased resistance and/or stress tolerance...
February 2, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226237/novel-insights-into-tree-biology-and-genome-evolution-as-revealed-through-genomics
#4
David B Neale, Pedro J Martínez-García, Amanda R De La Torre, Sara Montanari, Xiao-Xin Wei
Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226236/new-strategies-and-tools-in-quantitative-genetics-how-to-go-from-the-phenotype-to-the-genotype
#5
C Bazakos, M Hanemian, C Trontin, J M Jiménez-Gómez, O Loudet
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#6
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226234/zooming-in-on-plant-hormone-analysis-tissue-and-cell-specific-approaches
#7
Ondřej Novák, Richard Napier, Karin Ljung
Plant hormones are a group of naturally occurring, low-abundance organic compounds that influence physiological processes in plants. Our knowledge of the distribution profiles of phytohormones in plant organs, tissues, and cells is still incomplete, but advances in mass spectrometry have enabled significant advances in tissue- and cell-type-specific analyses of phytohormones over the last decade. Mass spectrometry is able to simultaneously identify and quantify hormones and their related substances. Biosensors, on the other hand, offer continuous monitoring; can visualize local distributions and realtime quantification; and, in the case of genetically encoded biosensors, are noninvasive...
February 10, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226233/chemical-genetic-dissection-of-membrane-trafficking
#8
Lorena Norambuena, Ricardo Tejos
The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking...
February 13, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226232/the-epigenome-and-transcriptional-dynamics-of-fruit-ripening
#9
James Giovannoni, Cuong Nguyen, Betsy Ampofo, Silin Zhong, Zhangjun Fei
Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226231/cell-biology-of-the-plant-nucleus
#10
Iris Meier, Eric J Richards, David E Evans
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226230/genomics-physiology-and-molecular-breeding-approaches-for-improving-salt-tolerance
#11
Abdelbagi M Ismail, Tomoaki Horie
Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are fairly well understood, involving numerous critical processes that are each controlled by multiple genes. Knowledge of the critical mechanisms controlling salt uptake and exclusion from functioning tissues, signaling of salt stress, and the arsenal of protective metabolites is advancing...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226229/a-perspective-on-the-role-of-computational-models-in-immunology
#12
Arup K Chakraborty
This is an exciting time for immunology because the future promises to be replete with exciting new discoveries that can be translated to improve health and treat disease in novel ways. Immunologists are attempting to answer increasingly complex questions concerning phenomena that range from the genetic, molecular, and cellular scales to that of organs, whole animals or humans, and populations of humans and pathogens. An important goal is to understand how the many different components involved interact with each other within and across these scales for immune responses to emerge, and how aberrant regulation of these processes causes disease...
February 6, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226228/antigen-presenting-cells-in-the-skin
#13
Sakeen W Kashem, Muzlifah Haniffa, Daniel H Kaplan
Professional antigen-presenting cells (APCs) in the skin include dendritic cells, monocytes, and macrophages. They are highly dynamic, with the capacity to enter skin from the peripheral circulation, patrol within tissue, and migrate through lymphatics to draining lymph nodes. Skin APCs are endowed with antigen sensing, processing, and presenting machinery and play key roles in initiating, modulating, and resolving cutaneous inflammation. Skin APCs are a highly heterogeneous population with functionally specialized subsets that are developmentally imprinted and modulated by local tissue microenvironmental and inflammatory cues...
February 6, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226227/protective-and-harmful-immunity-to-rsv-infection
#14
Peter J M Openshaw, Chris Chiu, Fiona J Culley, Cecilia Johansson
Respiratory syncytial virus (RSV) is an exceptional mucosal pathogen. It specializes in infection of the ciliated respiratory epithelium, causing disease of variable severity with little or no direct systemic effects. It infects virtually all children by the age of three years and then repeatedly infects throughout life; this it does despite relatively slight variations in antigenicity, apparently by inducing selective immunological amnesia. Inappropriate or dysregulated responses to RSV can be pathogenic, causing disease-enhancing inflammation that contributes to short- and long-term effects...
February 6, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226226/microglia-function-in-the-central-nervous-system-during-health-and-neurodegeneration
#15
Marco Colonna, Oleg Butovsky
Microglia are resident cells of the brain that regulate brain development, maintenance of neuronal networks, and injury repair. Microglia serve as brain macrophages but are distinct from other tissue macrophages owing to their unique homeostatic phenotype and tight regulation by the central nervous system (CNS) microenvironment. They are responsible for the elimination of microbes, dead cells, redundant synapses, protein aggregates, and other particulate and soluble antigens that may endanger the CNS. Furthermore, as the primary source of proinflammatory cytokines, microglia are pivotal mediators of neuroinflammation and can induce or modulate a broad spectrum of cellular responses...
February 9, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226225/thymic-epithelial-cells
#16
Jakub Abramson, Graham Anderson
IntrathymicTcell development is a complex process that depends upon continuous guidance from thymus stromal cell microenvironments. The thymic epithelium within the thymic stroma comprises highly specialized cells with a high degree of anatomic, phenotypic, and functional heterogeneity. These properties are collectively required to bias thymocyte development toward production of self-tolerant and functionally competent T cells. The importance of thymic epithelial cells (TECs) is evidenced by clear links between their dysfunction and multiple diseases where autoimmunity and immunodeficiency are major components...
February 10, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226223/progress-toward-a-molecular-mechanism-of-water-oxidation-in-photosystem-ii
#17
David J Vinyard, Gary W Brudvig
The active site of photosynthetic water oxidation is the oxygen-evolving complex (OEC) in the photosystem II (PSII) reaction center. The OEC is a Mn4CaO5 cluster embedded in the PSII protein matrix, and it cycles through redox intermediates known as Si states (i = 0-4). Significant progress has been made in understanding the inorganic and physical chemistry of states S0-S3 through experiment and theory. The chemical steps from S3 to S0 are more poorly understood, however, because the identity of the substrate water molecules and the mechanism of O-O bond formation are not well established...
February 2, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#18
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226221/development-of-new-density-functional-approximations
#19
Neil Qiang Su, Xin Xu
Kohn-Sham density functional theory has become the leading electronic structure method for atoms, molecules, and extended systems. It is in principle exact, but any practical application must rely on density functional approximations (DFAs) for the exchange-correlation energy. Here we emphasize four aspects of the subject: (a) philosophies and strategies for developing DFAs; (b) classification of DFAs; (c) major sources of error in existing DFAs; and (d) some recent developments and future directions. Expected final online publication date for the Annual Review of Physical Chemistry Volume 68 is April 20, 2017...
February 22, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226220/water-oxidation-mechanisms-of-metal-oxide-catalysts-by-vibrational-spectroscopy-of-transient-intermediates
#20
Miao Zhang, Heinz Frei
Water oxidation is an essential reaction of an artificial photosystem for solar fuel generation because it provides electrons needed to reduce carbon dioxide or protons to a fuel. Earth-abundant metal oxides are among the most attractive catalytic materials for this reaction because of their robustness and scalability, but their efficiency poses a challenge. Knowledge of catalytic surface intermediates gained by vibrational spectroscopy under reaction conditions plays a key role in uncovering kinetic bottlenecks and provides a basis for catalyst design improvements...
February 22, 2017: Annual Review of Physical Chemistry
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