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https://www.readbyqxmd.com/read/27933530/visualization-of-results-from-systems-genetics-studies-in-chromosomal-context
#1
Karen Y Oróstica, Ricardo A Verdugo
This chapter describes methods currently available for visualizing results from systems genetics experiments. Here, we abstract from the statistical methods used for genetic mapping, which are dependent on the specific resource being used, i.e. F2, RILs, or outbred populations among others. We use a public dataset with results from a mouse eQTL experiment for three examples of visualization: genome-wide dot plots of marker-by-gene association, karyotype-like plots, and circos plots. Dot plots give a first overview of the results from eQTL mapping, allowing detecting genome-wide patterns of cis- and trans-genetic association to transcription level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27932215/the-land-use-legacy-effect-towards-a-mechanistic-understanding-of-time-lagged-water-quality-responses-to-land-use-cover
#2
Sherry L Martin, Daniel B Hayes, Anthony D Kendall, David W Hyndman
Numerous studies have linked land use/land cover (LULC) to aquatic ecosystem responses, however only a few have included the dynamics of changing LULC in their analysis. In this study, we explicitly recognize changing LULC by linking mechanistic groundwater flow and travel time models to a historical time series of LULC, creating a land-use legacy map. We then illustrate the utility of legacy maps to explore relationships between dynamic LULC and lake water chemistry. We tested two main concepts about mechanisms linking LULC and lake water chemistry: groundwater pathways are an important mechanism driving legacy effects; and, LULC over multiple spatial scales is more closely related to lake chemistry than LULC over a single spatial scale...
December 5, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27931210/ontological-security-and-connectivity-provided-by-pets-a-study-in-the-self-management-of-the-everyday-lives-of-people-diagnosed-with-a-long-term-mental-health-condition
#3
Helen Brooks, Kelly Rushton, Sandra Walker, Karina Lovell, Anne Rogers
BACKGROUND: Despite evidence that connecting people to relevant wellbeing-related resources brings therapeutic benefit, there is limited understanding, in the context of mental health recovery, of the potential value and contribution of pet ownership to personal support networks for self-management. This study aimed to explore the role of pets in the support and management activities in the personal networks of people with long-term mental health problems. METHODS: Semi-structured interviews centred on 'ego' network mapping were conducted in two locations (in the North West and in the South of England) with 54 participants with a diagnosis of a long-term mental health problem...
December 9, 2016: BMC Psychiatry
https://www.readbyqxmd.com/read/27930958/protected-areas-and-agricultural-expansion-biodiversity-conservation-versus-economic-growth-in-the-southeast-of-brazil
#4
Mayra Cristina Prado de Moraes, Kaline de Mello, Rogério Hartung Toppa
The conversion of natural ecosystems to agricultural land and urban areas plays a threat to the protected areas and the natural ecosystems conservation. The aim of this paper is to provide an analysis of the agricultural expansion and its impact on the landscape spatial and temporal patterns in a buffer zone of a protected area located in the transition zone between the Atlantic Forest and Cerrado, in the State of São Paulo, Brazil. The land use and land cover were mapped between 1971 and 2008 and landscape metrics were calculated to provide a spatiotemporal analysis of the forest structure and the expansion of the croplands...
December 5, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27930915/anatomical-dysconnectivity-in-bipolar-disorder-compared-with-schizophrenia-a-selective-review-of-structural-network-analyses-using-diffusion-mri
#5
REVIEW
Stefani O'Donoghue, Laurena Holleran, Dara M Cannon, Colm McDonald
BACKGROUND: The dysconnectivity hypothesis suggests that psychotic illnesses arise not from regionally specific focal pathophysiology, but rather from impaired neuroanatomical integration across networks of brain regions. Decreased white matter organization has been hypothesized to be a feature of psychotic illnesses in general, which is supported by meta-analyses of DTI studies in bipolar disorder and schizophrenia. Although many diffusion MRI studies investigate bipolar disorder and schizophrenia alone, relatively few studies directly compare structural features in these psychotic illnesses...
November 17, 2016: Journal of Affective Disorders
https://www.readbyqxmd.com/read/27930690/structural-mapping-and-functional-characterization-of-zebrafish-class-b-g-protein-coupled-receptor-gpcr-with-dual-ligand-selectivity-towards-glp-1-and-glucagon
#6
Deena A Oren, Yang Wei, Luce Skrabanek, Billy K C Chow, Thomas Mommsen, Svetlana Mojsov
GLP-1 and glucagon regulate glucose metabolism through a network of metabolic pathways initiated upon binding to their specific receptors that belong to class B G-protein coupled receptors (GPCRs). The therapeutic potential of glucagon is currently being evaluated, while GLP-1 is already used in the treatment of type 2 diabetes and obesity. Development of a second generation of GLP-1 based therapeutics depends on a molecular and structural understanding of the interactions between the GLP-1 receptor (GLP-1R) and its ligand GLP-1...
2016: PloS One
https://www.readbyqxmd.com/read/27930095/multi-omics-data-integration-and-mapping-of-altered-kinases-to-pathways-reveal-gonadotropin-hormone-signaling-in-glioblastoma
#7
Savita Jayaram, Manoj Kumar Gupta, Rajesh Raju, Poonam Gautam, Ravi Sirdeshmukh
Glioblastoma multiforme (GBM) is one of the most lethal brain tumors with an inadequately understood pathophysiology. Biomarkers that guide accurate diagnosis and treatment decisions would greatly support precision medicine for GBM. Previous studies of GBM have focused on signaling pathways such as epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors (PDGFRs), notch, wnt, and others, identified with single omics technology platforms (genomics, transcriptomics, or proteomics), but not with their integrated use...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27925481/mitochondrial-ros-uncoupled-from-atp-synthesis-determine-endothelial-activation-for-both-physiological-recruitment-of-patrolling-cells-and-pathological-recruitment-of-inflammatory-cells
#8
Xinyuan Li, Pu Fang, William Y Yang, Kylie Chan, Muriel Lavallee, Keman Xu, Tracy Gao, Hong Wang, Xiaofeng Yang
Mitochondrial reactive oxygen species (mtROS) are signaling molecules, which drive inflammatory cytokine production and T cell activation. In addition, cardiovascular diseases, cancers, and autoimmune diseases all share a common feature of increased mtROS level. Both mtROS and ATP are produced as a result of electron transport chain activity, but it remains enigmatic whether mtROS could be generated independently from ATP synthesis. A recent study shed light on this important question and found that, during endothelial cell (EC) activation, mtROS could be upregulated in a proton leak-coupled, but ATP synthesis-uncoupled manner...
November 5, 2016: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/27924300/a-dataset-of-multiresolution-functional-brain-parcellations-in-an-elderly-population-with-no-or-mild-cognitive-impairment
#9
Angela Tam, Christian Dansereau, AmanPreet Badhwar, Pierre Orban, Sylvie Belleville, Howard Chertkow, Alain Dagher, Alexandru Hanganu, Oury Monchi, Pedro Rosa-Neto, Amir Shmuel, John Breitner, Pierre Bellec
We present group eight resolutions of brain parcellations for clusters generated from resting-state functional magnetic resonance images for 99 cognitively normal elderly persons and 129 patients with mild cognitive impairment, pooled from four independent datasets. This dataset was generated as part of the following study: Common Effects of Amnestic Mild Cognitive Impairment on Resting-State Connectivity Across Four Independent Studies (Tam et al., 2015) [1]. The brain parcellations have been registered to both symmetric and asymmetric MNI brain templates and generated using a method called bootstrap analysis of stable clusters (BASC) (Bellec et al...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27920740/spaces-in-the-brain-from-neurons-to-meanings
#10
REVIEW
Christian Balkenius, Peter Gärdenfors
Spaces in the brain can refer either to psychological spaces, which are derived from similarity judgments, or to neurocognitive spaces, which are based on the activities of neural structures. We want to show how psychological spaces naturally emerge from the underlying neural spaces by dimension reductions that preserve similarity structures and the relevant categorizations. Some neuronal representational formats that may generate the psychological spaces are presented, compared, and discussed in relation to the mathematical principles of monotonicity, continuity, and convexity...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27920095/functional-characterization-of-the-left-ventrolateral-premotor-cortex-in-humans-a-direct-electrophysiological-approach
#11
L Fornia, V Ferpozzi, M Montagna, M Rossi, M Riva, F Pessina, F Martinelli Boneschi, P Borroni, R N Lemon, L Bello, G Cerri
In monkeys, motor outputs from premotor cortex (PM) involve cortico-cortical connections with primary motor cortex (M1). However, in humans, the functional organization of PM and its relationship with the corticospinal tract (CST) is still uncertain. This study was carried out in 21 patients undergoing intraoperative brain mapping prior to tumor resection. The left ventrolateral premotor cortex (vlPM-BA6) was identified preoperatively by functional magnetic resonance imaging, and then investigated intraoperatively using high frequency direct electrical stimulation (HF-DES) of the convexity of M1 and vlPM-BA6, with simultaneous recording of motor-evoked potentials (MEPs) from oro-facial, hand and arm muscles...
December 5, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27919750/mapping-the-functional-connectome-in-traumatic-brain-injury-what-can-graph-metrics-tell-us
#12
Karen Caeyenberghs, Helena Verhelst, Adam Clemente, Peter H Wilson
OBJECTIVE: Traumatic brain injury (TBI) is associated with cognitive and motor deficits, and poses a significant personal, societal, and economic burden. One mechanism by which TBI is thought to affect cognition and behaviour is through changes in functional connectivity. Graph theory is a powerful framework for quantifying topological features of neuroimaging-derived functional networks. The objective of this paper is to review studies examining functional connectivity in TBI with an emphasis on graph theoretical analysis that is proving to be valuable in uncovering network abnormalities in this condition...
December 2, 2016: NeuroImage
https://www.readbyqxmd.com/read/27919546/brain-morphometry-predicts-individual-creative-potential-and-the-ability-to-combine-remote-ideas
#13
David Bendetowicz, Marika Urbanski, Clarisse Aichelburg, Richard Levy, Emmanuelle Volle
For complex mental functions such as creative thinking, inter-individual variability is useful to better understand the underlying cognitive components and brain anatomy. Associative theories propose that creative individuals have flexible semantic associations, which allows remote elements to be formed into new combinations. However, the structural brain variability associated with the ability to combine remote associates has not been explored. To address this question, we performed a voxel-based morphometry (VBM) study and explored the anatomical connectivity of significant regions...
November 15, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/27917569/distinct-intrinsic-functional-brain-network-abnormalities-in-methamphetamine-dependent-patients-with-and-without-a-history-of-psychosis
#14
Jonathan C Ipser, Anne Uhlmann, Paul Taylor, Brian H Harvey, Don Wilson, Dan J Stein
Chronic methamphetamine use is associated with executive functioning deficits that suggest dysfunctional cognitive control networks (CCNs) in the brain. Likewise, abnormal connectivity between intrinsic CCNs and default mode networks (DMNs) has also been associated with poor cognitive function in clinical populations. Accordingly, we tested the extent to which methamphetamine use predicts abnormal connectivity between these networks, and whether, as predicted, these abnormalities are compounded in patients with a history of methamphetamine-associated psychosis (MAP)...
December 5, 2016: Addiction Biology
https://www.readbyqxmd.com/read/27917194/a-network-approach-of-gene-co-expression-in-the-zea-mays-aspergillus-flavus-pathosystem-to-map-host-pathogen-interaction-pathways
#15
Bryan M Musungu, Deepak Bhatnagar, Robert L Brown, Gary A Payne, Greg OBrian, Ahmad M Fakhoury, Matt Geisler
A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27917112/reproducibility-and-reliability-of-quantitative-and-weighted-t1-and-t2-%C3%A2-mapping-for-myelin-based-cortical-parcellation-at-7-tesla
#16
Roy A M Haast, Dimo Ivanov, Elia Formisano, Kâmil Uludaǧ
Different magnetic resonance (MR) parameters, such as R1 (=1/T1) or T2(∗), have been used to visualize non-invasively the myelin distribution across the cortical sheet. Myelin contrast is consistently enhanced in the primary sensory and some higher order cortical areas (such as MT or the cingulate cortex), which renders it suitable for subject-specific anatomical cortical parcellation. However, no systematic comparison has been performed between the previously proposed MR parameters, i.e., the longitudinal and transversal relaxation values (or their ratios), for myelin mapping at 7 Tesla...
2016: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/27913359/network-unfolding-map-by-vertex-edge-dynamics-modeling
#17
Filipe Alves Neto Verri, Paulo Roberto Urio, Liang Zhao
The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique using distributed processing elements in a complex network, which are called particles, to solve semisupervised learning problems. Three actions govern the particles' dynamics: generation, walking, and absorption. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27912134/uncertainties-in-mapping-forest-carbon-in-urban-ecosystems
#18
Gang Chen, Emre Ozelkan, Kunwar K Singh, Jun Zhou, Marilyn R Brown, Ross K Meentemeyer
Spatially explicit urban forest carbon estimation provides a baseline map for understanding the variation in forest vertical structure, informing sustainable forest management and urban planning. While high-resolution remote sensing has proven promising for carbon mapping in highly fragmented urban landscapes, data cost and availability are the major obstacle prohibiting accurate, consistent, and repeated measurement of forest carbon pools in cities. This study aims to evaluate the uncertainties of forest carbon estimation in response to the combined impacts of remote sensing data resolution and neighborhood spatial patterns in Charlotte, North Carolina...
November 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27912109/characterization-and-fine-mapping-of-a-novel-premature-leaf-senescence-mutant-yellow-leaf-and-dwarf-1-in-rice
#19
Luchang Deng, Peng Qin, Zhi Liu, Geling Wang, Weilan Chen, Jianhua Tong, Langtao Xiao, Bin Tu, Yuantao Sun, Wei Yan, Hang He, Jun Tan, Xuewei Chen, Yuping Wang, Shigui Li, Bingtian Ma
Leaves are the main organs in which photosynthates are produced. Leaf senescence facilitates the translocation of photosynthates and nutrients from source to sink, which is important for plant development and especially for crop yield. However, the molecular mechanism of leaf senescence is unknown. Here, we identified a mutant, yellow leaf and dwarf 1 (yld1), which exhibited decreased plant height and premature leaf senescence. Nitroblue tetrazolium and diamiobenzidine staining analyses revealed that the concentrations of reactive oxygen species were higher in yld1 leaves than in wild type leaves...
November 22, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27911825/elucidating-the-druggable-interface-of-protein-protein-interactions-using-fragment-docking-and-coevolutionary-analysis
#20
Fang Bai, Faruck Morcos, Ryan R Cheng, Hualiang Jiang, José N Onuchic
Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
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