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Connectivity map Broad

Kathleen Whiting, Larry Y Liu, Mehmet Koyutürk, Günnur Karakurt
Intimate partner violence (IPV) is a serious problem with devastating health consequences. Screening procedures may overlook relationships between IPV and negative health effects. To identify IPV-associated women's health issues, we mined national, aggregated de-identified electronic health record data and compared female health issues of domestic abuse (DA) versus non-DA records, identifying terms significantly more frequent for the DA group. After coding these terms into 28 broad categories, we developed a network map to determine strength of relationships between categories in the context of DA, finding that acute conditions are strongly connected to cardiovascular, gastrointestinal, gynecological, and neurological conditions among victims...
2016: Pacific Symposium on Biocomputing
H A Marusak, M E Thomason, C Peters, C Zundel, F Elrahal, C A Rabinak
Connections between the amygdala and medial prefrontal cortex (mPFC) are considered critical for the expression and regulation of emotional behavior. Abnormalities in frontoamygdala circuitry are reported across several internalizing conditions and associated risk factors (for example, childhood trauma), which may underlie the strong phenotypic overlap and co-occurrence of internalizing conditions. However, it is unclear if these findings converge on the same localized areas of mPFC or adjacent anterior cingulate cortex (ACC)...
November 8, 2016: Translational Psychiatry
Katherine A Dunn, Jessica Moore-Connors, Brad MacIntyre, Andrew Stadnyk, Nikhil A Thomas, Angela Noble, Gamal Mahdi, Mohsin Rashid, Anthony R Otley, Joseph P Bielawski, Johan Van Limbergen
BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn's disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect. METHODS: Fecal samples were collected from 15 pediatric CD patients prior to and after EEN treatment, as well as from 5 healthy controls...
November 2016: Inflammatory Bowel Diseases
Rama Raghavan, Stephen Hyter, Harsh B Pathak, Andrew K Godwin, Gottfried Konecny, Chen Wang, Ellen L Goode, Brooke L Fridley
BACKGROUND: Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer death among women in the United States (5 % of cancer deaths). The standard treatment for patients with advanced EOC is initial debulking surgery followed by carboplatin-paclitaxel combination chemotherapy. Unfortunately, with chemotherapy most patients relapse and die resulting in a five-year overall survival around 45 %. Thus, finding novel therapeutics for treating EOC is essential. Connectivity Mapping (CMAP) has been used widely in cancer drug discovery and generally has relied on cancer cell line gene expression and drug phenotype data...
October 19, 2016: BMC Genomics
F Xavier Castellanos, Yuta Aoki
Functional magnetic resonance imaging (fMRI) without an explicit task, i.e., resting state fMRI, of individuals with Attention-Deficit/Hyperactivity Disorder (ADHD) is growing rapidly. Early studies were unaware of the vulnerability of this method to even minor degrees of head motion, a major concern in the field. Recent efforts are implementing various strategies to address this source of artifact along with a growing set of analytical tools. Availability of the ADHD-200 Consortium dataset, a large-scale multi-site repository, is facilitating increasingly sophisticated approaches...
May 2016: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Feixiong Cheng, James L Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H Rubin
Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap) host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins...
September 2016: PLoS Computational Biology
Lauren T Cordova, Hal S Alper
Central carbon metabolism is conserved among all organisms for cellular function and energy generation. The connectivity of this metabolic map gives rises to key metabolite nodes. Five of these nodes in particular, pyruvate, citric acid, tyrosine and aspartate, acetyl-CoA, serve as critical starting points for the generation of a broad class of relevant chemical molecules with ranging applications from fuels, pharmaceuticals and polymer precursors. This review highlights recent progress in converting these metabolite nodes into valuable products...
September 5, 2016: Current Opinion in Chemical Biology
Daniel L Albaugh, Andrew Salzwedel, Nathalie Van Den Berge, Wei Gao, Garret D Stuber, Yen-Yu Ian Shih
Deep brain stimulation of the nucleus accumbens (NAc-DBS) is an emerging therapy for diverse, refractory neuropsychiatric diseases. Although DBS therapy is broadly hypothesized to work through large-scale neural modulation, little is known regarding the neural circuits and networks affected by NAc-DBS. Using a healthy, sedated rat model of NAc-DBS, we employed both evoked- and functional connectivity (fc) MRI to examine the functional circuit and network changes achieved by electrical NAc stimulation. Optogenetic-fMRI experiments were also undertaken to evaluate the circuit modulation profile achieved by selective stimulation of NAc neurons...
September 7, 2016: Scientific Reports
Longwen Huang, Kevin Ung, Isabella Garcia, Kathleen B Quast, Keith Cordiner, Peter Saggau, Benjamin R Arenkiel
UNLABELLED: Elucidating patterns of functional synaptic connectivity and deciphering mechanisms of how plasticity influences such connectivity is essential toward understanding brain function. In the mouse olfactory bulb (OB), principal neurons (mitral/tufted cells) make reciprocal connections with local inhibitory interneurons, including granule cells (GCs) and external plexiform layer (EPL) interneurons. Our current understanding of the functional connectivity between these cell types, as well as their experience-dependent plasticity, remains incomplete...
August 24, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Emanuele Strano, Vishal Sood
Recent advances in the urban science make broad use of the notion of scaling. We focus here on the important scaling relationship between the gross metropolitan product (GMP) of a city and its population (pop). It has been demonstrated that GMP ∝ Y Ypopβ with β always greater than 1 and close to 1.2. This fundamental finding highlights a universal rule that holds across countries and cultures and might explain the very nature of cities. However, in an increasingly connected world, the hypothesis that the economy of a city solely depends on its population might be questionable...
2016: PloS One
Christian Arlt, Michael Götze, Christian H Ihling, Christoph Hage, Mathias Schäfer, Andrea Sinz
Cross-linking combined with mass spectrometry (MS) has evolved as an alternative strategy in structural biology for characterizing three-dimensional structures of protein assemblies and for mapping protein-protein interactions. Here, we describe an integrated workflow for an automated identification of cross-linked products that is based on the use of a tandem mass spectrometry (MS/MS) cleavable cross-linker (containing a 1,3-bis-(4-oxo-butyl)-urea group, BuUrBu) generating characteristic doublet patterns upon fragmentation...
August 16, 2016: Analytical Chemistry
Kellie A Park, Adema Ribic, Fabian M Laage Gaupp, Daniel Coman, Yuegao Huang, Chris G Dulla, Fahmeed Hyder, Thomas Biederer
UNLABELLED: Select adhesion proteins control the development of synapses and modulate their structural and functional properties. Despite these important roles, the extent to which different synapse-organizing mechanisms act across brain regions to establish connectivity and regulate network properties is incompletely understood. Further, their functional roles in different neuronal populations remain to be defined. Here, we applied diffusion tensor imaging (DTI), a modality of magnetic resonance imaging (MRI), to map connectivity changes in knock-out (KO) mice lacking the synaptogenic cell adhesion protein SynCAM 1...
July 13, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Houri Hintiryan, Nicholas N Foster, Ian Bowman, Maxwell Bay, Monica Y Song, Lin Gou, Seita Yamashita, Michael S Bienkowski, Brian Zingg, Muye Zhu, X William Yang, Jean C Shih, Arthur W Toga, Hong-Wei Dong
Different cortical areas are organized into distinct intracortical subnetworks. The manner in which descending pathways from the entire cortex interact subcortically as a network remains unclear. We developed an open-access comprehensive mesoscale mouse cortico-striatal projectome: a detailed connectivity projection map from the entire cerebral cortex to the dorsal striatum or caudoputamen (CP) in rodents. On the basis of these projections, we used new computational neuroanatomical tools to identify 29 distinct functional striatal domains...
August 2016: Nature Neuroscience
Zan Chen, Stefani N Thomas, David M Bolduc, Xuejun Jiang, Xiangbin Zhang, Cynthia Wolberger, Philip A Cole
PTEN is a lipid phosphatase that converts phosphatidylinositol 3,4,5-phosphate (PIP3) to phosphatidylinositol 4,5-phosphate (PIP2) and plays a critical role in the regulation of tumor growth. PTEN is subject to regulation by a variety of post-translational modifications, including phosphorylation on a C-terminal cluster of four Ser/Thr residues (380, 382, 383, and 385) and ubiquitylation by various E3 ligases, including NEDD4-1 and WWP2. It has previously been shown that C-terminal phosphorylation of PTEN can increase its cellular half-life...
July 5, 2016: Biochemistry
Daniel Wolf, Luis A Rodriguez, Armand Béché, Elsa Javon, Luis Serrano, Cesar Magen, Christophe Gatel, Axel Lubk, Hannes Lichte, Sara Bals, Gustaaf Van Tendeloo, Amalio Fernández-Pacheco, José M De Teresa, Etienne Snoeck
The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing...
October 13, 2015: Chemistry of Materials: a Publication of the American Chemical Society
Paul G O'Reilly, Qing Wen, Peter Bankhead, Philip D Dunne, Darragh G McArt, Suzanne McPherson, Peter W Hamilton, Ken I Mills, Shu-Dong Zhang
BACKGROUND: Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying potential small molecule compounds, which may be further investigated as candidates for repurposing to treat diseases. The public release of voluminous data from the Library of Integrated Cellular Signatures (LINCS) programme further enhanced the utilities and potentials of gene expression connectivity mapping in biomedicine...
2016: BMC Bioinformatics
Robert Marschall, Paul Tudzynski
NADPH oxidases (Nox) produce reactive oxygen species (ROS) in multicellular eukaryotic organisms. They trigger defense reactions ('oxidative burst') - in phagocytes and plant cells -, and are involved in a broad range of differentiation processes. Fungal Nox-complexes play a central role in vegetative, sexual and pathogenic processes. In contrast to mammalian systems, knowledge is limited about composition, localisation and connection to major signaling cascades in fungi. Here, we characterize a fungal homolog of the RasGAP scaffold protein IQGAP, which links several major signaling processes, including Nox in mammalian cell lines...
July 2016: Molecular Microbiology
Laura C Erickson, Josef P Rauschecker, Peter E Turkeltaub
The superior temporal sulcus (STS) is a critical region for multiple neural processes in the human brain Hein and Knight (J Cogn Neurosci 20(12): 2125-2136, 2008). To better understand the multiple functions of the STS it would be useful to know more about its consistent functional coactivations with other brain regions. We used the meta-analytic connectivity modeling technique to determine consistent functional coactivation patterns across experiments and behaviors associated with bilateral anterior, middle, and posterior anatomical STS subregions...
March 22, 2016: Brain Structure & Function
Matthew J Sutterer, Joel Bruss, Aaron D Boes, Michelle W Voss, Antoine Bechara, Daniel Tranel
Studies of patients with brain damage have highlighted a broad neural network of limbic and prefrontal areas as important for adaptive decision-making. However, some patients with damage outside these regions have impaired decision-making behavior, and the behavioral impairments observed in these cases are often attributed to the general variability in behavior following brain damage, rather than a deficit in a specific brain-behavior relationship. A novel approach, lesion-derived network mapping, uses healthy subject resting-state functional connectivity (RSFC) data to infer the areas that would be connected with each patient's lesion area in healthy adults...
May 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
Laura A Cocas, Gloria Fernandez, Mariya Barch, Jason Doll, Ivan Zamora Diaz, Samuel J Pleasure
UNLABELLED: The mammalian cerebral cortex is a dense network composed of local, subcortical, and intercortical synaptic connections. As a result, mapping cell type-specific neuronal connectivity in the cerebral cortex in vivo has long been a challenge for neurobiologists. In particular, the development of excitatory and inhibitory interneuron presynaptic input has been hard to capture. We set out to analyze the development of this connectivity in the first postnatal month using a murine model...
March 16, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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