Complement factor H family proteins in their non-canonical role as modulators of cellular functions.

PubMed

Józsi, Mihály; Schneider, Andrea E; Kárpáti, Éva; Sándor, Noémi

2018-01-04

Complement factor H is a major regulator of the alternative pathway of the complement system. The factor H-related proteins are less characterized, but recent data indicate that they rather promote complement activation. These proteins have some common ligands with factor H and have both overlapping and distinct functions depending on domain composition and the degree of conservation of amino acid sequence. Factor H and some of the factor H-related proteins also appear in a non-canonical function that is beyond their role in the modulation of complement activation. This review covers our current understanding on this emerging role of factor H family proteins in modulating the activation and function of various cells by binding to receptors or receptor ligands. Copyright © 2018 Elsevier Ltd. All rights reserved.

NASIS data base management system: IBM 360 TSS implementation. Volume 4: Program design specifications

NASA Technical Reports Server (NTRS)

1973-01-01

The design specifications for the programs and modules within the NASA Aerospace Safety Information System (NASIS) are presented. The purpose of the design specifications is to standardize the preparation of the specifications and to guide the program design. Each major functional module within the system is a separate entity for documentation purposes. The design specifications contain a description of, and specifications for, all detail processing which occurs in the module. Sub-models, reference tables, and data sets which are common to several modules are documented separately.

Experiment module concepts study. Volume 3: Module and subsystem design

NASA Technical Reports Server (NTRS)

Hunter, J. R.; Chiarappa, D. J.

1970-01-01

The final common module set exhibiting wide commonality is described. The set consists of three types of modules: one free flying module and two modules that operate attached to the space station. The common module designs provide for the experiment program as defined. The feasibility, economy, and practicality of these modules hinges on factors that do not affect the approach or results of the commonality process, but are important to the validity of the common module concepts. Implementation of the total experiment program requires thirteen common modules: five CM-1, five CM-3, and three CM-4 modules.

A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks.

PubMed

Gallos, Lazaros K; Makse, Hernán A; Sigman, Mariano

2012-02-21

The human brain is organized in functional modules. Such an organization presents a basic conundrum: Modules ought to be sufficiently independent to guarantee functional specialization and sufficiently connected to bind multiple processors for efficient information transfer. It is commonly accepted that small-world architecture of short paths and large local clustering may solve this problem. However, there is intrinsic tension between shortcuts generating small worlds and the persistence of modularity, a global property unrelated to local clustering. Here, we present a possible solution to this puzzle. We first show that a modified percolation theory can define a set of hierarchically organized modules made of strong links in functional brain networks. These modules are "large-world" self-similar structures and, therefore, are far from being small-world. However, incorporating weaker ties to the network converts it into a small world preserving an underlying backbone of well-defined modules. Remarkably, weak ties are precisely organized as predicted by theory maximizing information transfer with minimal wiring cost. This trade-off architecture is reminiscent of the "strength of weak ties" crucial concept of social networks. Such a design suggests a natural solution to the paradox of efficient information flow in the highly modular structure of the brain.

A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks

PubMed Central

Gallos, Lazaros K.; Makse, Hernán A.; Sigman, Mariano

2012-01-01

The human brain is organized in functional modules. Such an organization presents a basic conundrum: Modules ought to be sufficiently independent to guarantee functional specialization and sufficiently connected to bind multiple processors for efficient information transfer. It is commonly accepted that small-world architecture of short paths and large local clustering may solve this problem. However, there is intrinsic tension between shortcuts generating small worlds and the persistence of modularity, a global property unrelated to local clustering. Here, we present a possible solution to this puzzle. We first show that a modified percolation theory can define a set of hierarchically organized modules made of strong links in functional brain networks. These modules are “large-world” self-similar structures and, therefore, are far from being small-world. However, incorporating weaker ties to the network converts it into a small world preserving an underlying backbone of well-defined modules. Remarkably, weak ties are precisely organized as predicted by theory maximizing information transfer with minimal wiring cost. This trade-off architecture is reminiscent of the “strength of weak ties” crucial concept of social networks. Such a design suggests a natural solution to the paradox of efficient information flow in the highly modular structure of the brain. PMID:22308319

Diesel Exhaust Modulates Ozone-induced Lung Function Decrements in Healthy Human Volunteers

EPA Science Inventory

The potential effects of combinations of dilute whole diesel exhaust (DE) and ozone (03), each a common component of ambient airborne pollutant mixtures, on lung function were examined. Healthy young human volunteers were exposed for 2 hr to pollutants while exercising (~50 L/min...

Exploiting a Corpus of Business Letters from a Phraseological, Functional Perspective

ERIC Educational Resources Information Center

Flowerdew, Lynne

2012-01-01

This paper illustrates how a freely available online corpus has been exploited in a module on teaching business letters covering the following four speech acts (functions) commonly found in business letters: invitations, requests, complaints and refusals. It is proposed that different strategies are required for teaching potentially…

The National Transport Code Collaboration Module Library

NASA Astrophysics Data System (ADS)

Kritz, A. H.; Bateman, G.; Kinsey, J.; Pankin, A.; Onjun, T.; Redd, A.; McCune, D.; Ludescher, C.; Pletzer, A.; Andre, R.; Zakharov, L.; Lodestro, L.; Pearlstein, L. D.; Jong, R.; Houlberg, W.; Strand, P.; Wiley, J.; Valanju, P.; John, H. St.; Waltz, R.; Mandrekas, J.; Mau, T. K.; Carlsson, J.; Braams, B.

2004-12-01

This paper reports on the progress in developing a library of code modules under the auspices of the National Transport Code Collaboration (NTCC). Code modules are high quality, fully documented software packages with a clearly defined interface. The modules provide a variety of functions, such as implementing numerical physics models; performing ancillary functions such as I/O or graphics; or providing tools for dealing with common issues in scientific programming such as portability of Fortran codes. Researchers in the plasma community submit code modules, and a review procedure is followed to insure adherence to programming and documentation standards. The review process is designed to provide added confidence with regard to the use of the modules and to allow users and independent reviews to validate the claims of the modules' authors. All modules include source code; clear instructions for compilation of binaries on a variety of target architectures; and test cases with well-documented input and output. All the NTCC modules and ancillary information, such as current standards and documentation, are available from the NTCC Module Library Website http://w3.pppl.gov/NTCC. The goal of the project is to develop a resource of value to builders of integrated modeling codes and to plasma physics researchers generally. Currently, there are more than 40 modules in the module library.

Ras-sensitive IMP modulation of the Raf/MEK/ERK cascade through KSR1.

PubMed

Matheny, Sharon A; White, Michael A

2006-01-01

The E3 ubiquitin ligase IMP (impedes mitogenic signal propagation) was isolated as a novel Ras effector that negatively regulates ERK1/2 activation. Current evidence suggests that IMP limits the functional assembly of Raf/MEK complexes by inactivation of the KSR1 adaptor/scaffold protein. Interaction with Ras-GTP stimulates IMP autoubiquitination to relieve limitations on KSR function. The elevated sensitivity of IMP-depleted cells to ERK1/2 pathway activation suggests IMP acts as a signal threshold regulator by imposing reversible restrictions on the assembly of functional Raf/MEK/ERK kinase modules. These observations challenge commonly held concepts of signal transmission by Ras to the MAPK pathway and provide evidence for the role of amplitude modulation in tuning cellular responses to ERK1/2 pathway engagement. Here we describe details of the methods, including RNA interference, ubiquitin ligase assays, and protein complex analysis, that can be used to display the Ras-sensitive contribution of IMP to KSR-dependent modulation of the Raf/MEK/ERK pathway.

Increased neuromuscular consistency in gait and balance after partnered, dance-based rehabilitation in Parkinson's disease.

PubMed

Allen, Jessica L; McKay, J Lucas; Sawers, Andrew; Hackney, Madeleine E; Ting, Lena H

2017-07-01

Here we examined changes in muscle coordination associated with improved motor performance after partnered, dance-based rehabilitation in individuals with mild to moderate idiopathic Parkinson's disease. Using motor module (a.k.a. muscle synergy) analysis, we identified changes in the modular control of overground walking and standing reactive balance that accompanied clinically meaningful improvements in behavioral measures of balance, gait, and disease symptoms after 3 wk of daily Adapted Tango classes. In contrast to previous studies that revealed a positive association between motor module number and motor performance, none of the six participants in this pilot study increased motor module number despite improvements in behavioral measures of balance and gait performance. Instead, motor modules were more consistently recruited and distinctly organized immediately after rehabilitation, suggesting more reliable motor output. Furthermore, the pool of motor modules shared between walking and reactive balance increased after rehabilitation, suggesting greater generalizability of motor module function across tasks. Our work is the first to show that motor module distinctness, consistency, and generalizability are more sensitive to improvements in gait and balance function after short-term rehabilitation than motor module number. Moreover, as similar differences in motor module distinctness, consistency, and generalizability have been demonstrated previously in healthy young adults with and without long-term motor training, our work suggests commonalities in the structure of muscle coordination associated with differences in motor performance across the spectrum from motor impairment to expertise. NEW & NOTEWORTHY We demonstrate changes in neuromuscular control of gait and balance in individuals with Parkinson's disease after short-term, dance-based rehabilitation. Our work is the first to show that motor module distinctness, consistency, and generalizability across gait and balance are more sensitive than motor module number to improvements in motor performance following short-term rehabilitation. Our results indicate commonalities in muscle coordination improvements associated with motor skill reacquisition due to rehabilitation and motor skill acquisition in healthy individuals. Copyright © 2017 the American Physiological Society.

Common modulation of limbic network activation underlies musical emotions as they unfold.

PubMed

Singer, Neomi; Jacoby, Nori; Lin, Tamar; Raz, Gal; Shpigelman, Lavi; Gilam, Gadi; Granot, Roni Y; Hendler, Talma

2016-11-01

Music is a powerful means for communicating emotions among individuals. Here we reveal that this continuous stream of affective information is commonly represented in the brains of different listeners and that particular musical attributes mediate this link. We examined participants' brain responses to two naturalistic musical pieces using functional Magnetic Resonance imaging (fMRI). Following scanning, as participants listened to the musical pieces for a second time, they continuously indicated their emotional experience on scales of valence and arousal. These continuous reports were used along with a detailed annotation of the musical features, to predict a novel index of Dynamic Common Activation (DCA) derived from ten large-scale data-driven functional networks. We found an association between the unfolding music-induced emotionality and the DCA modulation within a vast network of limbic regions. The limbic-DCA modulation further corresponded with continuous changes in two temporal musical features: beat-strength and tempo. Remarkably, this "collective limbic sensitivity" to temporal features was found to mediate the link between limbic-DCA and the reported emotionality. An additional association with the emotional experience was found in a left fronto-parietal network, but only among a sub-group of participants with a high level of musical experience (>5years). These findings may indicate two processing-levels underlying the unfolding of common music emotionality; (1) a widely shared core-affective process that is confined to a limbic network and mediated by temporal regularities in music and (2) an experience based process that is rooted in a left fronto-parietal network that may involve functioning of the 'mirror-neuron system'. Copyright © 2016 Elsevier Inc. All rights reserved.

Finding a common path: predicting gene function using inferred evolutionary trees.

PubMed

Reynolds, Kimberly A

2014-07-14

Reporting in Cell, Li and colleagues (2014) describe an innovative method to functionally classify genes using evolutionary information. This approach demonstrates broad utility for eukaryotic gene annotation and suggests an intriguing new decomposition of pathways and complexes into evolutionarily conserved modules. Copyright © 2014 Elsevier Inc. All rights reserved.

Religion and psychosis: a common evolutionary trajectory?

PubMed

Dein, Simon; Littlewood, Roland

2011-07-01

In this article we propose that schizophrenia and religious cognition engage cognate mental modules in the over-attribution of agency and the overextension of theory of mind. We argue similarities and differences between assumptions of ultrahuman agents with omniscient minds and certain ''pathological'' forms of thinking in schizophrenia: thought insertion, withdrawal and broadcasting, and delusions of reference. In everyday religious cognition agency detection and theory of mind modules function ''normally,'' whereas in schizophrenia both modules are impaired. It is suggested that religion and schizophrenia have perhaps had a related evolutionary trajectory.

Advanced Transport Operating System (ATOPS) control display unit software description

NASA Technical Reports Server (NTRS)

Slominski, Christopher J.; Parks, Mark A.; Debure, Kelly R.; Heaphy, William J.

1992-01-01

The software created for the Control Display Units (CDUs), used for the Advanced Transport Operating Systems (ATOPS) project, on the Transport Systems Research Vehicle (TSRV) is described. Module descriptions are presented in a standardized format which contains module purpose, calling sequence, a detailed description, and global references. The global reference section includes subroutines, functions, and common variables referenced by a particular module. The CDUs, one for the pilot and one for the copilot, are used for flight management purposes. Operations performed with the CDU affects the aircraft's guidance, navigation, and display software.

Systematic analysis of microarray datasets to identify Parkinson's disease‑associated pathways and genes.

PubMed

Feng, Yinling; Wang, Xuefeng

2017-03-01

In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD. Functional enrichment analysis of commonly disturbed genes was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Co‑pathway relationships were identified with Pearson's correlation coefficient tests and a hypergeometric distribution‑based test. Common genes in pathway pairs were selected out and regarded as risk genes. A total of 17 microarray datasets from 7 platforms were retained for further analysis. Five gene coexpression modules were identified, containing 9,745, 736, 233, 101 and 93 genes, respectively. One module was significantly correlated with PD samples and thus the 736 genes it contained were considered to be candidate PD‑associated genes. Functional enrichment analysis demonstrated that these genes were implicated in oxidative phosphorylation and PD. A total of 44 pathway pairs and 52 risk genes were revealed, and a risk gene pathway relationship network was constructed. Eight modules were identified and were revealed to be associated with PD, cancers and metabolism. A number of disturbed pathways and risk genes were unveiled in PD, and these findings may help advance understanding of PD pathogenesis.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

PubMed Central

Iskar, Murat; Zeller, Georg; Blattmann, Peter; Campillos, Monica; Kuhn, Michael; Kaminska, Katarzyna H; Runz, Heiko; Gavin, Anne-Claude; Pepperkok, Rainer; van Noort, Vera; Bork, Peer

2013-01-01

In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug-induced transcriptional modules from genome-wide microarray data of drug-treated human cell lines and rat liver, and first characterized their conservation. Over 70% of these modules were common for multiple cell lines and 15% were conserved between the human in vitro and the rat in vivo system. We then illustrate the utility of conserved and cell-type-specific drug-induced modules by predicting and experimentally validating (i) gene functions, e.g., 10 novel regulators of cellular cholesterol homeostasis and (ii) new mechanisms of action for existing drugs, thereby providing a starting point for drug repositioning, e.g., novel cell cycle inhibitors and new modulators of α-adrenergic receptor, peroxisome proliferator-activated receptor and estrogen receptor. Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology. PMID:23632384

Class-specific effector functions of therapeutic antibodies.

PubMed

Pascal, Virginie; Laffleur, Brice; Cogné, Michel

2012-01-01

Physiology usually combines polyclonal antibodies of multiple classes in a single humoral response. Beyond their common ability to bind antigens, these various classes of human immunoglobulins carry specific functions which can each serve specific goals. In many cases, the function of a monoclonal therapeutic antibody may thus be modulated according to the class of its constant domains. Depending on the immunoglobulin class, different functional assays will be used in order to evaluate the functional activity of a monoclonal antibody.

Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila

PubMed Central

Oortveld, Merel A. W.; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G.; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A.; Schenck, Annette

2013-01-01

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. PMID:24204314

Human intellectual disability genes form conserved functional modules in Drosophila.

PubMed

Oortveld, Merel A W; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A; Schenck, Annette

2013-10-01

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features.

PubMed

Xu, Juan; Li, Chuan-Xing; Li, Yong-Sheng; Lv, Jun-Ying; Ma, Ye; Shao, Ting-Ting; Xu, Liang-De; Wang, Ying-Ying; Du, Lei; Zhang, Yun-Peng; Jiang, Wei; Li, Chun-Quan; Xiao, Yun; Li, Xia

2011-02-01

Synergistic regulations among multiple microRNAs (miRNAs) are important to understand the mechanisms of complex post-transcriptional regulations in humans. Complex diseases are affected by several miRNAs rather than a single miRNA. So, it is a challenge to identify miRNA synergism and thereby further determine miRNA functions at a system-wide level and investigate disease miRNA features in the miRNA-miRNA synergistic network from a new view. Here, we constructed a miRNA-miRNA functional synergistic network (MFSN) via co-regulating functional modules that have three features: common targets of corresponding miRNA pairs, enriched in the same gene ontology category and close proximity in the protein interaction network. Predicted miRNA synergism is validated by significantly high co-expression of functional modules and significantly negative regulation to functional modules. We found that the MFSN exhibits a scale free, small world and modular architecture. Furthermore, the topological features of disease miRNAs in the MFSN are distinct from non-disease miRNAs. They have more synergism, indicating their higher complexity of functions and are the global central cores of the MFSN. In addition, miRNAs associated with the same disease are close to each other. The structure of the MFSN and the features of disease miRNAs are validated to be robust using different miRNA target data sets.

Modular Activating Receptors in Innate and Adaptive Immunity.

PubMed

Berry, Richard; Call, Matthew E

2017-03-14

Triggering of cell-mediated immunity is largely dependent on the recognition of foreign or abnormal molecules by a myriad of cell surface-bound receptors. Many activating immune receptors do not possess any intrinsic signaling capacity but instead form noncovalent complexes with one or more dimeric signaling modules that communicate with a common set of kinases to initiate intracellular information-transfer pathways. This modular architecture, where the ligand binding and signaling functions are detached from one another, is a common theme that is widely employed throughout the innate and adaptive arms of immune systems. The evolutionary advantages of this highly adaptable platform for molecular recognition are visible in the variety of ligand-receptor interactions that can be linked to common signaling pathways, the diversification of receptor modules in response to pathogen challenges, and the amplification of cellular responses through incorporation of multiple signaling motifs. Here we provide an overview of the major classes of modular activating immune receptors and outline the current state of knowledge regarding how these receptors assemble, recognize their ligands, and ultimately trigger intracellular signal transduction pathways that activate immune cell effector functions.

Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

PubMed Central

Basu, Mahashweta; Bhattacharyya, Nitai P.; Mohanty, Pradeep K.

2013-01-01

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins. PMID:23741403

Quality of Life of Nepalese Women Post Mastectomy

PubMed

Maharjan, Muna; Thapa, Niresh; Adhikari, Raj Devi; Petrini, Marcia A; Amatya, Kapendra Shekhar

2018-04-25

Introduction: Worldwide breast cancer is the common invasive cancer among the females. The quality of life of women after treatment, which is often a mastectomy, is frequently decreased. Objective: To determine the life quality of Nepalese women post mastectomy. Materials and Methods: One hundred seven women after a mastectomy were selected and interviewed by using the European Organization for Research and Treatment of Cancer-Quality of Life Questionnaire and its Breast Specific Module to assess women’s quality of life. Result: The study findings revealed a good score on global health status/quality of life. The respondents performed well on functional and symptom scales. In the Breast Specific Module, all respondents performed poor regarding sexual function and sexual enjoyment. Global Health Status was found useful among the women involved in service/business/agriculture and the survivors using breast prosthesis. In Breast Specific Module, systemic therapy side effects showed strong statistical associations with age, marital status, occupation, education, use of breast prosthesis and co-morbidity. Body image was highly significant with age, occupation, education, use of breast prosthesis and co-morbidity. Conclusion: Based on the study findings, counseling, and a structured educational programme is recommended to improve the QOL of women after a mastectomy. Creative Commons Attribution License

Toolsets for Airborne Data (TAD): Customized Data Merging Function

NASA Astrophysics Data System (ADS)

Benson, A.; Peeters, M. C.; Perez, J.; Parker, L.; Chen, G.

2013-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. Prior to the actual toolset development, a comprehensive metadata database was created to compensate for the absence of standardization of the ICARTT data format in which the data is stored. This database tracks the Principal Investigator-provided metadata, and links the measurement variables to a common naming system that was developed as a part of this project. This database is used by the data merging module. Most aircraft data reported during a single flight is not on a consistent time base and is difficult to intercompare. This module provides the user with the ability to merge original data measurements from multiple data providers into a specified time interval or common time base. The database development, common naming scheme and data merge module development will be presented.

Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules.

PubMed

Xiao, Xiaolin; Moreno-Moral, Aida; Rotival, Maxime; Bottolo, Leonardo; Petretto, Enrico

2014-01-01

Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states). Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks) that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted) networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based) and humans (mRNA-sequencing-based) and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi-tissue subnetwork of co-expressed heat shock protein (Hsp) and cardiomyopathy genes (Bag3, Cryab, Kras, Emd, Plec), which was significantly replicated using separate failing heart and liver gene expression datasets in humans, thus revealing a conserved functional role for Hsp genes in cardiovascular disease.

Open Platform for Limit Protection with Carefree Maneuver Applications

NASA Technical Reports Server (NTRS)

Jeram, Geoffrey J.

2004-01-01

This Open Platform for Limit Protection guides the open design of maneuver limit protection systems in general, and manned, rotorcraft, aerospace applications in particular. The platform uses three stages of limit protection modules: limit cue creation, limit cue arbitration, and control system interface. A common set of limit cue modules provides commands that can include constraints, alerts, transfer functions, and friction. An arbitration module selects the "best" limit protection cues and distributes them to the most appropriate control path interface. This platform adopts a holistic approach to limit protection whereby it considers all potential interface points, including the pilot's visual, aural, and tactile displays; and automatic command restraint shaping for autonomous limit protection. For each functional module, this thesis guides the control system designer through the design choices and information interfaces among the modules. Limit cue module design choices include type of prediction, prediction mechanism, method of critical control calculation, and type of limit cue. Special consideration is given to the nature of the limit, particularly the level of knowledge about it, and the ramifications for limit protection design, especially with respect to intelligent control methods such as fuzzy inference systems and neural networks.

3D printed Lego®-like modular microfluidic devices based on capillary driving.

PubMed

Nie, Jing; Gao, Qing; Qiu, Jing-Jiang; Sun, Miao; Liu, An; Shao, Lei; Fu, Jian-Zhong; Zhao, Peng; He, Yong

2018-03-12

The field of how to rapidly assemble microfluidics with modular components continuously attracts researchers' attention, however, extra efforts must be devoted to solving the problems of leaking and aligning between individual modules. This paper presents a novel type of modular microfluidic device, driven by capillary force. There is no necessity for a strict seal or special alignment, and its open structures make it easy to integrate various stents and reactants. The key rationale for this method is to print different functional modules with a low-cost three-dimensional (3D) printer, then fill the channels with capillary materials and assemble them with plugs like Lego ® bricks. This rapidly reconstructed modular microfluidic device consists of a variety of common functional modules and other personalized modules, each module having a unified standard interface for easy assembly. As it can be printed by a desktop 3D printer, the manufacturing process is simple and efficient, with controllable regulation of the flow channel scale. Through diverse combinations of different modules, a variety of different functions can be achieved, without duplicating the manufacturing process. A single module can also be taken out for testing and analysis. What's more, combined with basic circuit components, it can serve as a low-cost Lego ® -like modular microfluidic circuits. As a proof of concept, the modular microfluidic device has been successfully demonstrated and used for stent degradation and cell cultures, revealing the potential use of this method in both chemical and biological research.

Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer.

PubMed

Li, Yongsheng; Chen, Juan; Zhang, Jinwen; Wang, Zishan; Shao, Tingting; Jiang, Chunjie; Xu, Juan; Li, Xia

2015-09-22

Long non-coding RNAs (lncRNAs) play key roles in diverse biological processes. Moreover, the development and progression of cancer often involves the combined actions of several lncRNAs. Here we propose a multi-step method for constructing lncRNA-lncRNA functional synergistic networks (LFSNs) through co-regulation of functional modules having three features: common coexpressed genes of lncRNA pairs, enrichment in the same functional category and close proximity within protein interaction networks. Applied to three cancers, we constructed cancer-specific LFSNs and found that they exhibit a scale free and modular architecture. In addition, cancer-associated lncRNAs tend to be hubs and are enriched within modules. Although there is little synergistic pairing of lncRNAs across cancers, lncRNA pairs involved in the same cancer hallmarks by regulating same or different biological processes. Finally, we identify prognostic biomarkers within cancer lncRNA expression datasets using modules derived from LFSNs. In summary, this proof-of-principle study indicates synergistic lncRNA pairs can be identified through integrative analysis of genome-wide expression data sets and functional information.

The differential role of motor cortex in the stretch reflex modulation induced by changes in environmental mechanics and verbal instruction

PubMed Central

Shemmell, Jonathan; An, Je Hi; Perreault, Eric J.

2009-01-01

The motor cortex assumes an increasingly important role in higher mammals relative to that in lower mammals. This is true to such an extent that the human motor cortex is deeply involved in reflex regulation and it is common to speak of “transcortical reflex loops”. Such loops appear to add flexibility to the human stretch reflex, once considered to be immutable, allowing it to adapt across a range of functional tasks. However, the purpose of this adaptation remains unclear. A common proposal is that stretch reflexes contribute to the regulation of limb stability; increased reflex sensitivity during tasks performed in unstable environments supports this hypothesis. Alternatively, prior to movement onset, stretch reflexes can assist an imposed stretch, opposite to what would be expected from a stabilizing response. Here we show that stretch reflex modulation in tasks that require changes in limb stability is mediated by motor cortical pathways, and that these differ from pathways contributing to reflex modulation that depends on how the subject is instructed to react to an imposed perturbation. By timing muscle stretches such that the modulated portion of the reflex occurred within a cortical silent period induced by transcranial magnetic stimulation, we abolished the increase in reflex sensitivity observed when individuals stabilized arm posture within a compliant environment. Conversely, reflex modulation caused by altered task instruction was unaffected by cortical silence. These results demonstrate that task-dependent changes in reflex function can be mediated through multiple neural pathways and that these pathways have task specific roles. PMID:19846713

The differential role of motor cortex in stretch reflex modulation induced by changes in environmental mechanics and verbal instruction.

PubMed

Shemmell, Jonathan; An, Je Hi; Perreault, Eric J

2009-10-21

The motor cortex assumes an increasingly important role in higher mammals relative to that in lower mammals. This is true to such an extent that the human motor cortex is deeply involved in reflex regulation and it is common to speak of "transcortical reflex loops." Such loops appear to add flexibility to the human stretch reflex, once considered to be immutable, allowing it to adapt across a range of functional tasks. However, the purpose of this adaptation remains unclear. A common proposal is that stretch reflexes contribute to the regulation of limb stability; increased reflex sensitivity during tasks performed in unstable environments supports this hypothesis. Alternatively, before movement onset, stretch reflexes can assist an imposed stretch, opposite to what would be expected from a stabilizing response. Here we show that stretch reflex modulation in tasks that require changes in limb stability is mediated by motor cortical pathways, and that these differ from pathways contributing to reflex modulation that depend on how the subject is instructed to react to an imposed perturbation. By timing muscle stretches such that the modulated portion of the reflex occurred within a cortical silent period induced by transcranial magnetic stimulation, we abolished the increase in reflex sensitivity observed when individuals stabilized arm posture within a compliant environment. Conversely, reflex modulation caused by altered task instruction was unaffected by cortical silence. These results demonstrate that task-dependent changes in reflex function can be mediated through multiple neural pathways and that these pathways have task-specific roles.

Conceptual design of the Space Station combustion module

NASA Technical Reports Server (NTRS)

Morilak, Daniel P.; Rohn, Dennis W.; Rhatigan, Jennifer L.

1994-01-01

The purpose of this paper is to describe the conceptual design of the Combustion Module for the International Space Station Alpha (ISSA). This module is part of the Space Station Fluids/Combustion Facility (SS FCF) under development at the NASA Lewis Research Center. The Fluids/Combustion Facility is one of several science facilities which are being developed to support microgravity science investigations in the US Laboratory Module of the ISSA. The SS FCF will support a multitude of fluids and combustion science investigations over the lifetime of the ISSA and return state-of-the-art science data in a timely and efficient manner to the scientific communities. This will be accomplished through modularization of hardware, with planned, periodic upgrades; modularization of like scientific investigations that make use of common facility functions; and through the use of orbital replacement units (ORU's) for incorporation of new technology and new functionality. The SS FCF is scheduled to become operational on-orbit in 1999. The Combustion Module is presently scheduled for launch to orbit and integration with the Fluids/Combustion Facility in 1999. The objectives of this paper are to describe the history of the Combustion Module concept, the types of combustion science investigations which will be accommodated by the module, the hardware design heritage, the hardware concept, and the hardware breadboarding efforts currently underway.

Conceptual Design of the Space Station Fluids Module

NASA Technical Reports Server (NTRS)

Rohn, Dennis W.; Morilak, Daniel P.; Rhatigan, Jennifer L.; Peterson, Todd T.

1994-01-01

The purpose of this paper is to describe the conceptual design of the Fluids Module for the International Space Station Alpha (ISSA). This module is part of the Space Station Fluids/Combustion Facility (SS FCF) under development at the NASA Lewis Research Center. The Fluids/Combustion Facility is one of several science facilities which are being developed to support microgravity science investigations in the US Laboratory Module of the ISSA. The SS FCF will support a multitude of fluids and combustion science investigations over the lifetime of the ISSA and return state-of-the-art science data in a timely and efficient manner to the scientific communities. This will be accomplished through modularization of hardware, with planned, periodic upgrades; modularization of like scientific investigations that make use of common facility functions; and use of orbital replacement units (ORU's) for incorporation of new technology and new functionality. Portions of the SS FCF are scheduled to become operational on-orbit in 1999. The Fluids Module is presently scheduled for launch to orbit and integration with the Fluids/Combustion Facility in 2001. The objectives of this paper are to describe the history of the Fluids Module concept, the types of fluids science investigations which will be accommodated by the module, the hardware design heritage, the hardware concept, and the hardware breadboarding efforts currently underway.

Task-dependent modulation of the visual sensory thalamus assists visual-speech recognition.

PubMed

Díaz, Begoña; Blank, Helen; von Kriegstein, Katharina

2018-05-14

The cerebral cortex modulates early sensory processing via feed-back connections to sensory pathway nuclei. The functions of this top-down modulation for human behavior are poorly understood. Here, we show that top-down modulation of the visual sensory thalamus (the lateral geniculate body, LGN) is involved in visual-speech recognition. In two independent functional magnetic resonance imaging (fMRI) studies, LGN response increased when participants processed fast-varying features of articulatory movements required for visual-speech recognition, as compared to temporally more stable features required for face identification with the same stimulus material. The LGN response during the visual-speech task correlated positively with the visual-speech recognition scores across participants. In addition, the task-dependent modulation was present for speech movements and did not occur for control conditions involving non-speech biological movements. In face-to-face communication, visual speech recognition is used to enhance or even enable understanding what is said. Speech recognition is commonly explained in frameworks focusing on cerebral cortex areas. Our findings suggest that task-dependent modulation at subcortical sensory stages has an important role for communication: Together with similar findings in the auditory modality the findings imply that task-dependent modulation of the sensory thalami is a general mechanism to optimize speech recognition. Copyright © 2018. Published by Elsevier Inc.

An Iterative Time Windowed Signature Algorithm for Time Dependent Transcription Module Discovery

PubMed Central

Meng, Jia; Gao, Shou-Jiang; Huang, Yufei

2010-01-01

An algorithm for the discovery of time varying modules using genome-wide expression data is present here. When applied to large-scale time serious data, our method is designed to discover not only the transcription modules but also their timing information, which is rarely annotated by the existing approaches. Rather than assuming commonly defined time constant transcription modules, a module is depicted as a set of genes that are co-regulated during a specific period of time, i.e., a time dependent transcription module (TDTM). A rigorous mathematical definition of TDTM is provided, which is serve as an objective function for retrieving modules. Based on the definition, an effective signature algorithm is proposed that iteratively searches the transcription modules from the time series data. The proposed method was tested on the simulated systems and applied to the human time series microarray data during Kaposi's sarcoma-associated herpesvirus (KSHV) infection. The result has been verified by Expression Analysis Systematic Explorer. PMID:21552463

Brain corticostriatal systems and the major clinical symptom dimensions of obsessive-compulsive disorder.

PubMed

Harrison, Ben J; Pujol, Jesus; Cardoner, Narcis; Deus, Joan; Alonso, Pino; López-Solà, Marina; Contreras-Rodríguez, Oren; Real, Eva; Segalàs, Cinto; Blanco-Hinojo, Laura; Menchon, José M; Soriano-Mas, Carles

2013-02-15

Functional neuroimaging studies have provided consistent support for the idea that obsessive-compulsive disorder (OCD) is associated with disturbances of brain corticostriatal systems. However, in general, these studies have not sought to account for the disorder's prominent clinical heterogeneity. To address these concerns, we investigated the influence of major OCD symptom dimensions on brain corticostriatal functional systems in a large sample of OCD patients (n = 74) and control participants (n = 74) examined with resting-state functional magnetic resonance imaging. We employed a valid method for mapping ventral and dorsal striatal functional connectivity, which supported both standard group comparisons and linear regression analyses with patients' scores on the Dimensional Yale-Brown Obsessive-Compulsive Scale. Consistent with past findings, patients demonstrated a common connectivity alteration involving the ventral striatum and orbitofrontal cortex that predicted overall illness severity levels. This common alteration was independent of the effect of particular symptom dimensions. Instead, we observed distinct anatomical relationships between the severity of symptom dimensions and striatal functional connectivity. Aggression symptoms modulated connectivity between the ventral striatum, amygdala, and ventromedial frontal cortex, while sexual/religious symptoms had a specific influence on ventral striatal-insular connectivity. Hoarding modulated the strength of ventral and dorsal striatal connectivity with distributed frontal regions. Taken together, these results suggest that pathophysiological changes among orbitofrontal-striatal regions may be common to all forms of OCD. They suggest that a further examination of certain dimensional relationships will also be relevant for advancing current neurobiological models of the disorder. Copyright © 2013 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Optimisation of a low cost SLM for diffraction efficiency and ghost order suppression

NASA Astrophysics Data System (ADS)

Bowman, R.; D'Ambrosio, V.; Rubino, E.; Jedrkiewicz, O.; di Trapani, P.; Padgett, M. J.

2011-11-01

Spatial Light Modulators (SLMs) are a powerful tool in many optics laboratories, but due to the technology required for their fabrication, they are usually very expensive. Recently some inexpensive devices have been produced, however their phase shift range is less than 2π, leading to a loss of diffraction efficiency for the SLM. We show how to improve the first order diffraction efficiency of such an SLM by adjusting the blazing function, and obtain a 1.5 times increase in first order diffracted power. Even a perfect SLM with 2π phase throw can produce undesired effects in some situations; for example in holographic optical tweezers it is common to find unwanted "ghost spots" near to the array of first-order spots. Modulating the amplitude, by spatially modulating the blazing function, allows us to suppress the ghost spots. This increases the contrast between desired and unwanted spots by more than an order of magnitude.

The redox-sensitive module of cyclophilin 20-3, 2-cysteine peroxiredoxin and cysteine synthase integrates sulfur metabolism and oxylipin signaling in the high light acclimation response.

PubMed

Müller, Sara M; Wang, Shanshan; Telman, Wilena; Liebthal, Michael; Schnitzer, Helena; Viehhauser, Andrea; Sticht, Carsten; Delatorre, Carolina; Wirtz, Markus; Hell, Rüdiger; Dietz, Karl-Josef

2017-09-01

The integration of redox- and reactive oxygen species-dependent signaling and metabolic activities is fundamental to plant acclimation to biotic and abiotic stresses. Previous data suggest the existence of a dynamically interacting module in the chloroplast stroma consisting of cyclophilin 20-3 (Cyp20-3), O-acetylserine(thiol)lyase B (OASTL-B), 2-cysteine peroxiredoxins A/B (2-CysPrx) and serine acetyltransferase 2;1 (SERAT2;1). The functionality of this COPS module is influenced by redox stimuli and oxophytodienoic acid (OPDA), which is the precursor for jasmonic acid. The concept of an integrating function of these proteins in stress signaling was challenged by combining transcriptome and biochemical analyses in Arabidopsis mutants devoid of oastlB, serat2;1, cyp20-3 and 2-cysprxA/B, and wild-type (WT). Leaf transcriptomes were analyzed 6 h after transfer to light intensity 10-fold in excess of growth light or under growth light. The survey of KEGG-based gene ontology groups showed common upregulation of translation- and protein homeostasis-associated transcripts under control conditions in all mutants compared with WT. The results revealed that the interference of the module was accompanied with disturbance of carbohydrate, sulfur and nitrogen metabolism, and also citric acid cycle intermediates. Apart from common regulation, specific responses at the transcriptome and metabolite level linked Cyp20-3 to cell wall-bound carbohydrates and oxylipin signaling, and 2-CysPrx to photosynthesis, sugar and amino acid metabolism. Deletion of either OASTL-B or SERAT2;1 frequently induced antagonistic changes in biochemical or molecular features. Enhanced sensitivity of mutant seedlings to OPDA and leaf discs to NaHS-administration confirmed the presumed functional interference of the COPS module in redox and oxylipin signaling. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Rationally engineered Troponin C modulates in vivo cardiac function and performance in health and disease.

PubMed

Shettigar, Vikram; Zhang, Bo; Little, Sean C; Salhi, Hussam E; Hansen, Brian J; Li, Ning; Zhang, Jianchao; Roof, Steve R; Ho, Hsiang-Ting; Brunello, Lucia; Lerch, Jessica K; Weisleder, Noah; Fedorov, Vadim V; Accornero, Federica; Rafael-Fortney, Jill A; Gyorke, Sandor; Janssen, Paul M L; Biesiadecki, Brandon J; Ziolo, Mark T; Davis, Jonathan P

2016-02-24

Treatment for heart disease, the leading cause of death in the world, has progressed little for several decades. Here we develop a protein engineering approach to directly tune in vivo cardiac contractility by tailoring the ability of the heart to respond to the Ca(2+) signal. Promisingly, our smartly formulated Ca(2+)-sensitizing TnC (L48Q) enhances heart function without any adverse effects that are commonly observed with positive inotropes. In a myocardial infarction (MI) model of heart failure, expression of TnC L48Q before the MI preserves cardiac function and performance. Moreover, expression of TnC L48Q after the MI therapeutically enhances cardiac function and performance, without compromising survival. We demonstrate engineering TnC can specifically and precisely modulate cardiac contractility that when combined with gene therapy can be employed as a therapeutic strategy for heart disease.

Rationally engineered Troponin C modulates in vivo cardiac function and performance in health and disease

PubMed Central

Shettigar, Vikram; Zhang, Bo; Little, Sean C.; Salhi, Hussam E.; Hansen, Brian J.; Li, Ning; Zhang, Jianchao; Roof, Steve R.; Ho, Hsiang-Ting; Brunello, Lucia; Lerch, Jessica K.; Weisleder, Noah; Fedorov, Vadim V.; Accornero, Federica; Rafael-Fortney, Jill A.; Gyorke, Sandor; Janssen, Paul M. L.; Biesiadecki, Brandon J.; Ziolo, Mark T.; Davis, Jonathan P.

2016-01-01

Treatment for heart disease, the leading cause of death in the world, has progressed little for several decades. Here we develop a protein engineering approach to directly tune in vivo cardiac contractility by tailoring the ability of the heart to respond to the Ca2+ signal. Promisingly, our smartly formulated Ca2+-sensitizing TnC (L48Q) enhances heart function without any adverse effects that are commonly observed with positive inotropes. In a myocardial infarction (MI) model of heart failure, expression of TnC L48Q before the MI preserves cardiac function and performance. Moreover, expression of TnC L48Q after the MI therapeutically enhances cardiac function and performance, without compromising survival. We demonstrate engineering TnC can specifically and precisely modulate cardiac contractility that when combined with gene therapy can be employed as a therapeutic strategy for heart disease. PMID:26908229

The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks

PubMed Central

2015-01-01

Background Cellular processes are known to be modular and are realized by groups of proteins implicated in common biological functions. Such groups of proteins are called functional modules, and many community detection methods have been devised for their discovery from protein interaction networks (PINs) data. In current agglomerative clustering approaches, vertices with just a very few neighbors are often classified as separate clusters, which does not make sense biologically. Also, a major limitation of agglomerative techniques is that their computational efficiency do not scale well to large PINs. Finally, PIN data obtained from large scale experiments generally contain many false positives, and this makes it hard for agglomerative clustering methods to find the correct clusters, since they are known to be sensitive to noisy data. Results We propose a local similarity premetric, the relative vertex clustering value, as a new criterion allowing to decide when a node can be added to a given node's cluster and which addresses the above three issues. Based on this criterion, we introduce a novel and very fast agglomerative clustering technique, FAC-PIN, for discovering functional modules and protein complexes from a PIN data. Conclusions Our proposed FAC-PIN algorithm is applied to nine PIN data from eight different species including the yeast PIN, and the identified functional modules are validated using Gene Ontology (GO) annotations from DAVID Bioinformatics Resources. Identified protein complexes are also validated using experimentally verified complexes. Computational results show that FAC-PIN can discover functional modules or protein complexes from PINs more accurately and more efficiently than HC-PIN and CNM, the current state-of-the-art approaches for clustering PINs in an agglomerative manner. PMID:25734691

Task-Driven Tube Current Modulation and Regularization Design in Computed Tomography with Penalized-Likelihood Reconstruction.

PubMed

Gang, G J; Siewerdsen, J H; Stayman, J W

2016-02-01

This work applies task-driven optimization to design CT tube current modulation and directional regularization in penalized-likelihood (PL) reconstruction. The relative performance of modulation schemes commonly adopted for filtered-backprojection (FBP) reconstruction were also evaluated for PL in comparison. We adopt a task-driven imaging framework that utilizes a patient-specific anatomical model and information of the imaging task to optimize imaging performance in terms of detectability index ( d' ). This framework leverages a theoretical model based on implicit function theorem and Fourier approximations to predict local spatial resolution and noise characteristics of PL reconstruction as a function of the imaging parameters to be optimized. Tube current modulation was parameterized as a linear combination of Gaussian basis functions, and regularization was based on the design of (directional) pairwise penalty weights for the 8 in-plane neighboring voxels. Detectability was optimized using a covariance matrix adaptation evolutionary strategy algorithm. Task-driven designs were compared to conventional tube current modulation strategies for a Gaussian detection task in an abdomen phantom. The task-driven design yielded the best performance, improving d' by ~20% over an unmodulated acquisition. Contrary to FBP, PL reconstruction using automatic exposure control and modulation based on minimum variance (in FBP) performed worse than the unmodulated case, decreasing d' by 16% and 9%, respectively. This work shows that conventional tube current modulation schemes suitable for FBP can be suboptimal for PL reconstruction. Thus, the proposed task-driven optimization provides additional opportunities for improved imaging performance and dose reduction beyond that achievable with conventional acquisition and reconstruction.

Sperm-binding fibronectin type II-module proteins are genetically linked and functionally related.

PubMed

Ekhlasi-Hundrieser, Mahnaz; Schäfer, Bettina; Philipp, Ute; Kuiper, Heidi; Leeb, Tosso; Mehta, Meenal; Kirchhoff, Christiane; Töpfer-Petersen, Edda

2007-05-01

Fibronectin type II (Fn2) module-containing proteins in the male genital tract are characterized by different numbers of Fn2 modules. Predominantly two classes exist which are distinct by having either two or four Fn2 modules. Minor variants with three Fn2 modules were also found in the human and the porcine epididymis. To reveal their relationship, mRNAs and proteins of representatives of these classes were studied in human, in Sus scrofa, and in rodents. Adult boars expressed members of both classes, i.e. ELSPBP1 and pB1, in subsequent regions of the epididymis, and both were under androgenic control. Human and rodent epididymides, on the other hand, alternatively contained only representatives of one of these two classes, i.e. ELSPBP1 in the human and two different pB1-related counterparts in rodents. ELSPBP1 and pB1-related genomic sequences were closely linked in chromosomal regions HSA 19q and SSC 6 q11-q21; conserved synteny between these regions is well established. On the other hand, in a syntenic region on mouse chromosome 7, ELSPBP1-related sequences were lacking. Tight binding to the sperm membrane via a choline-mediated mechanism was a common feature of the two classes of Fn2-module proteins, suggesting related function(s). However, differences in their regionalized expression patterns along the male genital tract as well as in association sites on the sperm surface suggested a species-specific sequential order in sperm binding.

Structural insight to mutation effects uncover a common allosteric site in class C GPCRs.

PubMed

Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian; Bräuner-Osborne, Hans; Gloriam, David E

2017-04-15

Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures. All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format. david.gloriam@sund.ku.dk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Broca's area: a supramodal hierarchical processor?

PubMed

Tettamanti, Marco; Weniger, Dorothea

2006-05-01

Despite the presence of shared characteristics across the different domains modulating Broca's area activity (e.g., structural analogies, as between language and music, or representational homologies, as between action execution and action observation), the question of what exactly the common denominator of such diverse brain functions is, with respect to the function of Broca's area, remains largely a debated issue. Here, we suggest that an important computational role of Broca's area may be to process hierarchical structures in a wide range of functional domains.

Top-down modulation: Bridging selective attention and working memory

PubMed Central

Gazzaley, Adam; Nobre, Anna C.

2012-01-01

Selective attention, the ability to focus our cognitive resources on information relevant to our goals, influences working memory (WM) performance. Indeed, attention and working memory are increasingly viewed as overlapping constructs. Here, we review recent evidence from human neurophysiological studies demonstrating that top-down modulation serves as a common neural mechanism underlying these two cognitive operations. The core features include activity modulation in stimulus-selective sensory cortices with concurrent engagement of prefrontal and parietal control regions that function as sources of top-down signals. Notably, top-down modulation is engaged during both stimulus-present and stimulus-absent stages of WM tasks, i.e., expectation of an ensuing stimulus to be remembered, selection and encoding of stimuli, maintenance of relevant information in mind and memory retrieval. PMID:22209601

Fear conditioning is associated with dynamic directed functional interactions between and within the human amygdala, hippocampus, and frontal lobe.

PubMed

Liu, C C; Crone, N E; Franaszczuk, P J; Cheng, D T; Schretlen, D S; Lenz, F A

2011-08-25

The current model of fear conditioning suggests that it is mediated through modules involving the amygdala (AMY), hippocampus (HIP), and frontal lobe (FL). We now test the hypothesis that habituation and acquisition stages of a fear conditioning protocol are characterized by different event-related causal interactions (ERCs) within and between these modules. The protocol used the painful cutaneous laser as the unconditioned stimulus and ERC was estimated by analysis of local field potentials recorded through electrodes implanted for investigation of epilepsy. During the prestimulus interval of the habituation stage FL>AMY ERC interactions were common. For comparison, in the poststimulus interval of the habituation stage, only a subdivision of the FL (dorsolateral prefrontal cortex, dlPFC) still exerted the FL>AMY ERC interaction (dlFC>AMY). For a further comparison, during the poststimulus interval of the acquisition stage, the dlPFC>AMY interaction persisted and an AMY>FL interaction appeared. In addition to these ERC interactions between modules, the results also show ERC interactions within modules. During the poststimulus interval, HIP>HIP ERC interactions were more common during acquisition, and deep hippocampal contacts exerted causal interactions on superficial contacts, possibly explained by connectivity between the perihippocampal gyrus and the HIP. During the prestimulus interval of the habituation stage, AMY>AMY ERC interactions were commonly found, while interactions between the deep and superficial AMY (indirect pathway) were independent of intervals and stages. These results suggest that the network subserving fear includes distributed or widespread modules, some of which are themselves "local networks." ERC interactions between and within modules can be either static or change dynamically across intervals or stages of fear conditioning. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Designing from minimum to optimum functionality

NASA Astrophysics Data System (ADS)

Bannova, Olga; Bell, Larry

2011-04-01

This paper discusses a multifaceted strategy to link NASA Minimal Functionality Habitable Element (MFHE) requirements to a compatible growth plan; leading forward to evolutionary, deployable habitats including outpost development stages. The discussion begins by reviewing fundamental geometric features inherent in small scale, vertical and horizontal, pressurized module configuration options to characterize applicability to meet stringent MFHE constraints. A proposed scenario to incorporate a vertical core MFHE concept into an expanded architecture to provide continuity of structural form and a logical path from "minimum" to "optimum" design of a habitable module. The paper describes how habitation and logistics accommodations could be pre-integrated into a common Hab/Log Module that serves both habitation and logistics functions. This is offered as a means to reduce unnecessary redundant development costs and to avoid EVA-intensive on-site adaptation and retrofitting requirements for augmented crew capacity. An evolutionary version of the hard shell Hab/Log design would have an expandable middle section to afford larger living and working accommodations. In conclusion, the paper illustrates that a number of cargo missions referenced for NASA's 4.0.0 Lunar Campaign Scenario could be eliminated altogether to expedite progress and reduce budgets. The plan concludes with a vertical growth geometry that provides versatile and efficient site development opportunities using a combination of hard Hab/Log modules and a hybrid expandable "CLAM" (Crew Lunar Accommodations Module) element.

Long-term meditation training induced changes in the operational synchrony of default mode network modules during a resting state.

PubMed

Fingelkurts, Andrew A; Fingelkurts, Alexander A; Kallio-Tamminen, Tarja

2016-02-01

Using theoretical analysis of self-consciousness concept and experimental evidence on the brain default mode network (DMN) that constitutes the neural signature of self-referential processes, we hypothesized that the anterior and posterior subnets comprising the DMN should show differences in their integrity as a function of meditation training. Functional connectivity within DMN and its subnets (measured by operational synchrony) has been measured in ten novice meditators using an electroencephalogram (EEG) recording in a pre-/post-meditation intervention design. We have found that while the whole DMN was clearly suppressed, different subnets of DMN responded differently after 4 months of meditation training: The strength of EEG operational synchrony in the right and left posterior modules of the DMN decreased in resting post-meditation condition compared to a pre-meditation condition, whereas the frontal DMN module on the contrary exhibited an increase in the strength of EEG operational synchrony. These findings combined with published data on functional-anatomic heterogeneity within the DMN and on trait subjective experiences commonly found following meditation allow us to propose that the first-person perspective and the sense of agency (the witnessing observer) are presented by the frontal DMN module, while the posterior modules of the DMN are generally responsible for the experience of the continuity of 'I' as embodied and localized within bodily space. Significance of these findings is discussed.

A Users Guide for the NASA ANOPP Propeller Analysis System

NASA Technical Reports Server (NTRS)

Nguygen, L. Cathy; Kelly, Jeffrey J.

1997-01-01

The purpose of this report is to document improvements to the Propeller Analysis System of the Aircraft Noise Prediction Program (PAS-ANOPP) and to serve as a users guide. An overview of the functional modules and modifications made to the Propeller ANOPP system are described. Propeller noise predictions are made by executing a sequence of functional modules through the use of ANOPP control statements. The most commonly used ANOPP control statements are discussed with detailed examples demonstrating the use of each control statement. Originally, the Propeller Analysis System included the angle-of-attack only in the performance module. Recently, modifications have been made to also include angle-of-attack in the noise prediction module. A brief description of PAS prediction capabilities is presented which illustrate the input requirements necessary to run the code by way of ten templates. The purpose of the templates are to provide PAS users with complete examples which can be modified to serve their particular purposes. The examples include the use of different approximations in the computation of the noise and the effects of synchrophasing. Since modifications have been made to the original PAS-ANOPP, comparisons of the modified ANOPP and wind tunnel data are also included. Two appendices are attached at the end of this report which provide useful reference material. One appendix summarizes the PAS functional modules while the second provides a detailed discussion of the TABLE control statement.

Neoagarotetraose protects mice against intense exercise induced stress by modulating gut microbial composition and function

USDA-ARS?s Scientific Manuscript database

Exhaustive exercise stress has emerged as an important health issue, and gastrointestinal problems are a common concern during intense exercise. In this study, we investigated potential anti-fatigue effects of neoagarotetraose (NAT) in mice under intense exercise stress. Exhaustive exercise stress s...

Brain-Behavior Relationships in Reading Acquisition Are Modulated by Socioeconomic Factors

ERIC Educational Resources Information Center

Noble, Kimberly G.; Wolmetz, Michael E.; Ochs, Lisa G.; Farah, Martha J.; McCandliss, Bruce D.

2006-01-01

Functional neuroimaging may provide insights into the achievement gap in reading skill commonly observed across socioeconomic status (SES). Brain activation during reading tasks is known to be associated with individual differences in children's phonological language skills. By selecting children of equivalent phonological skill, yet diverse…

Crystalline-silicon reliability lessons for thin-film modules

NASA Technical Reports Server (NTRS)

Ross, R. G., Jr.

1985-01-01

The reliability of crystalline silicon modules has been brought to a high level with lifetimes approaching 20 years, and excellent industry credibility and user satisfaction. The transition from crystalline modules to thin film modules is comparable to the transition from discrete transistors to integrated circuits. New cell materials and monolithic structures will require new device processing techniques, but the package function and design will evolve to a lesser extent. Although there will be new encapsulants optimized to take advantage of the mechanical flexibility and low temperature processing features of thin films, the reliability and life degradation stresses and mechanisms will remain mostly unchanged. Key reliability technologies in common between crystalline and thin film modules include hot spot heating, galvanic and electrochemical corrosion, hail impact stresses, glass breakage, mechanical fatigue, photothermal degradation of encapsulants, operating temperature, moisture sorption, circuit design strategies, product safety issues, and the process required to achieve a reliable product from a laboratory prototype.

Weighted gene co-expression network analysis of gene modules for the prognosis of esophageal cancer.

PubMed

Zhang, Cong; Sun, Qian

2017-06-01

Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas (TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival (PFS) or overall survival (OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that "glycoprotein binding" was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor (PTAFR) and feline Gardner-Rasheed (FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.

Excavation of attractor modules for nasopharyngeal carcinoma via integrating systemic module inference with attract method.

PubMed

Jiang, T; Jiang, C-Y; Shu, J-H; Xu, Y-J

2017-07-10

The molecular mechanism of nasopharyngeal carcinoma (NPC) is poorly understood and effective therapeutic approaches are needed. This research aimed to excavate the attractor modules involved in the progression of NPC and provide further understanding of the underlying mechanism of NPC. Based on the gene expression data of NPC, two specific protein-protein interaction networks for NPC and control conditions were re-weighted using Pearson correlation coefficient. Then, a systematic tracking of candidate modules was conducted on the re-weighted networks via cliques algorithm, and a total of 19 and 38 modules were separately identified from NPC and control networks, respectively. Among them, 8 pairs of modules with similar gene composition were selected, and 2 attractor modules were identified via the attract method. Functional analysis indicated that these two attractor modules participate in one common bioprocess of cell division. Based on the strategy of integrating systemic module inference with the attract method, we successfully identified 2 attractor modules. These attractor modules might play important roles in the molecular pathogenesis of NPC via affecting the bioprocess of cell division in a conjunct way. Further research is needed to explore the correlations between cell division and NPC.

A model for phase noise generation in amplifiers.

PubMed

Tomlin, T D; Fynn, K; Cantoni, A

2001-11-01

In this paper, a model is presented for predicting the phase modulation (PM) and amplitude modulation (AM) noise in bipolar junction transistor (BJT) amplifiers. The model correctly predicts the dependence of phase noise on the signal frequency (at a particular carrier offset frequency), explains the noise shaping of the phase noise about the signal frequency, and shows the functional dependence on the transistor parameters and the circuit parameters. Experimental studies on common emitter (CE) amplifiers have been used to validate the PM noise model at carrier frequencies between 10 and 100 MHz.

Security camera resolution measurements: Horizontal TV lines versus modulation transfer function measurements.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Birch, Gabriel Carisle; Griffin, John Clark

2015-01-01

The horizontal television lines (HTVL) metric has been the primary quantity used by division 6000 related to camera resolution for high consequence security systems. This document shows HTVL measurements are fundamen- tally insufficient as a metric to determine camera resolution, and propose a quantitative, standards based methodology by measuring the camera system modulation transfer function (MTF), the most common and accepted metric of res- olution in the optical science community. Because HTVL calculations are easily misinterpreted or poorly defined, we present several scenarios in which HTVL is frequently reported, and discuss their problems. The MTF metric is discussed, and scenariosmore » are presented with calculations showing the application of such a metric.« less

Cohesin Function in Cohesion, Condensation, and DNA Repair Is Regulated by Wpl1p via a Common Mechanism in Saccharomyces cerevisiae.

PubMed

Bloom, Michelle S; Koshland, Douglas; Guacci, Vincent

2018-01-01

Cohesin tethers DNA to mediate sister chromatid cohesion, chromosome condensation, and DNA repair. How the cell regulates cohesin to perform these distinct functions remains to be elucidated. One cohesin regulator, Wpl1p, was characterized in Saccharomyces cerevisiae as a promoter of efficient cohesion and an inhibitor of condensation. Wpl1p is also required for resistance to DNA-damaging agents. Here, we provide evidence that Wpl1p promotes the timely repair of DNA damage induced during S-phase. Previous studies have indicated that Wpl1p destabilizes cohesin's binding to DNA by modulating the interface between the cohesin subunits Mcd1p and Smc3p Our results suggest that Wpl1p likely modulates this interface to regulate all of cohesin's biological functions. Furthermore, we show that Wpl1p regulates cohesion and condensation through the formation of a functional complex with another cohesin-associated factor, Pds5p In contrast, Wpl1p regulates DNA repair independently of its interaction with Pds5p Together, these results suggest that Wpl1p regulates distinct biological functions of cohesin by Pds5p-dependent and -independent modulation of the Smc3p/Mcd1p interface. Copyright © 2018 by the Genetics Society of America.

Cohesin Function in Cohesion, Condensation, and DNA Repair Is Regulated by Wpl1p via a Common Mechanism in Saccharomyces cerevisiae

PubMed Central

Bloom, Michelle S.; Koshland, Douglas; Guacci, Vincent

2018-01-01

Cohesin tethers DNA to mediate sister chromatid cohesion, chromosome condensation, and DNA repair. How the cell regulates cohesin to perform these distinct functions remains to be elucidated. One cohesin regulator, Wpl1p, was characterized in Saccharomyces cerevisiae as a promoter of efficient cohesion and an inhibitor of condensation. Wpl1p is also required for resistance to DNA-damaging agents. Here, we provide evidence that Wpl1p promotes the timely repair of DNA damage induced during S-phase. Previous studies have indicated that Wpl1p destabilizes cohesin’s binding to DNA by modulating the interface between the cohesin subunits Mcd1p and Smc3p. Our results suggest that Wpl1p likely modulates this interface to regulate all of cohesin’s biological functions. Furthermore, we show that Wpl1p regulates cohesion and condensation through the formation of a functional complex with another cohesin-associated factor, Pds5p. In contrast, Wpl1p regulates DNA repair independently of its interaction with Pds5p. Together, these results suggest that Wpl1p regulates distinct biological functions of cohesin by Pds5p-dependent and -independent modulation of the Smc3p/Mcd1p interface. PMID:29158426

Pharmacological Tools to Study the Role of Astrocytes in Neural Network Functions.

PubMed

Peña-Ortega, Fernando; Rivera-Angulo, Ana Julia; Lorea-Hernández, Jonathan Julio

2016-01-01

Despite that astrocytes and microglia do not communicate by electrical impulses, they can efficiently communicate among them, with each other and with neurons, to participate in complex neural functions requiring broad cell-communication and long-lasting regulation of brain function. Glial cells express many receptors in common with neurons; secrete gliotransmitters as well as neurotrophic and neuroinflammatory factors, which allow them to modulate synaptic transmission and neural excitability. All these properties allow glial cells to influence the activity of neuronal networks. Thus, the incorporation of glial cell function into the understanding of nervous system dynamics will provide a more accurate view of brain function. Our current knowledge of glial cell biology is providing us with experimental tools to explore their participation in neural network modulation. In this chapter, we review some of the classical, as well as some recent, pharmacological tools developed for the study of astrocyte's influence in neural function. We also provide some examples of the use of these pharmacological agents to understand the role of astrocytes in neural network function and dysfunction.

Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in Neurospora crassa.

PubMed

Araujo-Palomares, Cynthia L; Richthammer, Corinna; Seiler, Stephan; Castro-Longoria, Ernestina

2011-01-01

Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.

Brain mitochondrial bioenergetics change with rapid and prolonged shifts in aggression in the honey bee, Apis mellifera.

PubMed

Rittschof, Clare C; Vekaria, Hemendra J; Palmer, Joseph H; Sullivan, Patrick G

2018-04-25

Neuronal function demands high-level energy production, and as such, a decline in mitochondrial respiration characterizes brain injury and disease. A growing number of studies, however, link brain mitochondrial function to behavioral modulation in non-diseased contexts. In the honey bee, we show for the first time that an acute social interaction, which invokes an aggressive response, may also cause a rapid decline in brain mitochondrial bioenergetics. The degree and speed of this decline has only been previously observed in the context of brain injury. Furthermore, in the honey bee, age-related increases in aggressive tendency are associated with increased baseline brain mitochondrial respiration, as well as increased plasticity in response to metabolic fuel type in vitro Similarly, diet restriction and ketone body feeding, which commonly enhance mammalian brain mitochondrial function in vivo , cause increased aggression. Thus, even in normal behavioral contexts, brain mitochondria show a surprising degree of variation in function over both rapid and prolonged time scales, with age predicting both baseline function and plasticity in function. These results suggest that mitochondrial function is integral to modulating aggression-related neuronal signaling. We hypothesize that variation in function reflects mitochondrial calcium buffering activity, and that shifts in mitochondrial function signal to the neuronal soma to regulate gene expression and neural energetic state. Modulating brain energetic state is emerging as a critical component of the regulation of behavior in non-diseased contexts. © 2018. Published by The Company of Biologists Ltd.

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

PubMed Central

Chen, Ming; Henry, Nathan; Almsaeed, Abdullah; Zhou, Xiao; Wegrzyn, Jill; Ficklin, Stephen

2017-01-01

Abstract Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression PMID:29220446

Pharmacological Modulation of GABA Function in Autism Spectrum Disorders: A Systematic Review of Human Studies

ERIC Educational Resources Information Center

Brondino, Natascia; Fusar-Poli, Laura; Panisi, Cristina; Damiani, Stefano; Barale, Francesco; Politi, Pierluigi

2016-01-01

Autism spectrum disorders are an emerging health problem worldwide, but little is known about their pathogenesis. It has been hypothesized that autism may result from an imbalance between excitatory glutamatergic and inhibitory GABAergic pathways. Commonly used medications such as valproate, acamprosate, and arbaclofen may act on the GABAergic…

Alpha-Tocopherol modulates transcriptional activities that affect essential biological processes in Bovine Cells

USDA-ARS?s Scientific Manuscript database

Alpha-tocopherol is the major isoform of vitamin E. after nearly 100 years of research and countless publications, the physiological functions of vitamin E remain mysterious to a certain degree. Nevertheless, vitamin E is one of the most commonly used single nutrient supplements. Recent data has su...

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

PubMed Central

O'Boyle, Noel M; Hutchison, Geoffrey R

2008-01-01

Background Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). Results We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. Conclusion By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit. PMID:19055766

Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell

PubMed Central

Lim, Wendell A.; Lee, Connie M.; Tang, Chao

2013-01-01

A challenge in biology is to understand how complex molecular networks in the cell execute sophisticated regulatory functions. Here we explore the idea that there are common and general principles that link network structures to biological functions, principles that constrain the design solutions that evolution can converge upon for accomplishing a given cellular task. We describe approaches for classifying networks based on abstract architectures and functions, rather than on the specific molecular components of the networks. For any common regulatory task, can we define the space of all possible molecular solutions? Such inverse approaches might ultimately allow the assembly of a design table of core molecular algorithms that could serve as a guide for building synthetic networks and modulating disease networks. PMID:23352241

Electronic health record analysis via deep poisson factor models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henao, Ricardo; Lu, James T.; Lucas, Joseph E.

Electronic Health Record (EHR) phenotyping utilizes patient data captured through normal medical practice, to identify features that may represent computational medical phenotypes. These features may be used to identify at-risk patients and improve prediction of patient morbidity and mortality. We present a novel deep multi-modality architecture for EHR analysis (applicable to joint analysis of multiple forms of EHR data), based on Poisson Factor Analysis (PFA) modules. Each modality, composed of observed counts, is represented as a Poisson distribution, parameterized in terms of hidden binary units. In-formation from different modalities is shared via a deep hierarchy of common hidden units. Activationmore » of these binary units occurs with probability characterized as Bernoulli-Poisson link functions, instead of more traditional logistic link functions. In addition, we demon-strate that PFA modules can be adapted to discriminative modalities. To compute model parameters, we derive efficient Markov Chain Monte Carlo (MCMC) inference that scales efficiently, with significant computational gains when compared to related models based on logistic link functions. To explore the utility of these models, we apply them to a subset of patients from the Duke-Durham patient cohort. We identified a cohort of over 12,000 patients with Type 2 Diabetes Mellitus (T2DM) based on diagnosis codes and laboratory tests out of our patient population of over 240,000. Examining the common hidden units uniting the PFA modules, we identify patient features that represent medical concepts. Experiments indicate that our learned features are better able to predict mortality and morbidity than clinical features identified previously in a large-scale clinical trial.« less

Electronic health record analysis via deep poisson factor models

DOE PAGES

Henao, Ricardo; Lu, James T.; Lucas, Joseph E.; ...

2016-01-01

Electronic Health Record (EHR) phenotyping utilizes patient data captured through normal medical practice, to identify features that may represent computational medical phenotypes. These features may be used to identify at-risk patients and improve prediction of patient morbidity and mortality. We present a novel deep multi-modality architecture for EHR analysis (applicable to joint analysis of multiple forms of EHR data), based on Poisson Factor Analysis (PFA) modules. Each modality, composed of observed counts, is represented as a Poisson distribution, parameterized in terms of hidden binary units. In-formation from different modalities is shared via a deep hierarchy of common hidden units. Activationmore » of these binary units occurs with probability characterized as Bernoulli-Poisson link functions, instead of more traditional logistic link functions. In addition, we demon-strate that PFA modules can be adapted to discriminative modalities. To compute model parameters, we derive efficient Markov Chain Monte Carlo (MCMC) inference that scales efficiently, with significant computational gains when compared to related models based on logistic link functions. To explore the utility of these models, we apply them to a subset of patients from the Duke-Durham patient cohort. We identified a cohort of over 12,000 patients with Type 2 Diabetes Mellitus (T2DM) based on diagnosis codes and laboratory tests out of our patient population of over 240,000. Examining the common hidden units uniting the PFA modules, we identify patient features that represent medical concepts. Experiments indicate that our learned features are better able to predict mortality and morbidity than clinical features identified previously in a large-scale clinical trial.« less

Pattern separation: a common function for new neurons in hippocampus and olfactory bulb.

PubMed

Sahay, Amar; Wilson, Donald A; Hen, René

2011-05-26

While adult-born neurons in the olfactory bulb (OB) and the dentate gyrus (DG) subregion of the hippocampus have fundamentally different properties, they may have more in common than meets the eye. Here, we propose that new granule cells in the OB and DG may function as modulators of principal neurons to influence pattern separation and that adult neurogenesis constitutes an adaptive mechanism to optimally encode contextual or olfactory information. See the related Perspective from Aimone, Deng, and Gage, "Resolving New Memories: A Critical Look at the Dentate Gyrus, Adult Neurogenesis, and Pattern Separation," in this issue of Neuron. Copyright © 2011 Elsevier Inc. All rights reserved.

A red orange extract modulates the vascular response to a recreational dive: a pilot study on the effect of anthocyanins on the physiological consequences of scuba diving.

PubMed

Balestra, C; Cimino, F; Theunissen, S; Snoeck, T; Provyn, S; Canali, R; Bonina, A; Virgili, F

2016-09-01

Nutritional antioxidants have been proposed as an expedient strategy to counter the potentially deleterious effects of scuba diving on endothelial function, flow-mediated dilation (FMD) and heart function. Sixteen volunteers performing a single standard dive (20 min at 33 m) according to US Navy diving procedures were randomly assigned to two groups: one was administered with two doses of 200 mg of an anthocyanins (AC)-rich extract from red oranges, 12 and 4 h before diving. Anthocyanins supplementation significantly modulated the effects of diving on haematocrit, body water distribution and FMD. AC administration significantly reduces the potentially harmful endothelial effects of a recreational single dive. The lack of any significant effect on the most common markers of plasma antioxidant capacity suggests that the mechanism underlying this protective activity is independent of the putative antioxidant effect of AC and possibly involves cellular signalling modulation of the response to high oxygen.

Functional heartburn: the stimulus, the pain, and the brain

PubMed Central

Fass, R; Tougas, G

2002-01-01

Functional heartburn is a common disorder and appears to be composed of several distinct subgroups. Identifying the different subgroups based on clinical history only is not achievable at present. The mechanisms responsible for pain, clinical characteristics, and the optimal therapeutic approach remain poorly understood. Response to potent antireflux treatment is relatively limited. Current and future treatment strategies for functional heartburn patients who have failed standard dose proton pump inhibitors (PPIs) include increased PPI dose in some, as well as addition of pain modulators in others. PMID:12427796

ISLE (Image and Signal Processing LISP Environment) reference manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherwood, R.J.; Searfus, R.M.

1990-01-01

ISLE is a rapid prototyping system for performing image and signal processing. It is designed to meet the needs of a person doing development of image and signal processing algorithms in a research environment. The image and signal processing modules in ISLE form a very capable package in themselves. They also provide a rich environment for quickly and easily integrating user-written software modules into the package. ISLE is well suited to applications in which there is a need to develop a processing algorithm in an interactive manner. It is straightforward to develop the algorithms, load it into ISLE, apply themore » algorithm to an image or signal, display the results, then modify the algorithm and repeat the develop-load-apply-display cycle. ISLE consists of a collection of image and signal processing modules integrated into a cohesive package through a standard command interpreter. ISLE developer elected to concentrate their effort on developing image and signal processing software rather than developing a command interpreter. A COMMON LISP interpreter was selected for the command interpreter because it already has the features desired in a command interpreter, it supports dynamic loading of modules for customization purposes, it supports run-time parameter and argument type checking, it is very well documented, and it is a commercially supported product. This manual is intended to be a reference manual for the ISLE functions The functions are grouped into a number of categories and briefly discussed in the Function Summary chapter. The full descriptions of the functions and all their arguments are given in the Function Descriptions chapter. 6 refs.« less

Functional neurological symptom disorder (conversion disorder): A role for microglial-based plasticity mechanisms?

PubMed

Stephenson, Chris P; Baguley, Ian J

2018-02-01

Functional Neurological Symptom Disorder (FND) is a relatively common neurological condition, accounting for approximately 3-6% of neurologist referrals. FND is considered a transient disorder of neuronal function, sometimes linked to physical trauma and psychological stress. Despite this, chronic disability is common, for example, around 40% of adults with motor FND have permanent disability. Building on current theoretical models, this paper proposes that microglial dysfunction could perpetuate functional changes within acute motor FND, thus providing a pathophysiological mechanism underlying the chronic stage of the motor FND phenotypes seen clinically. Core to our argument is microglia's dual role in modulating neuroimmunity and their control of synaptic plasticity, which places them at a pathophysiological nexus wherein coincident physical trauma and psychological stress could cause long-term change in neuronal networks without producing macroscopic structural abnormality. This model proposes a range of hypotheses that are testable with current technologies. Copyright © 2017. Published by Elsevier Ltd.

Solute solver 'what if' module for modeling urea kinetics.

PubMed

Daugirdas, John T

2016-11-01

The publicly available Solute Solver module allows calculation of a variety of two-pool urea kinetic measures of dialysis adequacy using pre- and postdialysis plasma urea and estimated dialyzer clearance or estimated urea distribution volumes as inputs. However, the existing program does not have a 'what if' module, which would estimate the plasma urea values as well as commonly used measures of hemodialysis adequacy for a patient with a given urea distribution volume and urea nitrogen generation rate dialyzed according to a particular dialysis schedule. Conventional variable extracellular volume 2-pool urea kinetic equations were used. A javascript-HTML Web form was created that can be used on any personal computer equipped with internet browsing software, to compute commonly used Kt/V-based measures of hemodialysis adequacy for patients with differing amounts of residual kidney function and following a variety of treatment schedules. The completed Web form calculator may be particularly useful in computing equivalent continuous clearances for incremental hemodialysis strategies. © The Author 2016. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

ATLAS, an integrated structural analysis and design system. Volume 2: System design document

NASA Technical Reports Server (NTRS)

Erickson, W. J. (Editor)

1979-01-01

ATLAS is a structural analysis and design system, operational on the Control Data Corporation 6600/CYBER computers. The overall system design, the design of the individual program modules, and the routines in the ATLAS system library are described. The overall design is discussed in terms of system architecture, executive function, data base structure, user program interfaces and operational procedures. The program module sections include detailed code description, common block usage and random access file usage. The description of the ATLAS program library includes all information needed to use these general purpose routines.

Medical Terminology: Using Some Common Prefixes, Suffixes, and Roots. Health Occupations Education Module.

ERIC Educational Resources Information Center

Temple Univ., Philadelphia, PA. Div. of Vocational Education.

This module on medical terminology (using common prefixes, suffixes, and root words) is one of 17 modules designed for individualized instruction in health occupations education programs at both the secondary and postsecondary levels. This module consists of an introduction to the module topic, a list of resources needed, and three learning…

The Role of Short Term Synaptic Plasticity in Temporal Coding of Neuronal Networks

ERIC Educational Resources Information Center

Chandrasekaran, Lakshmi

2008-01-01

Short term synaptic plasticity is a phenomenon which is commonly found in the central nervous system. It could contribute to functions of signal processing namely, temporal integration and coincidence detection by modulating the input synaptic strength. This dissertation has two parts. First, we study the effects of short term synaptic plasticity…

Crystalline-silicon reliability lessons for thin-film modules

NASA Technical Reports Server (NTRS)

Ross, Ronald G., Jr.

1985-01-01

Key reliability and engineering lessons learned from the 10-year history of the Jet Propulsion Laboratory's Flat-Plate Solar Array Project are presented and analyzed. Particular emphasis is placed on lessons applicable to the evolving new thin-film cell and module technologies and the organizations involved with these technologies. The user-specific demand for reliability is a strong function of the application, its location, and its expected duration. Lessons relative to effective means of specifying reliability are described, and commonly used test requirements are assessed from the standpoint of which are the most troublesome to pass, and which correlate best with field experience. Module design lessons are also summarized, including the significance of the most frequently encountered failure mechanisms and the role of encapsulant and cell reliability in determining module reliability. Lessons pertaining to research, design, and test approaches include the historical role and usefulness of qualification tests and field tests.

PV Reliability Development Lessons from JPL's Flat Plate Solar Array Project

NASA Technical Reports Server (NTRS)

Ross, Ronald G., Jr.

2013-01-01

Key reliability and engineering lessons learned from the 20-year history of the Jet Propulsion Laboratory's Flat-Plate Solar Array Project and thin film module reliability research activities are presented and analyzed. Particular emphasis is placed on lessons applicable to evolving new module technologies and the organizations involved with these technologies. The user-specific demand for reliability is a strong function of the application, its location, and its expected duration. Lessons relative to effective means of specifying reliability are described, and commonly used test requirements are assessed from the standpoint of which are the most troublesome to pass, and which correlate best with field experience. Module design lessons are also summarized, including the significance of the most frequently encountered failure mechanisms and the role of encapsulate and cell reliability in determining module reliability. Lessons pertaining to research, design, and test approaches include the historical role and usefulness of qualification tests and field tests.

The mechanics of state dependent neural correlations

PubMed Central

Doiron, Brent; Litwin-Kumar, Ashok; Rosenbaum, Robert; Ocker, Gabriel K.; Josić, Krešimir

2016-01-01

Simultaneous recordings from large neural populations are becoming increasingly common. An important feature of the population activity are the trial-to-trial correlated fluctuations of the spike train outputs of recorded neuron pairs. Like the firing rate of single neurons, correlated activity can be modulated by a number of factors, from changes in arousal and attentional state to learning and task engagement. However, the network mechanisms that underlie these changes are not fully understood. We review recent theoretical results that identify three separate biophysical mechanisms that modulate spike train correlations: changes in input correlations, internal fluctuations, and the transfer function of single neurons. We first examine these mechanisms in feedforward pathways, and then show how the same approach can explain the modulation of correlations in recurrent networks. Such mechanistic constraints on the modulation of population activity will be important in statistical analyses of high dimensional neural data. PMID:26906505

Vitamin D and the omega-3 fatty acids control serotonin synthesis and action, part 2: relevance for ADHD, bipolar disorder, schizophrenia, and impulsive behavior.

PubMed

Patrick, Rhonda P; Ames, Bruce N

2015-06-01

Serotonin regulates a wide variety of brain functions and behaviors. Here, we synthesize previous findings that serotonin regulates executive function, sensory gating, and social behavior and that attention deficit hyperactivity disorder, bipolar disorder, schizophrenia, and impulsive behavior all share in common defects in these functions. It has remained unclear why supplementation with omega-3 fatty acids and vitamin D improve cognitive function and behavior in these brain disorders. Here, we propose mechanisms by which serotonin synthesis, release, and function in the brain are modulated by vitamin D and the 2 marine omega-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Brain serotonin is synthesized from tryptophan by tryptophan hydroxylase 2, which is transcriptionally activated by vitamin D hormone. Inadequate levels of vitamin D (∼70% of the population) and omega-3 fatty acids are common, suggesting that brain serotonin synthesis is not optimal. We propose mechanisms by which EPA increases serotonin release from presynaptic neurons by reducing E2 series prostaglandins and DHA influences serotonin receptor action by increasing cell membrane fluidity in postsynaptic neurons. We propose a model whereby insufficient levels of vitamin D, EPA, or DHA, in combination with genetic factors and at key periods during development, would lead to dysfunctional serotonin activation and function and may be one underlying mechanism that contributes to neuropsychiatric disorders and depression. This model suggests that optimizing vitamin D and marine omega-3 fatty acid intake may help prevent and modulate the severity of brain dysfunction. © FASEB.

Statistical process control using optimized neural networks: a case study.

PubMed

Addeh, Jalil; Ebrahimzadeh, Ata; Azarbad, Milad; Ranaee, Vahid

2014-09-01

The most common statistical process control (SPC) tools employed for monitoring process changes are control charts. A control chart demonstrates that the process has altered by generating an out-of-control signal. This study investigates the design of an accurate system for the control chart patterns (CCPs) recognition in two aspects. First, an efficient system is introduced that includes two main modules: feature extraction module and classifier module. In the feature extraction module, a proper set of shape features and statistical feature are proposed as the efficient characteristics of the patterns. In the classifier module, several neural networks, such as multilayer perceptron, probabilistic neural network and radial basis function are investigated. Based on an experimental study, the best classifier is chosen in order to recognize the CCPs. Second, a hybrid heuristic recognition system is introduced based on cuckoo optimization algorithm (COA) algorithm to improve the generalization performance of the classifier. The simulation results show that the proposed algorithm has high recognition accuracy. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

The nexus between decision making and emotion regulation: a review of convergent neurocognitive substrates.

PubMed

Mitchell, Derek G V

2011-02-02

Emotional information, such as reward or punishment, gains rapid and often preferential access to neurocognitive resources. This ability to quickly evaluate and integrate emotion-related information is thought to benefit a range of behaviours critical for survival. Conversely, the improper use of, or preoccupation with, emotional information is associated with disruptions in functioning and psychiatric disorders. Optimally, an organism utilizes emotional information when it is significant, and minimizes its influence when it is not. Recently, similar regions of prefrontal cortex have been identified that are associated with regulating both behavioural conflict (motor response selection or inhibition) and affective conflict (emotional representation and awareness). In this review, data will be examined that concerns this convergence between decision making (modulating what we do) and emotion regulation (modulating how we feel) and an informal model will be proposed linking these processes at a neurocognitive level. The studies reviewed collectively support the conclusion that overlapping areas of prefrontal cortex perform similar computations whether the functional objective is to modulate an operant response, or an emotional one. Specifically, the idea is raised that key aspects of decision making and emotion regulation are bound by a common functional objective in which internal representations of conditioned stimuli and reinforcers are modulated to facilitate optimal behaviour or states. Emphasis is placed on dorsomedial, dorsolateral, ventrolateral, and ventromedial regions of prefrontal cortex. Copyright © 2010 Elsevier B.V. All rights reserved.

Long-range functional interactions of anterior insula and medial frontal cortex are differently modulated by visuospatial and inductive reasoning tasks.

PubMed

Ebisch, Sjoerd J H; Mantini, Dante; Romanelli, Roberta; Tommasi, Marco; Perrucci, Mauro G; Romani, Gian Luca; Colom, Roberto; Saggino, Aristide

2013-09-01

The brain is organized into functionally specific networks as characterized by intrinsic functional relationships within discrete sets of brain regions. However, it is poorly understood whether such functional networks are dynamically organized according to specific task-states. The anterior insular cortex (aIC)-dorsal anterior cingulate cortex (dACC)/medial frontal cortex (mFC) network has been proposed to play a central role in human cognitive abilities. The present functional magnetic resonance imaging (fMRI) study aimed at testing whether functional interactions of the aIC-dACC/mFC network in terms of temporally correlated patterns of neural activity across brain regions are dynamically modulated by transitory, ongoing task demands. For this purpose, functional interactions of the aIC-dACC/mFC network are compared during two distinguishable fluid reasoning tasks, Visualization and Induction. The results show an increased functional coupling of bilateral aIC with visual cortices in the occipital lobe during the Visualization task, whereas coupling of mFC with right anterior frontal cortex was enhanced during the Induction task. These task-specific modulations of functional interactions likely reflect ability related neural processing. Furthermore, functional connectivity strength between right aIC and right dACC/mFC reliably predicts general task performance. The findings suggest that the analysis of long-range functional interactions may provide complementary information about brain-behavior relationships. On the basis of our results, it is proposed that the aIC-dACC/mFC network contributes to the integration of task-common and task-specific information based on its within-network as well as its between-network dynamic functional interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Carbohydrate Recognition by an Architecturally Complex α-N-Acetylglucosaminidase from Clostridium perfringens

PubMed Central

Ficko-Blean, Elizabeth; Stuart, Christopher P.; Suits, Michael D.; Cid, Melissa; Tessier, Matthew; Woods, Robert J.; Boraston, Alisdair B.

2012-01-01

CpGH89 is a large multimodular enzyme produced by the human and animal pathogen Clostridium perfringens. The catalytic activity of this exo-α-d-N-acetylglucosaminidase is directed towards a rare carbohydrate motif, N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which is displayed on the class III mucins deep within the gastric mucosa. In addition to the family 89 glycoside hydrolase catalytic module this enzyme has six modules that share sequence similarity to the family 32 carbohydrate-binding modules (CBM32s), suggesting the enzyme has considerable capacity to adhere to carbohydrates. Here we suggest that two of the modules, CBM32-1 and CBM32-6, are not functional as carbohydrate-binding modules (CBMs) and demonstrate that three of the CBMs, CBM32-3, CBM32-4, and CBM32-5, are indeed capable of binding carbohydrates. CBM32-3 and CBM32-4 have a novel binding specificity for N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which thus complements the specificity of the catalytic module. The X-ray crystal structure of CBM32-4 in complex with this disaccharide reveals a mode of recognition that is based primarily on accommodation of the unique bent shape of this sugar. In contrast, as revealed by a series of X-ray crystal structures and quantitative binding studies, CBM32-5 displays the structural and functional features of galactose binding that is commonly associated with CBM family 32. The functional CBM32s that CpGH89 contains suggest the possibility for multivalent binding events and the partitioning of this enzyme to highly specific regions within the gastrointestinal tract. PMID:22479408

Beam Instrument Development System

DOE Office of Scientific and Technical Information (OSTI.GOV)

DOOLITTLE, LAWRENCE; HUANG, GANG; DU, QIANG

Beam Instrumentation Development System (BIDS) is a collection of common support libraries and modules developed during a series of Low-Level Radio Frequency (LLRF) control and timing/synchronization projects. BIDS includes a collection of Hardware Description Language (HDL) libraries and software libraries. The BIDS can be used for the development of any FPGA-based system, such as LLRF controllers. HDL code in this library is generic and supports common Digital Signal Processing (DSP) functions, FPGA-specific drivers (high-speed serial link wrappers, clock generation, etc.), ADC/DAC drivers, Ethernet MAC implementation, etc.

Modulation instability in high power laser amplifiers.

PubMed

Rubenchik, Alexander M; Turitsyn, Sergey K; Fedoruk, Michail P

2010-01-18

The modulation instability (MI) is one of the main factors responsible for the degradation of beam quality in high-power laser systems. The so-called B-integral restriction is commonly used as the criteria for MI control in passive optics devices. For amplifiers the adiabatic model, assuming locally the Bespalov-Talanov expression for MI growth, is commonly used to estimate the destructive impact of the instability. We present here the exact solution of MI development in amplifiers. We determine the parameters which control the effect of MI in amplifiers and calculate the MI growth rate as a function of those parameters. The safety range of operational parameters is presented. The results of the exact calculations are compared with the adiabatic model, and the range of validity of the latest is determined. We demonstrate that for practical situations the adiabatic approximation noticeably overestimates MI. The additional margin of laser system design is quantified.

3D printing of tissue-simulating phantoms as a traceable standard for biomedical optical measurement

NASA Astrophysics Data System (ADS)

Dong, Erbao; Wang, Minjie; Shen, Shuwei; Han, Yilin; Wu, Qiang; Xu, Ronald

2016-01-01

Optical phantoms are commonly used to validate and calibrate biomedical optical devices in order to ensure accurate measurement of optical properties in biological tissue. However, commonly used optical phantoms are based on homogenous materials that reflect neither optical properties nor multi-layer heterogeneities of biological tissue. Using these phantoms for optical calibration may result in significant bias in biological measurement. We propose to characterize and fabricate tissue simulating phantoms that simulate not only the multi-layer heterogeneities but also optical properties of biological tissue. The tissue characterization module detects tissue structural and functional properties in vivo. The phantom printing module generates 3D tissue structures at different scales by layer-by-layer deposition of phantom materials with different optical properties. The ultimate goal is to fabricate multi-layer tissue simulating phantoms as a traceable standard for optimal calibration of biomedical optical spectral devices.

[Common intralobular microcirculatory module peculliarities in cholestasis in white rats].

PubMed

Sulaberidze, G D; Kardzvia, D Dzh; Kikalishvili, L A; Khomeriki, Ts T

2006-03-01

The dynamics of intralobular microcirculatory module transformation in cholestasis was investigated. The liver tissues of 54 white Wistar rats were studied by Histology, TEM, TEM after injection of 1% Pb(NO(3))(3), vie common bile duct (CBD), SEM of corrosion casts prepared after methylmethacrylate injection vie CBD. It is demonstrated that liver is the basis of microcirculation of 4 different liquids: blood, bile, connective tissue liquid and lymph. Accordingly, in normal condition 4 different well formed compartments bordered from each-others by different types of cells exist. In the yearly stages of cholestasis (3-6 days) the function of bile drainage is partially overtaken by lymph pathways. This is accompanied by the beginning of the destruction of structures bordering above-mentioned microcirculatory beds. In the later stages of cholestasis (12-18 days) the final disorganization of microcirculatory compartments with mixture of all liquids is observed. It is accompanied by increased dystrophy of liver cells population.

Design of Mobile Health Tools to Promote Goal Achievement in Self-Management Tasks

PubMed Central

Henderson, Geoffrey; Parmanto, Bambang

2017-01-01

Background Goal-setting within rehabilitation is a common practice ultimately geared toward helping patients make functional progress. Objective The purposes of this study were to (1) qualitatively analyze data from a wellness program for patients with spina bifida (SB) and spinal cord injury (SCI) in order to generate software requirements for a goal-setting module to support their complex goal-setting routines, (2) design a prototype of a goal-setting module within an existing mobile health (mHealth) system, and (3) identify what educational content might be necessary to integrate into the system. Methods A total of 750 goals were analyzed from patients with SB and SCI enrolled in a wellness program. These goals were qualitatively analyzed in order to operationalize a set of software requirements for an mHealth goal-setting module and identify important educational content. Results Those of male sex (P=.02) and with SCI diagnosis (P<.001) were more likely to achieve goals than females or those with SB. Temporality (P<.001) and type (P<.001) of goal were associated with likelihood that the goal would be achieved. Nearly all (210/213; 98.6%) of the fact-finding goals were achieved. There was no significant difference in achievement based on goal theme. Checklists, data tracking, and fact-finding tools were identified as three functionalities that could support goal-setting and achievement in an mHealth system. Based on the qualitative analysis, a list of software requirements for a goal-setting module was generated, and a prototype was developed. Targets for educational content were also generated. Conclusions Innovative mHealth tools can be developed to support commonly set goals by individuals with disabilities. PMID:28739558

Functions of intrinsic disorder in transmembrane proteins.

PubMed

Kjaergaard, Magnus; Kragelund, Birthe B

2017-09-01

Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding protein disorder.

Variation in the miRNA-433 Binding Site of FGF20 Confers Risk for Parkinson Disease by Overexpression of α-Synuclein

PubMed Central

Wang, Gaofeng; van der Walt, Joelle M.; Mayhew, Gregory; Li, Yi-Ju; Züchner, Stephan; Scott, William K.; Martin, Eden R.; Vance, Jeffery M.

2008-01-01

Parkinson disease (PD) is a common neurodegenerative disorder caused by environmental and genetic factors. We have previously shown linkage of PD to chromosome 8p. Subsequently, fibroblast growth factor 20 (FGF20) at 8p21.3–22 was identified as a risk factor in several association studies. To identify the risk-conferring polymorphism in FGF20, we performed genetic and functional analysis of single-nucleotide polymorphisms within the gene. In a sample of 729 nuclear families with 1089 affected and 1165 unaffected individuals, the strongest evidence of association came from rs12720208 in the 3′ untranslated region of FGF20. We show in several functional assays that the risk allele for rs12720208 disrupts a binding site for microRNA-433, increasing translation of FGF20 in vitro and in vivo. In a cell-based system and in PD brains, this increase in translation of FGF20 is correlated with increased α-synuclein expression, which has previously been shown to cause PD through both overexpression and point mutations. We suggest a novel mechanism of action for PD risk in which the modulation of the susceptibility gene's translation by common variations interfere with the regulation mechanisms of microRNA. We propose this is likely to be a common mechanism of genetic modulation of individual susceptibility to complex disease. PMID:18252210

Using the Generic Mapping Tools From Within the MATLAB, Octave and Julia Computing Environments

NASA Astrophysics Data System (ADS)

Luis, J. M. F.; Wessel, P.

2016-12-01

The Generic Mapping Tools (GMT) is a widely used software infrastructure tool set for analyzing and displaying geoscience data. Its power to analyze and process data and produce publication-quality graphics has made it one of several standard processing toolsets used by a large segment of the Earth and Ocean Sciences. GMT's strengths lie in superior publication-quality vector graphics, geodetic-quality map projections, robust data processing algorithms scalable to enormous data sets, and ability to run under all common operating systems. The GMT tool chest offers over 120 modules sharing a common set of command options, file structures, and documentation. GMT modules are command line tools that accept input and write output, and this design allows users to write scripts in which one module's output becomes another module's input, creating highly customized GMT workflows. With the release of GMT 5, these modules are high-level functions with a C API, potentially allowing users access to high-level GMT capabilities from any programmable environment. Many scientists who use GMT also use other computational tools, such as MATLAB® and its clone Octave. We have built a MATLAB/Octave interface on top of the GMT 5 C API. Thus, MATLAB or Octave now has full access to all GMT modules as well as fundamental input/output of GMT data objects via a MEX function. Internally, the GMT/MATLAB C API defines six high-level composite data objects that handle input and output of data via individual GMT modules. These are data tables, grids, text tables (text/data mixed records), color palette tables, raster images (1-4 color bands), and PostScript. The API is responsible for translating between the six GMT objects and the corresponding native MATLAB objects. References to data arrays are passed if transposing of matrices is not required. The GMT and MATLAB/Octave combination is extremely flexible, letting the user harvest the general numerical and graphical capabilities of both systems, and represents a giant step forward in interoperability between GMT and other software package. We will present examples of the symbiotic benefits of combining these platforms. Two other extensions are also in the works: a nearly finished Julia wrapper and an embryonic Python module. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto D. Luiz

Epigenetics in Prostate Cancer

PubMed Central

Albany, Costantine; Alva, Ajjai S.; Aparicio, Ana M.; Singal, Rakesh; Yellapragada, Sarvari; Sonpavde, Guru; Hahn, Noah M.

2011-01-01

Prostate cancer (PC) is the most commonly diagnosed nonskin malignancy and the second most common cause of cancer death among men in the United States. Epigenetics is the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequences. Two common epigenetic mechanisms, DNA methylation and histone modification, have demonstrated critical roles in prostate cancer growth and metastasis. DNA hypermethylation of cytosine-guanine (CpG) rich sequence islands within gene promoter regions is widespread during neoplastic transformation of prostate cells, suggesting that treatment-induced restoration of a “normal” epigenome could be clinically beneficial. Histone modification leads to altered tumor gene function by changing chromosome structure and the level of gene transcription. The reversibility of epigenetic aberrations and restoration of tumor suppression gene function have made them attractive targets for prostate cancer treatment with modulators that demethylate DNA and inhibit histone deacetylases. PMID:22191037

Epigenetics in prostate cancer.

PubMed

Albany, Costantine; Alva, Ajjai S; Aparicio, Ana M; Singal, Rakesh; Yellapragada, Sarvari; Sonpavde, Guru; Hahn, Noah M

2011-01-01

Prostate cancer (PC) is the most commonly diagnosed nonskin malignancy and the second most common cause of cancer death among men in the United States. Epigenetics is the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequences. Two common epigenetic mechanisms, DNA methylation and histone modification, have demonstrated critical roles in prostate cancer growth and metastasis. DNA hypermethylation of cytosine-guanine (CpG) rich sequence islands within gene promoter regions is widespread during neoplastic transformation of prostate cells, suggesting that treatment-induced restoration of a "normal" epigenome could be clinically beneficial. Histone modification leads to altered tumor gene function by changing chromosome structure and the level of gene transcription. The reversibility of epigenetic aberrations and restoration of tumor suppression gene function have made them attractive targets for prostate cancer treatment with modulators that demethylate DNA and inhibit histone deacetylases.

Advanced Transport Operating System (ATOPS) color displays software description: MicroVAX system

NASA Technical Reports Server (NTRS)

Slominski, Christopher J.; Plyler, Valerie E.; Dickson, Richard W.

1992-01-01

This document describes the software created for the Display MicroVAX computer used for the Advanced Transport Operating Systems (ATOPS) project on the Transport Systems Research Vehicle (TSRV). The software delivery of February 27, 1991, known as the 'baseline display system', is the one described in this document. Throughout this publication, module descriptions are presented in a standardized format which contains module purpose, calling sequence, detailed description, and global references. The global references section includes subroutines, functions, and common variables referenced by a particular module. The system described supports the Research Flight Deck (RFD) of the TSRV. The RFD contains eight Cathode Ray Tubes (CRTs) which depict a Primary Flight Display, Navigation Display, System Warning Display, Takeoff Performance Monitoring System Display, and Engine Display.

Allosteric Modulation of Metabotropic Glutamate Receptors

PubMed Central

Sheffler, Douglas J.; Gregory, Karen J.; Rook, Jerri M.; Conn, P. Jeffrey

2013-01-01

The development of receptor subtype-selective ligands by targeting allosteric sites of G protein-coupled receptors (GPCRs) has proven highly successful in recent years. One GPCR family that has greatly benefited from this approach is the metabotropic glutamate receptors (mGlus). These family C GPCRs participate in the neuromodulatory actions of glutamate throughout the CNS, where they play a number of key roles in regulating synaptic transmission and neuronal excitability. A large number of mGlu subtype-selective allosteric modulators have been identified, the majority of which are thought to bind within the transmembrane regions of the receptor. These modulators can either enhance or inhibit mGlu functional responses and, together with mGlu knockout mice, have furthered the establishment of the physiologic roles of many mGlu subtypes. Numerous pharmacological and receptor mutagenesis studies have been aimed at providing a greater mechanistic understanding of the interaction of mGlu allosteric modulators with the receptor, which have revealed evidence for common allosteric binding sites across multiple mGlu subtypes and the presence for multiple allosteric sites within a single mGlu subtype. Recent data have also revealed that mGlu allosteric modulators can display functional selectivity toward particular signal transduction cascades downstream of an individual mGlu subtype. Studies continue to validate the therapeutic utility of mGlu allosteric modulators as a potential therapeutic approach for a number of disorders including anxiety, schizophrenia, Parkinson’s disease, and Fragile X syndrome. PMID:21907906

Common drive to the upper airway muscle genioglossus during inspiratory loading

PubMed Central

Woods, Michael J.; Nicholas, Christian L.; Semmler, John G.; Chan, Julia K. M.; Jordan, Amy S.

2015-01-01

Common drive is thought to constitute a central mechanism by which the efficiency of a motor neuron pool is increased. This study tested the hypothesis that common drive to the upper airway muscle genioglossus (GG) would increase with increased respiratory drive in response to an inspiratory load. Respiration, GG electromyographic (EMG) activity, single-motor unit activity, and coherence in the 0–5 Hz range between pairs of GG motor units were assessed for the 30 s before an inspiratory load, the first and second 30 s of the load, and the 30 s after the load. Twelve of twenty young, healthy male subjects provided usable data, yielding 77 pairs of motor units: 2 Inspiratory Phasic, 39 Inspiratory Tonic, 15 Expiratory Tonic, and 21 Tonic. Respiratory and GG inspiratory activity significantly increased during the loads and returned to preload levels during the postload periods (all showed significant quadratic functions over load trials, P < 0.05). As hypothesized, common drive increased during the load in inspiratory modulated motor units to a greater extent than in expiratory/tonic motor units (significant load × discharge pattern interaction, P < 0.05). Furthermore, this effect persisted during the postload period. In conclusion, common drive to inspiratory modulated motor units was elevated in response to increased respiratory drive. The postload elevation in common drive was suggestive of a poststimulus activation effect. PMID:26378207

Knowledge-based geographic information systems on the Macintosh computer: a component of the GypsES project

Treesearch

Gregory Elmes; Thomas Millette; Charles B. Yuill

1991-01-01

GypsES, a decision-support and expert system for the management of Gypsy Moth addresses five related research problems in a modular, computer-based project. The modules are hazard rating, monitoring, prediction, treatment decision and treatment implementation. One common component is a geographic information system designed to function intelligently. We refer to this...

Using Multiple FPGA Architectures for Real-time Processing of Low-level Machine Vision Functions

Treesearch

Thomas H. Drayer; William E. King; Philip A. Araman; Joseph G. Tront; Richard W. Conners

1995-01-01

In this paper, we investigate the use of multiple Field Programmable Gate Array (FPGA) architectures for real-time machine vision processing. The use of FPGAs for low-level processing represents an excellent tradeoff between software and special purpose hardware implementations. A library of modules that implement common low-level machine vision operations is presented...

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference

PubMed Central

Stone, Eric A.; Ayroles, Julien F.

2009-01-01

In recent years, the advent of high-throughput assays, coupled with their diminishing cost, has facilitated a systems approach to biology. As a consequence, massive amounts of data are currently being generated, requiring efficient methodology aimed at the reduction of scale. Whole-genome transcriptional profiling is a standard component of systems-level analyses, and to reduce scale and improve inference clustering genes is common. Since clustering is often the first step toward generating hypotheses, cluster quality is critical. Conversely, because the validation of cluster-driven hypotheses is indirect, it is critical that quality clusters not be obtained by subjective means. In this paper, we present a new objective-based clustering method and demonstrate that it yields high-quality results. Our method, modulated modularity clustering (MMC), seeks community structure in graphical data. MMC modulates the connection strengths of edges in a weighted graph to maximize an objective function (called modularity) that quantifies community structure. The result of this maximization is a clustering through which tightly-connected groups of vertices emerge. Our application is to systems genetics, and we quantitatively compare MMC both to the hierarchical clustering method most commonly employed and to three popular spectral clustering approaches. We further validate MMC through analyses of human and Drosophila melanogaster expression data, demonstrating that the clusters we obtain are biologically meaningful. We show MMC to be effective and suitable to applications of large scale. In light of these features, we advocate MMC as a standard tool for exploration and hypothesis generation. PMID:19424432

A-7E Software Module Guide.

DTIC Science & Technology

1981-12-08

o 14 A& B:2.1 Function Driver Module.. ..... .... 14’ ’: B:2.2 Shared Services Module . . . o o . 0 -15 M’ 5:3 Software Decision Module...2.1.13 Weapon Release Functions... ........24 C:2.l.14 Ground Test Functions .. ........... 24 C:2.2 Shared Services Module Decomposition. ........24 C...Driver (FD) Module supported by a Shared Services (SS) Module. B:2.1 FUNCTION DRIVER MODULE The Function Driver Module consists of a set of individual

Optimum Adaptive Modulation and Channel Coding Scheme for Frequency Domain Channel-Dependent Scheduling in OFDM Based Evolved UTRA Downlink

NASA Astrophysics Data System (ADS)

Miki, Nobuhiko; Kishiyama, Yoshihisa; Higuchi, Kenichi; Sawahashi, Mamoru; Nakagawa, Masao

In the Evolved UTRA (UMTS Terrestrial Radio Access) downlink, Orthogonal Frequency Division Multiplexing (OFDM) based radio access was adopted because of its inherent immunity to multipath interference and flexible accommodation of different spectrum arrangements. This paper presents the optimum adaptive modulation and channel coding (AMC) scheme when resource blocks (RBs) is simultaneously assigned to the same user when frequency and time domain channel-dependent scheduling is assumed in the downlink OFDMA radio access with single-antenna transmission. We start by presenting selection methods for the modulation and coding scheme (MCS) employing mutual information both for RB-common and RB-dependent modulation schemes. Simulation results show that, irrespective of the application of power adaptation to RB-dependent modulation, the improvement in the achievable throughput of the RB-dependent modulation scheme compared to that for the RB-common modulation scheme is slight, i.e., 4 to 5%. In addition, the number of required control signaling bits in the RB-dependent modulation scheme becomes greater than that for the RB-common modulation scheme. Therefore, we conclude that the RB-common modulation and channel coding rate scheme is preferred, when multiple RBs of the same coded stream are assigned to one user in the case of single-antenna transmission.

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

PubMed

Rittschof, Clare C; Bukhari, Syed Abbas; Sloofman, Laura G; Troy, Joseph M; Caetano-Anollés, Derek; Cash-Ahmed, Amy; Kent, Molly; Lu, Xiaochen; Sanogo, Yibayiri O; Weisner, Patricia A; Zhang, Huimin; Bell, Alison M; Ma, Jian; Sinha, Saurabh; Robinson, Gene E; Stubbs, Lisa

2014-12-16

Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.

Think like a sponge: The genetic signal of sensory cells in sponges.

PubMed

Mah, Jasmine L; Leys, Sally P

2017-11-01

A complex genetic repertoire underlies the apparently simple body plan of sponges. Among the genes present in poriferans are those fundamental to the sensory and nervous systems of other animals. Sponges are dynamic and sensitive animals and it is intuitive to link these genes to behaviour. The proposal that ctenophores are the earliest diverging metazoan has led to the question of whether sponges possess a 'pre-nervous' system or have undergone nervous system loss. Both lines of thought generally assume that the last common ancestor of sponges and eumetazoans possessed the genetic modules that underlie sensory abilities. By corollary extant sponges may possess a sensory cell homologous to one present in the last common ancestor, a hypothesis that has been studied by gene expression. We have performed a meta-analysis of all gene expression studies published to date to explore whether gene expression is indicative of a feature's sensory function. In sponges we find that eumetazoan sensory-neural markers are not particularly expressed in structures with known sensory functions. Instead it is common for these genes to be expressed in cells with no known or uncharacterized sensory function. Indeed, many sensory-neural markers so far studied are expressed during development, perhaps because many are transcription factors. This suggests that the genetic signal of a sponge sensory cell is dissimilar enough to be unrecognizable when compared to a bilaterian sensory or neural cell. It is possible that sensory-neural markers have as yet unknown functions in sponge cells, such as assembling an immunological synapse in the larval globular cell. Furthermore, the expression of sensory-neural markers in non-sensory cells, such as adult and larval epithelial cells, suggest that these cells may have uncharacterized sensory functions. While this does not rule out the co-option of ancestral sensory modules in later evolving groups, a distinct genetic foundation may underlie the sponge sensory system. Copyright © 2017 Elsevier Inc. All rights reserved.

Shaping reverberating sound fields with an actively tunable metasurface.

PubMed

Ma, Guancong; Fan, Xiying; Sheng, Ping; Fink, Mathias

2018-06-26

A reverberating environment is a common complex medium for airborne sound, with familiar examples such as music halls and lecture theaters. The complexity of reverberating sound fields has hindered their meaningful control. Here, by combining acoustic metasurface and adaptive wavefield shaping, we demonstrate the versatile control of reverberating sound fields in a room. This is achieved through the design and the realization of a binary phase-modulating spatial sound modulator that is based on an actively reconfigurable acoustic metasurface. We demonstrate useful functionalities including the creation of quiet zones and hotspots in a typical reverberating environment. Copyright © 2018 the Author(s). Published by PNAS.

Pd-Metalated Conjugated Nanoporous Polycarbazoles for Additive-Free Cyanation of Aryl Halides: Boosting Catalytic Efficiency through Spatial Modulation

DOE PAGES

Ding, Shunmin; Tian, Chengcheng; Zhu, Xiang; ...

2017-03-23

Transition-metal-catalyzed cyanation of aryl halides is a common route to benzonitriles, which are integral to many industrial procedures. However, traditional homogeneous catalysts for such processes are expensive and suffer poor recyclability, so a heterogeneous analogue is highly desired. A novel spatial modulation approach has been developed in this paper to fabricate a heterogeneous Pd-metalated nanoporous polymer, which catalyzes the cyanation of aryl halides without need for ligands. Finally, the catalyst displays high activity in the synthesis of benzonitriles, including high product yields, excellent stability and recycling, and broad functional-group tolerance.

Eosinophils in Autoimmune Diseases

PubMed Central

Diny, Nicola L.; Rose, Noel R.; Čiháková, Daniela

2017-01-01

Eosinophils are multifunctional granulocytes that contribute to initiation and modulation of inflammation. Their role in asthma and parasitic infections has long been recognized. Growing evidence now reveals a role for eosinophils in autoimmune diseases. In this review, we summarize the function of eosinophils in inflammatory bowel diseases, neuromyelitis optica, bullous pemphigoid, autoimmune myocarditis, primary biliary cirrhosis, eosinophilic granulomatosis with polyangiitis, and other autoimmune diseases. Clinical studies, eosinophil-targeted therapies, and experimental models have contributed to our understanding of the regulation and function of eosinophils in these diseases. By examining the role of eosinophils in autoimmune diseases of different organs, we can identify common pathogenic mechanisms. These include degranulation of cytotoxic granule proteins, induction of antibody-dependent cell-mediated cytotoxicity, release of proteases degrading extracellular matrix, immune modulation through cytokines, antigen presentation, and prothrombotic functions. The association of eosinophilic diseases with autoimmune diseases is also examined, showing a possible increase in autoimmune diseases in patients with eosinophilic esophagitis, hypereosinophilic syndrome, and non-allergic asthma. Finally, we summarize key future research needs. PMID:28496445

TALE transcription factors during early development of the vertebrate brain and eye.

PubMed

Schulte, Dorothea; Frank, Dale

2014-01-01

Our brain's cognitive performance arises from the coordinated activities of billions of nerve cells. Despite a high degree of morphological and functional differences, all neurons of the vertebrate central nervous system (CNS) arise from a common field of multipotent progenitors. Cell fate specification and differentiation are directed by multistep processes that include inductive/external cues, such as the extracellular matrix or growth factors, and cell-intrinsic determinants, such as transcription factors and epigenetic modulators of proteins and DNA. Here we review recent findings implicating TALE-homeodomain proteins in these processes. Although originally identified as HOX-cofactors, TALE proteins also contribute to many physiological processes that do not require HOX-activity. Particular focus is, therefore, given to HOX-dependent and -independent functions of TALE proteins during early vertebrate brain development. Additionally, we provide an overview about known upstream and downstream factors of TALE proteins in the developing vertebrate brain and discuss general concepts of how TALE proteins function to modulate neuronal cell fate specification. Copyright © 2013 Wiley Periodicals, Inc.

Disrupted functional connectivity of the periaqueductal gray in chronic low back pain

PubMed Central

Yu, Rongjun; Gollub, Randy L.; Spaeth, Rosa; Napadow, Vitaly; Wasan, Ajay; Kong, Jian

2014-01-01

Chronic low back pain is a common neurological disorder. The periaqueductal gray (PAG) plays a key role in the descending modulation of pain. In this study, we investigated brain resting state PAG functional connectivity (FC) differences between patients with chronic low back pain (cLBP) in low pain or high pain condition and matched healthy controls (HCs). PAG seed based functional connectivity (FC) analysis of the functional MR imaging data was performed to investigate the difference among the connectivity maps in the cLBP in the low or high pain condition and HC groups as well as within the cLBP at differing endogenous back pain intensities. Results showed that FC between the PAG and the ventral medial prefrontal cortex (vmPFC)/rostral anterior cingulate cortex (rACC) increased in cLBP patients compared to matched controls. In addition, we also found significant negative correlations between pain ratings and PAG–vmPFC/rACC FC in cLBP patients after pain-inducing maneuver. The duration of cLBP was negatively correlated with PAG–insula and PAG–amygdala FC before pain-inducing maneuver in the patient group. These findings are in line with the impairments of the descending pain modulation reported in patients with cLBP. Our results provide evidence showing that cLBP patients have abnormal FC in PAG centered pain modulation network during rest. PMID:25379421

MAPI: towards the integrated exploitation of bioinformatics Web Services.

PubMed

Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

2011-10-27

Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

Neural architectures for stereo vision.

PubMed

Parker, Andrew J; Smith, Jackson E T; Krug, Kristine

2016-06-19

Stereoscopic vision delivers a sense of depth based on binocular information but additionally acts as a mechanism for achieving correspondence between patterns arriving at the left and right eyes. We analyse quantitatively the cortical architecture for stereoscopic vision in two areas of macaque visual cortex. For primary visual cortex V1, the result is consistent with a module that is isotropic in cortical space with a diameter of at least 3 mm in surface extent. This implies that the module for stereo is larger than the repeat distance between ocular dominance columns in V1. By contrast, in the extrastriate cortical area V5/MT, which has a specialized architecture for stereo depth, the module for representation of stereo is about 1 mm in surface extent, so the representation of stereo in V5/MT is more compressed than V1 in terms of neural wiring of the neocortex. The surface extent estimated for stereo in V5/MT is consistent with measurements of its specialized domains for binocular disparity. Within V1, we suggest that long-range horizontal, anatomical connections form functional modules that serve both binocular and monocular pattern recognition: this common function may explain the distortion and disruption of monocular pattern vision observed in amblyopia.This article is part of the themed issue 'Vision in our three-dimensional world'. © 2016 The Authors.

Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon.

PubMed

Spieler, Derek; Kaffe, Maria; Knauf, Franziska; Bessa, José; Tena, Juan J; Giesert, Florian; Schormair, Barbara; Tilch, Erik; Lee, Heekyoung; Horsch, Marion; Czamara, Darina; Karbalai, Nazanin; von Toerne, Christine; Waldenberger, Melanie; Gieger, Christian; Lichtner, Peter; Claussnitzer, Melina; Naumann, Ronald; Müller-Myhsok, Bertram; Torres, Miguel; Garrett, Lillian; Rozman, Jan; Klingenspor, Martin; Gailus-Durner, Valérie; Fuchs, Helmut; Hrabě de Angelis, Martin; Beckers, Johannes; Hölter, Sabine M; Meitinger, Thomas; Hauck, Stefanie M; Laumen, Helmut; Wurst, Wolfgang; Casares, Fernando; Gómez-Skarmeta, Jose Luis; Winkelmann, Juliane

2014-04-01

Genome-wide association studies (GWAS) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and their functional relevance remain unknown. This locus contains a large number of highly conserved noncoding regions (HCNRs) potentially functioning as cis-regulatory modules. We analyzed these HCNRs for allele-dependent enhancer activity in zebrafish and mice and found that the risk allele of the lead SNP rs12469063 reduces enhancer activity in the Meis1 expression domain of the murine embryonic ganglionic eminences (GE). CREB1 binds this enhancer and rs12469063 affects its binding in vitro. In addition, MEIS1 target genes suggest a role in the specification of neuronal progenitors in the GE, and heterozygous Meis1-deficient mice exhibit hyperactivity, resembling the RLS phenotype. Thus, in vivo and in vitro analysis of a common SNP with small effect size showed allele-dependent function in the prospective basal ganglia representing the first neurodevelopmental region implicated in RLS.

Identification of Unstable Network Modules Reveals Disease Modules Associated with the Progression of Alzheimer’s Disease

PubMed Central

Kikuchi, Masataka; Ogishima, Soichi; Miyamoto, Tadashi; Miyashita, Akinori; Kuwano, Ryozo; Nakaya, Jun; Tanaka, Hiroshi

2013-01-01

Alzheimer’s disease (AD), the most common cause of dementia, is associated with aging, and it leads to neuron death. Deposits of amyloid β and aberrantly phosphorylated tau protein are known as pathological hallmarks of AD, but the underlying mechanisms have not yet been revealed. A high-throughput gene expression analysis previously showed that differentially expressed genes accompanying the progression of AD were more down-regulated than up-regulated in the later stages of AD. This suggested that the molecular networks and their constituent modules collapsed along with AD progression. In this study, by using gene expression profiles and protein interaction networks (PINs), we identified the PINs expressed in three brain regions: the entorhinal cortex (EC), hippocampus (HIP) and superior frontal gyrus (SFG). Dividing the expressed PINs into modules, we examined the stability of the modules with AD progression and with normal aging. We found that in the AD modules, the constituent proteins, interactions and cellular functions were not maintained between consecutive stages through all brain regions. Interestingly, the modules were collapsed with AD progression, specifically in the EC region. By identifying the modules that were affected by AD pathology, we found the transcriptional regulation-associated modules that interact with the proteasome-associated module via UCHL5 hub protein, which is a deubiquitinating enzyme. Considering PINs as a system made of network modules, we found that the modules relevant to the transcriptional regulation are disrupted in the EC region, which affects the ubiquitin-proteasome system. PMID:24348898

Toward a convergence of regenerative medicine, rehabilitation, and neuroprosthetics.

PubMed

Aravamudhan, Shyam; Bellamkonda, Ravi V

2011-11-01

No effective therapeutic interventions exist for severe neural pathologies, despite significant advances in regenerative medicine, rehabilitation, and neuroprosthetics. Our current hypothesis is that a specific combination of tissue engineering, pharmacology, cell replacement, drug delivery, and electrical stimulation, together with plasticity-promoting and locomotor training (neurorehabilitation) is necessary to interact synergistically in order to activate and enable all damaged circuits. We postulate that various convergent themes exist among the different therapeutic fields. Therefore, the objective of this review is to highlight the convergent themes, which we believe have a common goal of restoring function after neural damage. The convergent themes discussed in this review include modulation of inflammation and secondary damage, encouraging endogenous repair/regeneration (using scaffolds, cell transplantation, and drug delivery), application of electrical fields to modulate healing and/or activity, and finally modulation of plasticity.

Targeting Metabolic Plasticity in Breast Cancer Cells via Mitochondrial Complex I Modulation

PubMed Central

Xu, Qijin; Biener-Ramanujan, Eva; Yang, Wei; Ramanujan, V Krishnan

2016-01-01

Purpose Heterogeneity commonly observed in clinical tumors stems both from the genetic diversity as well as from the differential metabolic adaptation of multiple cancer types during their struggle to maintain uncontrolled proliferation and invasion in vivo. This study aims to identify a potential metabolic window of such adaptation in aggressive human breast cancer cell lines. Methods With a multidisciplinary approach using high resolution imaging, cell metabolism assays, proteomic profiling and animal models of human tumor xenografts and via clinically-relevant, pharmacological approach for modulating mitochondrial complex I function in human breast cancer cell lines, we report a novel route to target metabolic plasticity in human breast cancer cells. Results By a systematic modulation of mitochondrial function and by mitigating metabolic switch phenotype in aggressive human breast cancer cells, we demonstrate that the resulting metabolic adaptation signatures can predictably decrease tumorigenic potential in vivo. Proteomic profiling of the metabolic adaptation in these cells further revealed novel protein-pathway interactograms highlighting the importance of antioxidant machinery in the observed metabolic adaptation. Conclusions Improved metabolic adaptation potential in aggressive human breast cancer cells contribute to improving mitochondrial function and reducing metabolic switch phenotype –which may be vital for targeting primary tumor growth in vivo. PMID:25677747

The Millennium Cohort Family Study: A Prospective Evaluation of the Health and Well-Being of Military Service Members and Their Families

DTIC Science & Technology

2014-06-10

psychology , family, military, epidemiology, mental health, deployments Correspondence Nancy Crum-Cianflone, Deployment Health Research Department...American Psychological Association, 2007; Siegel et al., 2013; US Army Medical Research and Materiel Command, 2013). Although studies on military...functional health Modules on common types of mental disorders: depression, anxiety, panic syndrome, somatoform symptoms, alcohol abuse, bulimia nervosa

Universal sensor interface module (USIM)

NASA Astrophysics Data System (ADS)

King, Don; Torres, A.; Wynn, John

1999-01-01

A universal sensor interface model (USIM) is being developed by the Raytheon-TI Systems Company for use with fields of unattended distributed sensors. In its production configuration, the USIM will be a multichip module consisting of a set of common modules. The common module USIM set consists of (1) a sensor adapter interface (SAI) module, (2) digital signal processor (DSP) and associated memory module, and (3) a RF transceiver model. The multispectral sensor interface is designed around a low-power A/D converted, whose input/output interface consists of: -8 buffered, sampled inputs from various devices including environmental, acoustic seismic and magnetic sensors. The eight sensor inputs are each high-impedance, low- capacitance, differential amplifiers. The inputs are ideally suited for interface with discrete or MEMS sensors, since the differential input will allow direct connection with high-impedance bridge sensors and capacitance voltage sources. Each amplifier is connected to a 22-bit (Delta) (Sigma) A/D converter to enable simultaneous samples. The low power (Delta) (Sigma) converter provides 22-bit resolution at sample frequencies up to 142 hertz (used for magnetic sensors) and 16-bit resolution at frequencies up to 1168 hertz (used for acoustic and seismic sensors). The video interface module is based around the TMS320C5410 DSP. It can provide sensor array addressing, video data input, data calibration and correction. The processor module is based upon a MPC555. It will be used for mode control, synchronization of complex sensors, sensor signal processing, array processing, target classification and tracking. Many functions of the A/D, DSP and transceiver can be powered down by using variable clock speeds under software command or chip power switches. They can be returned to intermediate or full operation by DSP command. Power management may be based on the USIM's internal timer, command from the USIM transceiver, or by sleep mode processing management. The low power detection mode is implemented by monitoring any of the sensor analog outputs at lower sample rates for detection over a software controllable threshold.

Defense system shortcuts and limits of scope.

PubMed

Rewald, E; Francischetti, M M

2000-10-01

Defense, as a key factor of life, shares the biological tendencies of simplicity and energy saving. We propose that, like the mind, defense tends to rely on shortcuts via immune memes. Also, response repetition may induce the formation of virtual 'modules' [toolkits] to simplify and perfect performance. Engaged modules may expand by proliferating or by capturing immune components from the 'dormant' and even perhaps from active ones. With regard to recovery and/or survival, complexity of the integrated defense system (IDS) (1) requires to be inside of what we call the 'functional window'. In contrast to the physiological and common disease repair, energy is squandered when IDS perceives real danger. Our concern is the uncertain transition to conditions that do not fit into the IDS routine and, even worse, that are outside the functional window where the system is lacking. Copyright 2000 Harcourt Publishers Ltd.

Monetary reward magnitude effects on behavior and brain function during goal-directed behavior.

PubMed

Rosell-Negre, P; Bustamante, J C; Fuentes-Claramonte, P; Costumero, V; Benabarre, S; Barrós-Loscertales, A

2017-08-01

Reward may modulate the cognitive processes required for goal achievement, while individual differences in personality may affect reward modulation. Our aim was to test how different monetary reward magnitudes modulate brain activation and performance during goal-directed behavior, and whether individual differences in reward sensitivity affect this modulation. For this purpose, we scanned 37 subjects with a parametric design in which we varied the magnitude of monetary rewards (€0, €0.01, €0.5, €1 or €1.5) in a blocked fashion while participants performed an interference counting-Stroop condition. The results showed that the brain activity of left dorsolateral prefrontal cortex (DLPFC) and the striatum were modulated by increasing and decreasing reward magnitudes, respectively. Behavioral performance improved as the magnitude of monetary reward increased while comparing the non reward (€0) condition to any other reward condition, or the lower €0.01 to any other reward condition, and this improvement was related with individual differences in reward sensitivity. In conclusion, the locus of influence of monetary incentives overlaps the activity of the regions commonly involved in cognitive control.

SpecBit, DecayBit and PrecisionBit: GAMBIT modules for computing mass spectra, particle decay rates and precision observables

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Kvellestad, Anders; McKay, James; Putze, Antje; Rogan, Chris; Scott, Pat; Weniger, Christoph; White, Martin

2018-01-01

We present the GAMBIT modules SpecBit, DecayBit and PrecisionBit. Together they provide a new framework for linking publicly available spectrum generators, decay codes and other precision observable calculations in a physically and statistically consistent manner. This allows users to automatically run various combinations of existing codes as if they are a single package. The modular design allows software packages fulfilling the same role to be exchanged freely at runtime, with the results presented in a common format that can easily be passed to downstream dark matter, collider and flavour codes. These modules constitute an essential part of the broader GAMBIT framework, a major new software package for performing global fits. In this paper we present the observable calculations, data, and likelihood functions implemented in the three modules, as well as the conventions and assumptions used in interfacing them with external codes. We also present 3-BIT-HIT, a command-line utility for computing mass spectra, couplings, decays and precision observables in the MSSM, which shows how the three modules can easily be used independently of GAMBIT.

Magnetoelectric gradiometer with enhanced vibration rejection efficiency under H-field modulation

NASA Astrophysics Data System (ADS)

Xu, Junran; Zhuang, Xin; Leung, Chung Ming; Staruch, Margo; Finkel, Peter; Li, Jiefang; Viehland, D.

2018-03-01

A magnetoelectric (ME) gradiometer consisting of two Metglas/Pb(Zr,Ti)O3 fiber-based sensors has been developed. The equivalent magnetic noise of both sensors was first determined to be about 60 pT/√Hz while using an H-field modulation technique. The common mode rejection ratio of a gradiometer based on these two sensors was determined to be 74. The gradiometer response curve was then measured, which provided the dependence of the gradiometer output as a function of the source-gradiometer-normalized distance. Investigations in the presence of vibration noise revealed that a ME gradiometer consisting of two ME magnetometers working under H-field modulation was capable of significant vibration rejection. The results were compared to similar studies of ME gradiometers operated in a passive working mode. Our findings demonstrate that this active gradiometer has a good vibration rejection capability in the presence of both magnetic signals and vibration noise/interferences by using two magnetoelectric sensors operated under H-field modulation.

Descending pain modulation in irritable bowel syndrome (IBS): a systematic review and meta-analysis.

PubMed

Chakiath, Rosemary J; Siddall, Philip J; Kellow, John E; Hush, Julia M; Jones, Mike P; Marcuzzi, Anna; Wrigley, Paul J

2015-12-10

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. While abdominal pain is a dominant symptom of IBS, many sufferers also report widespread hypersensitivity and present with other chronic pain conditions. The presence of widespread hypersensitivity and extra-intestinal pain conditions suggests central nervous dysfunction. While central nervous system dysfunction may involve the spinal cord (central sensitisation) and brain, this review will focus on one brain mechanism, descending pain modulation. We will conduct a comprehensive search for the articles indexed in the databases Ovid MEDLINE, Ovid Embase, Ovid PsycINFO and Cochrane Central Register of Controlled Trial (CENTRAL) from their inception to August 2015, that report on any aspect of descending pain modulation in irritable bowel syndrome. Two independent reviewers will screen studies for eligibility, assess risk of bias and extract relevant data. Results will be tabulated and, if possible, a meta-analysis will be carried out. The systematic review outlined in this protocol aims to summarise current knowledge regarding descending pain modulation in IBS. PROSPERO CRD42015024284.

Design of an Optical System for Phase Retrieval based on a Spatial Light Modulator

NASA Astrophysics Data System (ADS)

Falldorf, Claas; Agour, Mostafa; von Kopylow, Christoph; Bergmann, Ralf B.

2010-04-01

We present an optical configuration for phase retrieval from a sequence of intensity measurements. The setup is based on a 4f-configuration with a phase modulating spatial light modulator (SLM) located in the Fourier domain. The SLM is used to modulate the incoming light with the transfer function of propagation, thus a sequence of propagated representations of the subjected wave field can be captured across a common sensor plane. The main advantage of this technique is the greatly reduced measurement time, since no mechanical adjustment of the camera sensor is required throughout the measurement process. The treatise is focused on the analysis of the wave field in the sensor domain. From the discussion a set of parameters is derived in order to minimize disturbing effects arising from the discrete nature of the SLM. Finally, the big potential of this approach is demonstrated by means of experimental investigations with regard to wave field sensing.

Experiment/facility requirements document for the Space Station Furnace Facility. Section 1: Integrated configuration

NASA Astrophysics Data System (ADS)

1992-05-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules which will be operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidification conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment; and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace. The SSFF support functions are provided by the following Core subsystems: power conditioning and distribution subsystem (SSFF PCDS); data management subsystem (SSFF DMS); thermal control Subsystem (SSFF TCS); gas distribution subsystem (SSFF GDS); and mechanical structures subsystem (SSFF MSS).

Experiment/facility requirements document for the Space Station Furnace Facility. Section 1: Integrated configuration

NASA Technical Reports Server (NTRS)

1992-01-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules which will be operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidification conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment; and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace. The SSFF support functions are provided by the following Core subsystems: power conditioning and distribution subsystem (SSFF PCDS); data management subsystem (SSFF DMS); thermal control Subsystem (SSFF TCS); gas distribution subsystem (SSFF GDS); and mechanical structures subsystem (SSFF MSS).

Methylphenidate Modulates Functional Network Connectivity to Enhance Attention

PubMed Central

Zhang, Sheng; Hsu, Wei-Ting; Scheinost, Dustin; Finn, Emily S.; Shen, Xilin; Constable, R. Todd; Li, Chiang-Shan R.; Chun, Marvin M.

2016-01-01

Recent work has demonstrated that human whole-brain functional connectivity patterns measured with fMRI contain information about cognitive abilities, including sustained attention. To derive behavioral predictions from connectivity patterns, our group developed a connectome-based predictive modeling (CPM) approach (Finn et al., 2015; Rosenberg et al., 2016). Previously using CPM, we defined a high-attention network, comprising connections positively correlated with performance on a sustained attention task, and a low-attention network, comprising connections negatively correlated with performance. Validating the networks as generalizable biomarkers of attention, models based on network strength at rest predicted attention-deficit/hyperactivity disorder (ADHD) symptoms in an independent group of individuals (Rosenberg et al., 2016). To investigate whether these networks play a causal role in attention, here we examined their strength in healthy adults given methylphenidate (Ritalin), a common ADHD treatment, compared with unmedicated controls. As predicted, individuals given methylphenidate showed patterns of connectivity associated with better sustained attention: higher high-attention and lower low-attention network strength than controls. There was significant overlap between the high-attention network and a network with greater strength in the methylphenidate group, and between the low-attention network and a network with greater strength in the control group. Network strength also predicted behavior on a stop-signal task, such that participants with higher go response rates showed higher high-attention and lower low-attention network strength. These results suggest that methylphenidate acts by modulating functional brain networks related to sustained attention, and that changing whole-brain connectivity patterns may help improve attention. SIGNIFICANCE STATEMENT Recent work identified a promising neuromarker of sustained attention based on whole-brain functional connectivity networks. To investigate the causal role of these networks in attention, we examined their response to a dose of methylphenidate, a common and effective treatment for attention-deficit/hyperactivity disorder, in healthy adults. As predicted, individuals on methylphenidate showed connectivity signatures of better sustained attention: higher high-attention and lower low-attention network strength than controls. These results suggest that methylphenidate acts by modulating strength in functional brain networks related to attention, and that changing whole-brain connectivity patterns may improve attention. PMID:27629707

Methylphenidate Modulates Functional Network Connectivity to Enhance Attention.

PubMed

Rosenberg, Monica D; Zhang, Sheng; Hsu, Wei-Ting; Scheinost, Dustin; Finn, Emily S; Shen, Xilin; Constable, R Todd; Li, Chiang-Shan R; Chun, Marvin M

2016-09-14

Recent work has demonstrated that human whole-brain functional connectivity patterns measured with fMRI contain information about cognitive abilities, including sustained attention. To derive behavioral predictions from connectivity patterns, our group developed a connectome-based predictive modeling (CPM) approach (Finn et al., 2015; Rosenberg et al., 2016). Previously using CPM, we defined a high-attention network, comprising connections positively correlated with performance on a sustained attention task, and a low-attention network, comprising connections negatively correlated with performance. Validating the networks as generalizable biomarkers of attention, models based on network strength at rest predicted attention-deficit/hyperactivity disorder (ADHD) symptoms in an independent group of individuals (Rosenberg et al., 2016). To investigate whether these networks play a causal role in attention, here we examined their strength in healthy adults given methylphenidate (Ritalin), a common ADHD treatment, compared with unmedicated controls. As predicted, individuals given methylphenidate showed patterns of connectivity associated with better sustained attention: higher high-attention and lower low-attention network strength than controls. There was significant overlap between the high-attention network and a network with greater strength in the methylphenidate group, and between the low-attention network and a network with greater strength in the control group. Network strength also predicted behavior on a stop-signal task, such that participants with higher go response rates showed higher high-attention and lower low-attention network strength. These results suggest that methylphenidate acts by modulating functional brain networks related to sustained attention, and that changing whole-brain connectivity patterns may help improve attention. Recent work identified a promising neuromarker of sustained attention based on whole-brain functional connectivity networks. To investigate the causal role of these networks in attention, we examined their response to a dose of methylphenidate, a common and effective treatment for attention-deficit/hyperactivity disorder, in healthy adults. As predicted, individuals on methylphenidate showed connectivity signatures of better sustained attention: higher high-attention and lower low-attention network strength than controls. These results suggest that methylphenidate acts by modulating strength in functional brain networks related to attention, and that changing whole-brain connectivity patterns may improve attention. Copyright © 2016 the authors 0270-6474/16/369547-11$15.00/0.

Standardized Solution for Management Controller for MTCA.4

NASA Astrophysics Data System (ADS)

Makowski, D.; Fenner, M.; Ludwig, F.; Mavrič, U.; Mielczarek, A.; Napieralski, A.; Perek, P.; Schlarb, H.

2015-06-01

The Micro Telecommunications Computing Architecture (MTCA) standard is a modern platform that is gaining popularity in the area of High Energy Physics (HEP) experiments. The standard provides extensive management, monitoring and diagnostics functionalities. The hardware control and monitoring is based on the Intelligent Platform Management Interface (IPMI), that was initially developed for supervision of complex computers operation. The original IPMI specification was extended to support functions required by the MTCA specification. The Module Management Controller (MMC) is required on each Advanced Mezzanine Card (AMC) installed in MTCA chassis. The Rear Transition Modules (RTMs) have to be equipped with RTM Management Controllers (RMCs) which is required by the MTCA.4 subsidiary specification. The commercially available implementations of MMC and RMC are expensive and do not provide the complete functionality that is required by specific HEP applications. Therefore, many research centers and commercial companies work on their own implementation of AMC and RTM controllers. The available implementations suffer because of lack of common approach and interoperability problems. Since both Lodz University of Technology (TUL) and Deutsches Elektronen-Synchrotron (DESY) have long-term experience in developing ATCA and MTCA hardware, the authors decided to develop a unified solution of management controller fully compliant with AMC and MTCA.4 standards. The MMC v1.00 solution is dedicated for management of AMC and RTM modules. The MMC v1.00 is based on Atmel ATxmega MCUs and can be fully customized by the user or used as a drop-in-module without any modifications. The paper discusses the functionality of the MMC v1.00 solution. The implementation was verified with developed evaluation kits for AMC and RTM cards.

Instructional strategies to improve women's attitudes toward science

NASA Astrophysics Data System (ADS)

Newbill, Phyllis Leary

Although negative attitudes toward science are common among women and men in undergraduate introductory science classes, women's attitudes toward science tend to be more negative than men's. The reasons for women's negative attitudes toward science include lack of self-confidence, fear of association with social outcasts, lack of women role models in science, and the fundamental differences between traditional scientific and feminist values. Attitudes are psychological constructs theorized to be composed of emotional, cognitive, and behavioral components. Attitudes serve functions, including social expressive, value expressive, utilitarian, and defensive functions, for the people who hold them. To change attitudes, the new attitudes must serve the same function as the old one, and all three components must be treated. Instructional designers can create instructional environments to effect attitude change. In designing instruction to improve women's attitudes toward science, instructional designers should (a) address the emotions that are associated with existing attitudes, (b) involve credible, attractive women role models, and (c) address the functions of the existing attitudes. Two experimental instructional modules were developed based on these recommendations, and two control modules were developed that were not based on these recommendations. The asynchronous, web-based modules were administered to 281 undergraduate geology and chemistry students at two universities. Attitude assessment revealed that attitudes toward scientists improved significantly more in the experimental group, although there was no significant difference in overall attitudes toward science. Women's attitudes improved significantly more than men's in both the experimental and control groups. Students whose attitudes changed wrote significantly more in journaling activities associated with the modules. Qualitative analysis of journals revealed that the guidelines worked exactly as predicted for some students.

Biological mechanism analysis of acute renal allograft rejection: integrated of mRNA and microRNA expression profiles.

PubMed

Huang, Shi-Ming; Zhao, Xia; Zhao, Xue-Mei; Wang, Xiao-Ying; Li, Shan-Shan; Zhu, Yu-Hui

2014-01-01

Renal transplantation is the preferred method for most patients with end-stage renal disease, however, acute renal allograft rejection is still a major risk factor for recipients leading to renal injury. To improve the early diagnosis and treatment of acute rejection, study on the molecular mechanism of it is urgent. MicroRNA (miRNA) expression profile and mRNA expression profile of acute renal allograft rejection and well-functioning allograft downloaded from ArrayExpress database were applied to identify differentially expressed (DE) miRNAs and DE mRNAs. DE miRNAs targets were predicted by combining five algorithm. By overlapping the DE mRNAs and DE miRNAs targets, common genes were obtained. Differentially co-expressed genes (DCGs) were identified by differential co-expression profile (DCp) and differential co-expression enrichment (DCe) methods in Differentially Co-expressed Genes and Links (DCGL) package. Then, co-expression network of DCGs and the cluster analysis were performed. Functional enrichment analysis for DCGs was undergone. A total of 1270 miRNA targets were predicted and 698 DE mRNAs were obtained. While overlapping miRNA targets and DE mRNAs, 59 common genes were gained. We obtained 103 DCGs and 5 transcription factors (TFs) based on regulatory impact factors (RIF), then built the regulation network of miRNA targets and DE mRNAs. By clustering the co-expression network, 5 modules were obtained. Thereinto, module 1 had the highest degree and module 2 showed the most number of DCGs and common genes. TF CEBPB and several common genes, such as RXRA, BASP1 and AKAP10, were mapped on the co-expression network. C1R showed the highest degree in the network. These genes might be associated with human acute renal allograft rejection. We conducted biological analysis on integration of DE mRNA and DE miRNA in acute renal allograft rejection, displayed gene expression patterns and screened out genes and TFs that may be related to acute renal allograft rejection.

Biological mechanism analysis of acute renal allograft rejection: integrated of mRNA and microRNA expression profiles

PubMed Central

Huang, Shi-Ming; Zhao, Xia; Zhao, Xue-Mei; Wang, Xiao-Ying; Li, Shan-Shan; Zhu, Yu-Hui

2014-01-01

Objectives: Renal transplantation is the preferred method for most patients with end-stage renal disease, however, acute renal allograft rejection is still a major risk factor for recipients leading to renal injury. To improve the early diagnosis and treatment of acute rejection, study on the molecular mechanism of it is urgent. Methods: MicroRNA (miRNA) expression profile and mRNA expression profile of acute renal allograft rejection and well-functioning allograft downloaded from ArrayExpress database were applied to identify differentially expressed (DE) miRNAs and DE mRNAs. DE miRNAs targets were predicted by combining five algorithm. By overlapping the DE mRNAs and DE miRNAs targets, common genes were obtained. Differentially co-expressed genes (DCGs) were identified by differential co-expression profile (DCp) and differential co-expression enrichment (DCe) methods in Differentially Co-expressed Genes and Links (DCGL) package. Then, co-expression network of DCGs and the cluster analysis were performed. Functional enrichment analysis for DCGs was undergone. Results: A total of 1270 miRNA targets were predicted and 698 DE mRNAs were obtained. While overlapping miRNA targets and DE mRNAs, 59 common genes were gained. We obtained 103 DCGs and 5 transcription factors (TFs) based on regulatory impact factors (RIF), then built the regulation network of miRNA targets and DE mRNAs. By clustering the co-expression network, 5 modules were obtained. Thereinto, module 1 had the highest degree and module 2 showed the most number of DCGs and common genes. TF CEBPB and several common genes, such as RXRA, BASP1 and AKAP10, were mapped on the co-expression network. C1R showed the highest degree in the network. These genes might be associated with human acute renal allograft rejection. Conclusions: We conducted biological analysis on integration of DE mRNA and DE miRNA in acute renal allograft rejection, displayed gene expression patterns and screened out genes and TFs that may be related to acute renal allograft rejection. PMID:25664019

Ion Channel Modulators in Cystic Fibrosis.

PubMed

Gentzsch, Martina; Mall, Marcus A

2018-05-08

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and remains one of the most common life-shortening genetic diseases affecting the lung and other organs. CFTR functions as a cAMP-dependent anion channel that transports chloride and bicarbonate across epithelial surfaces and disruption of these ion transport processes plays a central role in the pathogenesis of CF. These findings provided the rationale for pharmacological modulation of ion transport, either by targeting mutant CFTR or alternative ion channels that can compensate for CFTR dysfunction, as a promising therapeutic approach. High throughput screening has supported the development of CFTR modulator compounds. CFTR correctors are designed to improve defective protein processing, trafficking and cell surface expression, whereas potentiators increase the activity of mutant CFTR at the cell surface. The approval of the first potentiator ivacaftor for the treatment of patients with specific CFTR mutations and, more recently the corrector lumacaftor in combination with ivacaftor for patients homozygous for the common F508del mutation, were major breakthroughs on the path to causal therapies for all patients with CF. In this review, we focus on recent developments and remaining challenges of CFTR-directed therapies, as well as modulators of other ion channels such as alternative chloride channels and the epithelial sodium channel (ENaC) as additional targets in CF lung disease. Further, we discuss how patient-derived precision medicine models may aid the translation of emerging next generation ion channel modulators from the laboratory to the clinic and tailor their use for optimal therapeutic benefits in individual patients with CF. Copyright © 2018. Published by Elsevier Inc.

htsint: a Python library for sequencing pipelines that combines data through gene set generation.

PubMed

Richards, Adam J; Herrel, Anthony; Bonneaud, Camille

2015-09-24

Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint.

Identification of common coexpression modules based on quantitative network comparison.

PubMed

Jo, Yousang; Kim, Sanghyeon; Lee, Doheon

2018-06-13

Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington's disease and brain aging by the new method. We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington's disease-aging coexpression module pairs. We identified similar Huntington's disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex.

A Multi-Purpose Modular Electronics Integration Node for Exploration Extravehicular Activity

NASA Technical Reports Server (NTRS)

Hodgson, Edward; Papale, William; Wichowski, Robert; Rosenbush, David; Hawes, Kevin; Stankiewicz, Tom

2013-01-01

As NASA works to develop an effective integrated portable life support system design for exploration Extravehicular activity (EVA), alternatives to the current system s electrical power and control architecture are needed to support new requirements for flexibility, maintainability, reliability, and reduced mass and volume. Experience with the current Extravehicular Mobility Unit (EMU) has demonstrated that the current architecture, based in a central power supply, monitoring and control unit, with dedicated analog wiring harness connections to active components in the system has a significant impact on system packaging and seriously constrains design flexibility in adapting to component obsolescence and changing system needs over time. An alternative architecture based in the use of a digital data bus offers possible wiring harness and system power savings, but risks significant penalties in component complexity and cost. A hybrid architecture that relies on a set of electronic and power interface nodes serving functional models within the Portable Life Support System (PLSS) is proposed to minimize both packaging and component level penalties. A common interface node hardware design can further reduce penalties by reducing the nonrecurring development costs, making miniaturization more practical, maximizing opportunities for maturation and reliability growth, providing enhanced fault tolerance, and providing stable design interfaces for system components and a central control. Adaptation to varying specific module requirements can be achieved with modest changes in firmware code within the module. A preliminary design effort has developed a common set of hardware interface requirements and functional capabilities for such a node based on anticipated modules comprising an exploration PLSS, and a prototype node has been designed assembled, programmed, and tested. One instance of such a node has been adapted to support testing the swingbed carbon dioxide and humidity control element in NASA s advanced PLSS 2.0 test article. This paper will describe the common interface node design concept, results of the prototype development and test effort, and plans for use in NASA PLSS 2.0 integrated tests.

Readout from iconic memory and selective spatial attention involve similar neural processes.

PubMed

Ruff, Christian C; Kristjánsson, Arni; Driver, Jon

2007-10-01

Iconic memory and spatial attention are often considered separately, but they may have functional similarities. Here we provide functional magnetic resonance imaging evidence for some common underlying neural effects. Subjects judged three visual stimuli in one hemifield of a bilateral array comprising six stimuli. The relevant hemifield for partial report was indicated by an auditory cue, administered either before the visual array (precue, spatial attention) or shortly after the array (postcue, iconic memory). Pre- and postcues led to similar activity modulations in lateral occipital cortex contralateral to the cued side. This finding indicates that readout from iconic memory can have some neural effects similar to those of spatial attention. We also found common bilateral activation of a fronto-parietal network for postcue and precue trials. These neuroimaging data suggest that some common neural mechanisms underlie selective spatial attention and readout from iconic memory. Some differences were also found; compared with precues, postcues led to higher activity in the right middle frontal gyrus.

Readout From Iconic Memory and Selective Spatial Attention Involve Similar Neural Processes

PubMed Central

Ruff, Christian C; Kristjánsson, Árni; Driver, Jon

2007-01-01

Iconic memory and spatial attention are often considered separately, but they may have functional similarities. Here we provide functional magnetic resonance imaging evidence for some common underlying neural effects. Subjects judged three visual stimuli in one hemifield of a bilateral array comprising six stimuli. The relevant hemifield for partial report was indicated by an auditory cue, administered either before the visual array (precue, spatial attention) or shortly after the array (postcue, iconic memory). Pre- and postcues led to similar activity modulations in lateral occipital cortex contralateral to the cued side. This finding indicates that readout from iconic memory can have some neural effects similar to those of spatial attention. We also found common bilateral activation of a fronto-parietal network for postcue and precue trials. These neuroimaging data suggest that some common neural mechanisms underlie selective spatial attention and readout from iconic memory. Some differences were also found; compared with precues, postcues led to higher activity in the right middle frontal gyrus. PMID:17894608

Performance effects of nicotine during selective attention, divided attention, and simple stimulus detection: an fMRI study.

PubMed

Hahn, Britta; Ross, Thomas J; Wolkenberg, Frank A; Shakleya, Diaa M; Huestis, Marilyn A; Stein, Elliot A

2009-09-01

Attention-enhancing effects of nicotine appear to depend on the nature of the attentional function. Underlying neuroanatomical mechanisms, too, may vary depending on the function modulated. This functional magnetic resonance imaging study recorded blood oxygen level-dependent (BOLD) activity in minimally deprived smokers during tasks of simple stimulus detection, selective attention, or divided attention after single-blind application of a transdermal nicotine (21 mg) or placebo patch. Smokers' performance in the placebo condition was unimpaired as compared with matched nonsmokers. Nicotine reduced reaction time (RT) in the stimulus detection and selective attention but not divided attention condition. Across all task conditions, nicotine reduced activation in frontal, temporal, thalamic, and visual regions and enhanced deactivation in so-called "default" regions. Thalamic effects correlated with RT reduction selectively during stimulus detection. An interaction with task condition was observed in middle and superior frontal gyri, where nicotine reduced activation only during stimulus detection. A visuomotor control experiment provided evidence against nonspecific effects of nicotine. In conclusion, although prefrontal activity partly displayed differential modulation by nicotine, most BOLD effects were identical across tasks, despite differential performance effects, suggesting that common neuronal mechanisms can selectively benefit different attentional functions. Overall, the effects of nicotine may be explained by increased functional efficiency and downregulated task-independent "default" functions.

Automatic Traffic-Based Internet Control Message Protocol (ICMP) Model Generation for ns-3

DTIC Science & Technology

2015-12-01

through visiting the inferred automata o Fuzzing of an implementation by generating altered message formats We tested with 3 versions of Netzob. First...relationships. Afterwards, we used the Automata module to generate state machines using different functions: “generateChainedStateAutomata...The “generatePTAAutomata” takes as input several communication sessions and then identifies common paths and merges these into a single automata . The

A Common Interface Real-Time Multiprocessor Operating System for Embedded Systems

DTIC Science & Technology

1991-03-04

Pressman , a design methodology should show hierarchical organization, lead to modules exhibiting independent functional characteristics, and be derived...Boehm, Barry W. "Software Engineering," Tutorial: Software Design Strategies, 2nd Edition. 35-50. Los Angeles CA: IEEE Computer Society Press, 1981... Pressman , Roger S. Software Engineering: A Practitioner’s Approach, Second Edi- tion. McGraw-Hill Book Company, New York, 1988. 59. Quinn, Michael J

Improving Legacy Aircraft Systems Through Condition-Based Maintenance: An H-60 Case Study

DTIC Science & Technology

2014-09-01

level functions. These decompositions are equivalent to a detailed design effort in systems engineering. NAMPSOPs have a common architectural structure...Assembly Power Available Spindle Cables No.1 Engine Load Demand Spindle Control Cables Engine Pneumatic Starters Auxiliary Power Unit IRCM FLIR Mission...Analysis Fuel System Main Rotor Head Main Module Main Gear Box Radiator Engine Output Shaft Auxiliary Power Unit Flight Control Cables Tail Landing

Using Tradtional Ecological Knowledge to Protect Wetlands: the Swinomish Tribe's Wetland Cultural Assessment Project

NASA Astrophysics Data System (ADS)

Mitchell, T.

2017-12-01

"Traditional" wetland physical assessment modules do not adequately identify Tribal cultural values of wetlands and thus wetlands may not be adequately protected for cultural uses. This Swinomish Wetlands Cultural Assessment Project has developed a cultural resource scoring module that can be incorporated into wetland assessments to better inform wetland protections. Local native knowledge was gathered about the traditional uses of 99 native wetland plant species. A cultural scoring matrix was developed based on the presence of traditionally used plants in several use categories including: construction, ceremonial, subsistence, medicinal, common use, plant rarity, and place of value for each wetland. The combined score of the cultural and physcial modules provides an overall wetland score that relates to proscribed buffer protection widths. With this local native knowledge incorporated into wetland assessments, we are protecting and preserving Swinomish Reservation wetlands for both cultural uses and ecological functionality through the Tribe's wetland protection law.

simBio: a Java package for the development of detailed cell models.

PubMed

Sarai, Nobuaki; Matsuoka, Satoshi; Noma, Akinori

2006-01-01

Quantitative dynamic computer models, which integrate a variety of molecular functions into a cell model, provide a powerful tool to create and test working hypotheses. We have developed a new modeling tool, the simBio package (freely available from ), which can be used for constructing cell models, such as cardiac cells (the Kyoto model from Matsuoka et al., 2003, 2004 a, b, the LRd model from Faber and Rudy, 2000, and the Noble 98 model from Noble et al., 1998), epithelial cells (Strieter et al., 1990) and pancreatic beta cells (Magnus and Keizer, 1998). The simBio package is written in Java, uses XML and can solve ordinary differential equations. In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models. This way of building models, through the combination of various modules, is enabled through the use of object-oriented programming concepts. Thus, simBio is a straightforward system for the creation of a variety of cell models on a common database of functional modules.

Sexy DEG/ENaC channels involved in gustatory detection of fruit fly pheromones.

PubMed

Pikielny, Claudio W

2012-11-06

Hydrocarbon pheromones on the cuticle of Drosophila melanogaster modulate the complex courtship behavior of males. Recently, three members of the degenerin/epithelial Na+ channel (DEG/ENaC) family of sodium channel subunits, Ppk25, Ppk23, and Ppk29 (also known as Nope), have been shown to function in gustatory perception of courtship-modulating contact pheromones. All three proteins are required for the activation of male courtship by female pheromones. Specific interactions between two of them have been demonstrated in cultured cells, suggesting that, in a subset of cells where they are coexpressed, these three subunits function within a common heterotrimeric DEG/ENaC channel. Such a DEG/ENaC channel may be gated by pheromones, either directly or indirectly, or alternatively may control the excitability of pheromone-sensing cells. In addition, these studies identify taste neurons that respond specifically to courtship-modulating pheromones and mediate their effects on male behavior. Two types of pheromone-sensing taste neurons, F and M cells, have been defined on the basis of their specific response to either female or male pheromones. These reports set the stage for the dissection of the molecular and cellular mechanisms that mediate gustatory detection of contact pheromones.

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.

PubMed

Wang, Jianxin; Zhong, Jiancheng; Chen, Gang; Li, Min; Wu, Fang-xiang; Pan, Yi

2015-01-01

Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

Dissociable influences of opiates and expectations on pain

PubMed Central

Atlas, Lauren Y.; Whittington, Robert A.; Lindquist, Martin A.; Wielgosz, Joe; Sonty, Nomita; Wager, Tor D.

2012-01-01

Placebo treatments and opiate drugs are thought to have common effects on the opioid system and pain-related brain processes. This has created excitement about the potential for expectations to modulate drug effects themselves. If drug effects differ as a function of belief, this would challenge the assumptions underlying the standard clinical trial. We conducted two studies to directly examine the relationship between expectations and opioid analgesia. We administered the opioid agonist remifentanil to human subjects during experimental thermal pain and manipulated participants’ knowledge of drug delivery using an open-hidden design. This allowed us to test drug effects, expectancy (knowledge) effects, and their interactions on pain reports and pain-related responses in the brain. Remifentanil and expectancy both reduced pain, but drug effects on pain reports and fMRI activity did not interact with expectancy. Regions associated with pain processing showed drug-induced modulation during both Open and Hidden conditions, with no differences in drug effects as a function of expectation. Instead, expectancy modulated activity in frontal cortex, with a separable time course from drug effects. These findings reveal that opiates and placebo treatments both influence clinically relevant outcomes and operate without mutual interference. PMID:22674280

Dietary Additive Probiotics Modulation of the Intestinal Microbiota.

PubMed

Hu, Shenglan; Wang, Li; Jiang, Zongyong

2017-01-01

The importance of the intestinal microbiota of animals is widely acknowledged because of its vital role in the health of animals. There are complex communities of microbiota, which colonize the gastrointestinal tract. Intestinal microbiota are conductive to animal health and the development of the host immune system. Probiotics are commonly used dietary additives where they provide the host with many beneficial functions, such as modulating intestinal homeostasis and promoting gut health. These beneficial effects of probiotics may accrue from the inhibiting the growth of pathogenic bacteria and promoting the growth of beneficial flora in the gastrointestinal tract. Probiotics colonization and its impact on gut microbiota members are highly species specific. Different probiotics have been shown to have dramatically different capacities of modulation physiological function. This review summarizes existing studies of the influence of dietary additive probiotics on the gut microbiota in different animals, such as humans, mice, pigs and chickens, to clarify the contribution of different kinds of probiotics to the intestinal microbiota. Moreover, the probable mechanism for the benefits of dietary supplementation with probiotics will be discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Honey Bee Allatostatins Target Galanin/Somatostatin-Like Receptors and Modulate Learning: A Conserved Function?

PubMed Central

Urlacher, Elodie; Soustelle, Laurent; Parmentier, Marie-Laure; Verlinden, Heleen; Gherardi, Marie-Julie; Fourmy, Daniel; Mercer, Alison R.

2016-01-01

Sequencing of the honeybee genome revealed many neuropeptides and putative neuropeptide receptors, yet functional characterization of these peptidic systems is scarce. In this study, we focus on allatostatins, which were first identified as inhibitors of juvenile hormone synthesis, but whose role in the adult honey bee (Apis mellifera) brain remains to be determined. We characterize the bee allatostatin system, represented by two families: allatostatin A (Apime-ASTA) and its receptor (Apime-ASTA-R); and C-type allatostatins (Apime-ASTC and Apime-ASTCC) and their common receptor (Apime-ASTC-R). Apime-ASTA-R and Apime-ASTC-R are the receptors in bees most closely related to vertebrate galanin and somatostatin receptors, respectively. We examine the functional properties of the two honeybee receptors and show that they are transcriptionally expressed in the adult brain, including in brain centers known to be important for learning and memory processes. Thus we investigated the effects of exogenously applied allatostatins on appetitive olfactory learning in the bee. Our results show that allatostatins modulate learning in this insect, and provide important insights into the evolution of somatostatin/allatostatin signaling. PMID:26741132

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.

PubMed

Machiela, Mitchell J; Chanock, Stephen J

2015-11-01

Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. mitchell.machiela@nih.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Cortical organization of inhibition-related functions and modulation by psychopathology

PubMed Central

Warren, Stacie L.; Crocker, Laura D.; Spielberg, Jeffery M.; Engels, Anna S.; Banich, Marie T.; Sutton, Bradley P.; Miller, Gregory A.; Heller, Wendy

2013-01-01

Individual differences in inhibition-related functions have been implicated as risk factors for a broad range of psychopathology, including anxiety and depression. Delineating neural mechanisms of distinct inhibition-related functions may clarify their role in the development and maintenance of psychopathology. The present study tested the hypothesis that activity in common and distinct brain regions would be associated with an ecologically sensitive, self-report measure of inhibition and a laboratory performance measure of prepotent response inhibition. Results indicated that sub-regions of DLPFC distinguished measures of inhibition, whereas left inferior frontal gyrus and bilateral inferior parietal cortex were associated with both types of inhibition. Additionally, co-occurring anxiety and depression modulated neural activity in select brain regions associated with response inhibition. Results imply that specific combinations of anxiety and depression dimensions are associated with failure to implement top-down attentional control as reflected in inefficient recruitment of posterior DLPFC and increased activation in regions associated with threat (MTG) and worry (BA10). Present findings elucidate possible neural mechanisms of interference that could help explain executive control deficits in psychopathology. PMID:23781192

Cortical organization of inhibition-related functions and modulation by psychopathology.

PubMed

Warren, Stacie L; Crocker, Laura D; Spielberg, Jeffery M; Engels, Anna S; Banich, Marie T; Sutton, Bradley P; Miller, Gregory A; Heller, Wendy

2013-01-01

Individual differences in inhibition-related functions have been implicated as risk factors for a broad range of psychopathology, including anxiety and depression. Delineating neural mechanisms of distinct inhibition-related functions may clarify their role in the development and maintenance of psychopathology. The present study tested the hypothesis that activity in common and distinct brain regions would be associated with an ecologically sensitive, self-report measure of inhibition and a laboratory performance measure of prepotent response inhibition. Results indicated that sub-regions of DLPFC distinguished measures of inhibition, whereas left inferior frontal gyrus and bilateral inferior parietal cortex were associated with both types of inhibition. Additionally, co-occurring anxiety and depression modulated neural activity in select brain regions associated with response inhibition. Results imply that specific combinations of anxiety and depression dimensions are associated with failure to implement top-down attentional control as reflected in inefficient recruitment of posterior DLPFC and increased activation in regions associated with threat (MTG) and worry (BA10). Present findings elucidate possible neural mechanisms of interference that could help explain executive control deficits in psychopathology.

Hormones and the hippocampus.

PubMed

Lathe, R

2001-05-01

Hippocampal lesions produce memory deficits, but the exact function of the hippocampus remains obscure. Evidence is presented that its role in memory may be ancillary to physiological regulation. Molecular studies demonstrate that the hippocampus is a primary target for ligands that reflect body physiology, including ion balance and blood pressure, immunity, pain, reproductive status, satiety and stress. Hippocampal receptors are functional, probably accessible to their ligands, and mediate physiological and cognitive changes. This argues that an early role of the hippocampus may have been in sensing soluble molecules (termed here 'enteroception') in blood and cerebrospinal fluid, perhaps reflecting a common evolutionary origin with the olfactory system ('exteroception'). Functionally, hippocampal enteroception may reflect feedback control; evidence is reviewed that the hippocampus modulates body physiology, including the activity of the hypothalamus-pituitary-adrenal axis, blood pressure, immunity, and reproductive function. It is suggested that the hippocampus operates, in parallel with the amygdala, to modulate body physiology in response to cognitive stimuli. Hippocampal outputs are predominantly inhibitory on downstream neuroendocrine activity; increased synaptic efficacy in the hippocampus (e.g. long-term potentiation) could facilitate throughput inhibition. This may have implications for the role of the hippocampus and long-term potentiation in memory.

White matter hyperintensities and cognitive reserve during a working memory task: a functional magnetic resonance imaging study in cognitively normal older adults.

PubMed

Fernández-Cabello, Sara; Valls-Pedret, Cinta; Schurz, Matthias; Vidal-Piñeiro, Dídac; Sala-Llonch, Roser; Bargallo, Nuria; Ros, Emilio; Bartrés-Faz, David

2016-12-01

Cognitive reserve (CR) models posit that lifestyle factors such as education modulate the relationship between brain damage and cognition. However, the functional correlates of CR in healthy aging are still under investigation. White matter hyperintensities (WMHs) are a common age-associated finding that impacts cognition. In this study, we used functional magnetic resonance imaging to characterize the patterns of brain activation during a working memory task in older participants with high and low levels of education (as a proxy of CR) and high and low WMH volumes. Ninety older volunteers (aged 63-76 years) and 16 young adults (aged 21-27) completed the study. We found that older adults with higher education had better working memory performance than their less educated peers. Among the highly educated participants, those with WMH over-recruited areas engaged by young volunteers and showed activation in additional cortical and subcortical structures. However, those with low WMH differed little with respect to their younger counterparts. Our findings demonstrate that the functional mechanisms subtending the effects of education, as a proxy of CR, are modulated according to the WMH burden. Copyright © 2016 Elsevier Inc. All rights reserved.

A Calmodulin C-Lobe Ca2+-Dependent Switch Governs Kv7 Channel Function.

PubMed

Chang, Aram; Abderemane-Ali, Fayal; Hura, Greg L; Rossen, Nathan D; Gate, Rachel E; Minor, Daniel L

2018-02-21

Kv7 (KCNQ) voltage-gated potassium channels control excitability in the brain, heart, and ear. Calmodulin (CaM) is crucial for Kv7 function, but how this calcium sensor affects activity has remained unclear. Here, we present X-ray crystallographic analysis of CaM:Kv7.4 and CaM:Kv7.5 AB domain complexes that reveal an Apo/CaM clamp conformation and calcium binding preferences. These structures, combined with small-angle X-ray scattering, biochemical, and functional studies, establish a regulatory mechanism for Kv7 CaM modulation based on a common architecture in which a CaM C-lobe calcium-dependent switch releases a shared Apo/CaM clamp conformation. This C-lobe switch inhibits voltage-dependent activation of Kv7.4 and Kv7.5 but facilitates Kv7.1, demonstrating that mechanism is shared by Kv7 isoforms despite the different directions of CaM modulation. Our findings provide a unified framework for understanding how CaM controls different Kv7 isoforms and highlight the role of membrane proximal domains for controlling voltage-gated channel function. VIDEO ABSTRACT. Copyright © 2018 Elsevier Inc. All rights reserved.

Brain networks and their origins. Comment on “Understanding brain networks and brain organization” by Luiz Pessoa

NASA Astrophysics Data System (ADS)

Cisek, Paul

2014-09-01

Nearly every textbook on psychology or neuroscience contains theories of function described with box and arrow diagrams. Sometimes, the boxes stand for purely theoretical constructs, such as attention or working memory, and sometimes they also correspond to specific brain regions or systems, such as parietal or prefrontal cortex, and the arrows between them to known anatomical pathways. It is common for scientists (present company included) to summarize their theories in this way and to think of the brain as a set of interacting modules with clearly distinguishable functions.

A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2

PubMed Central

Hambly, Emma; Tétart, Francoise; Desplats, Carine; Wilson, William H.; Krisch, Henry M.; Mann, Nicholas H.

2001-01-01

Sequence analysis of a 10-kb region of the genome of the marine cyanomyovirus S-PM2 reveals a homology to coliphage T4 that extends as a contiguous block from gene (g)18 to g23. The order of the S-PM2 genes in this region is similar to that of T4, but there are insertions and deletions of small ORFs of unknown function. In T4, g18 codes for the tail sheath, g19, the tail tube, g20, the head portal protein, g21, the prohead core protein, g22, a scaffolding protein, and g23, the major capsid protein. Thus, the entire module that determines the structural components of the phage head and contractile tail is conserved between T4 and this cyanophage. The significant differences in the morphology of these phages must reflect the considerable divergence of the amino acid sequence of their homologous virion proteins, which uniformly exceeds 50%. We suggest that their enormous diversity in the sea could be a result of genetic shuffling between disparate phages mediated by such commonly shared modules. These conserved sequences could facilitate genetic exchange by providing partially homologous substrates for recombination between otherwise divergent phage genomes. Such a mechanism would thus expand the pool of phage genes accessible by recombination to all those phages that share common modules. PMID:11553768

Cell Elasticity Determines Macrophage Function

PubMed Central

Patel, Naimish R.; Bole, Medhavi; Chen, Cheng; Hardin, Charles C.; Kho, Alvin T.; Mih, Justin; Deng, Linhong; Butler, James; Tschumperlin, Daniel; Fredberg, Jeffrey J.; Krishnan, Ramaswamy; Koziel, Henry

2012-01-01

Macrophages serve to maintain organ homeostasis in response to challenges from injury, inflammation, malignancy, particulate exposure, or infection. Until now, receptor ligation has been understood as being the central mechanism that regulates macrophage function. Using macrophages of different origins and species, we report that macrophage elasticity is a major determinant of innate macrophage function. Macrophage elasticity is modulated not only by classical biologic activators such as LPS and IFN-γ, but to an equal extent by substrate rigidity and substrate stretch. Macrophage elasticity is dependent upon actin polymerization and small rhoGTPase activation, but functional effects of elasticity are not predicted by examination of gene expression profiles alone. Taken together, these data demonstrate an unanticipated role for cell elasticity as a common pathway by which mechanical and biologic factors determine macrophage function. PMID:23028423

TMEM237 Is Mutated in Individuals with a Joubert Syndrome Related Disorder and Expands the Role of the TMEM Family at the Ciliary Transition Zone

PubMed Central

Huang, Lijia; Szymanska, Katarzyna; Jensen, Victor L.; Janecke, Andreas R.; Innes, A. Micheil; Davis, Erica E.; Frosk, Patrick; Li, Chunmei; Willer, Jason R.; Chodirker, Bernard N.; Greenberg, Cheryl R.; McLeod, D. Ross; Bernier, Francois P.; Chudley, Albert E.; Müller, Thomas; Shboul, Mohammad; Logan, Clare V.; Loucks, Catrina M.; Beaulieu, Chandree L.; Bowie, Rachel V.; Bell, Sandra M.; Adkins, Jonathan; Zuniga, Freddi I.; Ross, Kevin D.; Wang, Jian; Ban, Matthew R.; Becker, Christian; Nürnberg, Peter; Douglas, Stuart; Craft, Cheryl M.; Akimenko, Marie-Andree; Hegele, Robert A.; Ober, Carole; Utermann, Gerd; Bolz, Hanno J.; Bulman, Dennis E.; Katsanis, Nicholas; Blacque, Oliver E.; Doherty, Dan; Parboosingh, Jillian S.; Leroux, Michel R.; Johnson, Colin A.; Boycott, Kym M.

2011-01-01

Joubert syndrome related disorders (JSRDs) have broad but variable phenotypic overlap with other ciliopathies. The molecular etiology of this overlap is unclear but probably arises from disrupting common functional module components within primary cilia. To identify additional module elements associated with JSRDs, we performed homozygosity mapping followed by next-generation sequencing (NGS) and uncovered mutations in TMEM237 (previously known as ALS2CR4). We show that loss of the mammalian TMEM237, which localizes to the ciliary transition zone (TZ), results in defective ciliogenesis and deregulation of Wnt signaling. Furthermore, disruption of Danio rerio (zebrafish) tmem237 expression produces gastrulation defects consistent with ciliary dysfunction, and Caenorhabditis elegans jbts-14 genetically interacts with nphp-4, encoding another TZ protein, to control basal body-TZ anchoring to the membrane and ciliogenesis. Both mammalian and C. elegans TMEM237/JBTS-14 require RPGRIP1L/MKS5 for proper TZ localization, and we demonstrate additional functional interactions between C. elegans JBTS-14 and MKS-2/TMEM216, MKSR-1/B9D1, and MKSR-2/B9D2. Collectively, our findings integrate TMEM237/JBTS-14 in a complex interaction network of TZ-associated proteins and reveal a growing contribution of a TZ functional module to the spectrum of ciliopathy phenotypes. PMID:22152675

Viva La Diferencia! Segundo Modulo de una Serie para Maestros de Escuela Elemental (Long Live the Difference! Second Module of a Series for Elementary School Teachers).

ERIC Educational Resources Information Center

Molina, Carmen Eneida, Ed.; And Others

This guide, in English and Spanish, is designed to provide teachers with a scientific basis for identifying myths and distortions about men and women. A pre-test and post-test are included to measure the user's awareness of stereotypes. Object lessons address the following areas: (1) common sexual stereotypes; (2) sexual functions; (3) the…

Modular avionics packaging standardization

NASA Astrophysics Data System (ADS)

Austin, M.; McNichols, J. K.

The Modular Avionics Packaging (MAP) Program for packaging future military avionics systems with the objective of improving reliability, maintainability, and supportability, and reducing equipment life cycle costs is addressed. The basic MAP packaging concepts called the Standard Avionics Module, the Standard Enclosure, and the Integrated Rack are summarized, and the benefits of modular avionics packaging, including low risk design, technology independence with common functions, improved maintainability and life cycle costs are discussed. Progress made in MAP is briefly reviewed.

Emerging concepts in effector biology of plant-associated organisms.

PubMed

Hogenhout, Saskia A; Van der Hoorn, Renier A L; Terauchi, Ryohei; Kamoun, Sophien

2009-02-01

Plant-associated organisms secrete proteins and other molecules to modulate plant defense circuitry and enable colonization of plant tissue. Understanding the molecular function of these secreted molecules, collectively known as effectors, became widely accepted as essential for a mechanistic understanding of the processes underlying plant colonization. This review summarizes recent findings in the field of effector biology and highlights the common concepts that have emerged from the study of cellular plant pathogen effectors.

Glutamate-Modulating Drugs as a Potential Therapeutic Strategy in Obsessive-Compulsive Disorder

PubMed Central

Marinova, Zoya; Chuang, De-Maw; Fineberg, Naomi

2017-01-01

Objective: Abstract: Obsessive-compulsive disorder (OCD) is a mental disease commonly associated with severe distress and impairment of social functioning. Serotonin reuptake inhibitors and/or cognitive behavioural therapy are the therapy of choice, however up to 40% of patients do not respond to treatment. Glutamatergic signalling has also been implicated in OCD. The aim of the current study was to review the clinical evidence for therapeutic utility of glutamate-modulating drugs as an augmentation or monotherapy in OCD patients. Methods: We conducted a search of the MEDLINE database for clinical studies evaluating the effect of glutamate-modulating drugs in OCD. Results: Memantine is the compound most consistently showing a positive effect as an augmentation therapy in OCD. Anti-convulsant drugs (lamotrigine, topiramate) and riluzole may also provide therapeutic benefit to some OCD patients. Finally, ketamine may be of interest due to its potential for a rapid onset of action. Conclusion: Further randomized placebo-controlled trials in larger study populations are necessary in order to draw definitive conclusions on the utility of glutamate-modulating drugs in OCD. Furthermore, genetic and epigenetic factors, clinical symptoms and subtypes predicting treatment response to glutamate-modulating drugs need to be investigated systematically. PMID:28322166

Neural activations associated with feedback and retrieval success

NASA Astrophysics Data System (ADS)

Wiklund-Hörnqvist, Carola; Andersson, Micael; Jonsson, Bert; Nyberg, Lars

2017-11-01

There is substantial behavioral evidence for a phenomenon commonly called "the testing effect", i.e. superior memory performance after repeated testing compared to re-study of to-be-learned materials. However, considerably less is known about the underlying neuro-cognitive processes that are involved in the initial testing phase, and thus underlies the actual testing effect. Here, we investigated functional brain activity related to test-enhanced learning with feedback. Subjects learned foreign vocabulary across three consecutive tests with correct-answer feedback. Functional brain-activity responses were analyzed in relation to retrieval and feedback events, respectively. Results revealed up-regulated activity in fronto-striatal regions during the first successful retrieval, followed by a marked reduction in activity as a function of improved learning. Whereas feedback improved behavioral performance across consecutive tests, feedback had a negligable role after the first successful retrieval for functional brain-activity modulations. It is suggested that the beneficial effects of test-enhanced learning is regulated by feedback-induced updating of memory representations, mediated via the striatum, that might underlie the stabilization of memory commonly seen in behavioral studies of the testing effect.

Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.

PubMed

Zinkgraf, Matthew; Liu, Lijun; Groover, Andrew; Filkov, Vladimir

2017-06-01

Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies. No claim to original US government works. New Phytologist © 2017 New Phytologist Trust.

Structural Basis of Clostridium perfringens Toxin Complex Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams,J.; Gregg, K.; Bayer, E.

2008-01-01

The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between themore » X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.« less

Representations of pitch and slow modulation in auditory cortex

PubMed Central

Barker, Daphne; Plack, Christopher J.; Hall, Deborah A.

2013-01-01

Iterated ripple noise (IRN) is a type of pitch-evoking stimulus that is commonly used in neuroimaging studies of pitch processing. When contrasted with a spectrally matched Gaussian noise, it is known to produce a consistent response in a region of auditory cortex that includes an area antero-lateral to the primary auditory fields (lateral Heschl's gyrus). The IRN-related response has often been attributed to pitch, although recent evidence suggests that it is more likely driven by slowly varying spectro-temporal modulations not related to pitch. The present functional magnetic resonance imaging (fMRI) study showed that both pitch-related temporal regularity and slow modulations elicited a significantly greater response than a baseline Gaussian noise in an area that has been pre-defined as pitch-responsive. The region was sensitive to both pitch salience and slow modulation salience. The responses to pitch and spectro-temporal modulations interacted in a saturating manner, suggesting that there may be an overlap in the populations of neurons coding these features. However, the interaction may have been influenced by the fact that the two pitch stimuli used (IRN and unresolved harmonic complexes) differed in terms of pitch salience. Finally, the results support previous findings suggesting that the cortical response to IRN is driven in part by slow modulations, not by pitch. PMID:24106464

A novel functional electrical stimulation-control system for restoring motor function of post-stroke hemiplegic patients

PubMed Central

Huang, Zonghao; Wang, Zhigong; Lv, Xiaoying; Zhou, Yuxuan; Wang, Haipeng; Zong, Sihao

2014-01-01

Hemiparesis is one of the most common consequences of stroke. Advanced rehabilitation techniques are essential for restoring motor function in hemiplegic patients. Functional electrical stimulation applied to the affected limb based on myoelectric signal from the unaffected limb is a promising therapy for hemiplegia. In this study, we developed a prototype system for evaluating this novel functional electrical stimulation-control strategy. Based on surface electromyography and a vector machine model, a self-administered, multi-movement, force-modulation functional electrical stimulation-prototype system for hemiplegia was implemented. This paper discusses the hardware design, the algorithm of the system, and key points of the self-oscillation-prone system. The experimental results demonstrate the feasibility of the prototype system for further clinical trials, which is being conducted to evaluate the efficacy of the proposed rehabilitation technique. PMID:25657728

Method to determine the true modulation ratio for comprehensive two-dimensional gas chromatography.

PubMed

Pinkerton, David K; Parsons, Brendon A; Synovec, Robert E

2016-12-09

A new method is presented to determine the true modulation ratio, M R , from the measurable effective modulation ratio, M R *, in comprehensive two-dimensional gas chromatography, GC×GC, without the requirement for a detector at the end of the primary column. The method was developed through the investigation of modulator induced band broadening, as a function of 1 W b and the selected modulation period, P M , for simulated GC×GC data, by first defining primary column 1 D peak(s) and simulating the modulation process. Gaussian curve fitting is used to model each modulated secondary column separation peaklet, 2 D, in the unfolded GC×GC data to accurately determine the maxima of the peaklet distribution, followed by Gaussian curve fitting to the maxima to determine the effective 1 D peak profile and width, 1 W b *. The relationship between 1 W b and 1 W b * is studied as a function of the effective modulation ratio, M R *, which is 1 W b * divided by P M , in order to determine the true modulation ratio, M R , which is 1 W b divided by P M . We explore how peak sampling phase (in-phase and out-of-phase) plays a role in the relationship between M R and M R *. Experimental validation of the simulated results is also provided, to span a range of commonly implemented conditions with typical 1 W b (2-4.5s) and P M (0.25-8s). Use of M R <2 significantly broadens the 1 D peak (M R *≥1.2M R ) corresponding to a loss in 1 D peak capacity, 1 n c ≥20%. The new method relies upon mapping from M R * to M R , which is discussed in relation to peak capacity theories for GC×GC. It is found that optimizing 1 n c in GC×GC requires that 1 W b is minimized and must be sampled with a sufficiently short P M (1-2s) to minimize modulator induced band broadening and a subsequent reduction in the effective 1 D peak capacity. Copyright © 2016 Elsevier B.V. All rights reserved.

1H, 15N and 13C backbone and side-chain resonance assignments of a family 32 carbohydrate-binding module from the Clostridium perfringens NagH.

PubMed

Grondin, Julie M; Chitayat, Seth; Ficko-Blean, Elizabeth; Boraston, Alisdair B; Smith, Steven P

2012-10-01

The Gram-positive anaerobe Clostridium perfringens is an opportunistic bacterial pathogen that secretes a battery of enzymes involved in glycan degradation. These glycoside hydrolases are thought to be involved in turnover of mucosal layer glycans, and in the spread of major toxins commonly associated with the development of gastrointestinal diseases and gas gangrene in humans. These enzymes employ multi-modularity and carbohydrate-binding function to degrade extracellular eukaryotic host sugars. Here, we report the full (1)H, (15)N and (13)C chemical shift resonance assignments of the first family 32 carbohydrate-binding module from NagH, a secreted family 84 glycoside hydrolase.

Modulation of apoptosis sensitivity through the interplay with autophagic and proteasomal degradation pathways

PubMed Central

Delgado, M E; Dyck, L; Laussmann, M A; Rehm, M

2014-01-01

Autophagic and proteasomal degradation constitute the major cellular proteolysis pathways. Their physiological and pathophysiological adaptation and perturbation modulates the relative abundance of apoptosis-transducing proteins and thereby can positively or negatively adjust cell death susceptibility. In addition to balancing protein expression amounts, components of the autophagic and proteasomal degradation machineries directly interact with and co-regulate apoptosis signal transduction. The influence of autophagic and proteasomal activity on apoptosis susceptibility is now rapidly gaining more attention as a significant modulator of cell death signalling in the context of human health and disease. Here we present a concise and critical overview of the latest knowledge on the molecular interplay between apoptosis signalling, autophagy and proteasomal protein degradation. We highlight that these three pathways constitute an intricate signalling triangle that can govern and modulate cell fate decisions between death and survival. Owing to rapid research progress in recent years, it is now possible to provide detailed insight into the mechanisms of pathway crosstalk, common signalling nodes and the role of multi-functional proteins in co-regulating both protein degradation and cell death. PMID:24457955

Influence of White and Gray Matter Connections on Endogenous Human Cortical Oscillations

PubMed Central

Hawasli, Ammar H.; Kim, DoHyun; Ledbetter, Noah M.; Dahiya, Sonika; Barbour, Dennis L.; Leuthardt, Eric C.

2016-01-01

Brain oscillations reflect changes in electrical potentials summated across neuronal populations. Low- and high-frequency rhythms have different modulation patterns. Slower rhythms are spatially broad, while faster rhythms are more local. From this observation, we hypothesized that low- and high-frequency oscillations reflect white- and gray-matter communications, respectively, and synchronization between low-frequency phase with high-frequency amplitude represents a mechanism enabling distributed brain-networks to coordinate local processing. Testing this common understanding, we selectively disrupted white or gray matter connections to human cortex while recording surface field potentials. Counter to our original hypotheses, we found that cortex consists of independent oscillatory-units (IOUs) that maintain their own complex endogenous rhythm structure. IOUs are differentially modulated by white and gray matter connections. White-matter connections maintain topographical anatomic heterogeneity (i.e., separable processing in cortical space) and gray-matter connections segregate cortical synchronization patterns (i.e., separable temporal processing through phase-power coupling). Modulation of distinct oscillatory modules enables the functional diversity necessary for complex processing in the human brain. PMID:27445767

The anticonvulsant stiripentol acts directly on the GABAA receptor as a positive allosteric modulator

PubMed Central

Fisher, Janet L.

2009-01-01

SUMMARY Stiripentol(STP) has been used as co-therapy for treatment of epilepsy for many years. Its mechanism of action has long been considered to be indirect, as it inhibits the enzymes responsible for metabolism of other anticonvulsant agents. However, a recent report suggested that STP might also act at the neuronal level, increasing inhibitory GABAergic neurotransmission. We examined the effect of STP on the functional properties of recombinant GABAA receptors (GABARs) and found that it was a positive allosteric modulator of these ion channels. Its activity showed some dependence on subunit composition, with greater potentiation of α3-containing receptors and reduced potentiation when the β1 or ε subunits were present. STP caused a leftward shift in the GABA concentration-response relationship, but did not increase the peak response of the receptors to a maximal GABA concentration. Although STP shares some functional characteristics with the neurosteroids, its activity was not inhibited by a neurosteroid site antagonist and was unaffected by a mutation in the α3 subunit that reduced positive modulation by neurosteroids. The differential effect of STP on β1- and β2/β3-containing receptors was not altered by mutations within the second transmembrane domain that affect modulation by loreclezole. These findings suggest that STP acts as a direct allosteric modulator of the GABAR at a site distinct from many commonly used anti-convulsant, sedative and anxiolytic drugs. Its higher activity at α3-containing receptors as well as its activity at δ-containing receptors may provide a unique opportunity to target selected populations of GABARs. PMID:18585399

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data.

PubMed

Zhu, Mingzhu; Dahmen, Jeremy L; Stacey, Gary; Cheng, Jianlin

2013-09-22

High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to generate experimental data in the last few years, few computational methods are available to analyze this huge amount of transcription data. The computational methods for constructing gene regulatory networks from RNA-Seq expression data of hundreds or even thousands of genes are particularly lacking and urgently needed. We developed an automated bioinformatics method to predict gene regulatory networks from the quantitative expression values of differentially expressed genes based on RNA-Seq transcriptome data of a cell in different stages and conditions, integrating transcriptional, genomic and gene function data. We applied the method to the RNA-Seq transcriptome data generated for soybean root hair cells in three different development stages of nodulation after rhizobium infection. The method predicted a soybean nodulation-related gene regulatory network consisting of 10 regulatory modules common for all three stages, and 24, 49 and 70 modules separately for the first, second and third stage, each containing both a group of co-expressed genes and several transcription factors collaboratively controlling their expression under different conditions. 8 of 10 common regulatory modules were validated by at least two kinds of validations, such as independent DNA binding motif analysis, gene function enrichment test, and previous experimental data in the literature. We developed a computational method to reliably reconstruct gene regulatory networks from RNA-Seq transcriptome data. The method can generate valuable hypotheses for interpreting biological data and designing biological experiments such as ChIP-Seq, RNA interference, and yeast two hybrid experiments.

Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules.

PubMed

Tikka, Saara; Monogioudi, Evanthia; Gotsopoulos, Athanasios; Soliymani, Rabah; Pezzini, Francesco; Scifo, Enzo; Uusi-Rauva, Kristiina; Tyynelä, Jaana; Baumann, Marc; Jalanko, Anu; Simonati, Alessandro; Lalowski, Maciej

2016-03-01

Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood encephalopathy.

Structure and Functional Characterization of the RNA-Binding Element of the NLRX1 Innate Immune Modulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Minsun; Yoon, Sung-il; Wilson, Ian A.

2012-06-20

Mitochondrial NLRX1 is a member of the family of nucleotide-binding domain and leucine-rich-repeat-containing proteins (NLRs) that mediate host innate immunity as intracellular surveillance sensors against common molecular patterns of invading pathogens. NLRX1 functions in antiviral immunity, but the molecular mechanism of its ligand-induced activation is largely unknown. The crystal structure of the C-terminal fragment (residues 629975) of human NLRX1 (cNLRX1) at 2.65 {angstrom} resolution reveals that cNLRX1 consists of an N-terminal helical (LRRNT) domain, central leucine-rich repeat modules (LRRM), and a C-terminal three-helix bundle (LRRCT). cNLRX1 assembles into a compact hexameric architecture that is stabilized by intersubunit and interdomain interactionsmore » of LRRNT and LRRCT in the trimer and dimer components of the hexamer, respectively. Furthermore, we find that cNLRX1 interacts directly with RNA and supports a role for NLRX1 in recognition of intracellular viral RNA in antiviral immunity.« less

Progesterone receptor modulates estrogen receptor-α action in breast cancer

PubMed Central

Mohammed, Hisham; Russell, I. Alasdair; Stark, Rory; Rueda, Oscar M.; Hickey, Theresa E.; Tarulli, Gerard A.; Serandour, Aurelien A. A.; Birrell, Stephen N.; Bruna, Alejandra; Saadi, Amel; Menon, Suraj; Hadfield, James; Pugh, Michelle; Raj, Ganesh V.; Brown, Gordon D.; D’Santos, Clive; Robinson, Jessica L. L.; Silva, Grace; Launchbury, Rosalind; Perou, Charles M.; Stingl, John; Caldas, Carlos; Tilley, Wayne D.; Carroll, Jason S.

2015-01-01

Summary Progesterone receptor (PR) expression is employed as a biomarker of estrogen receptor-α (ERα) function and breast cancer prognosis. We now show that PR is not merely an ERα-induced gene target, but is also an ERα-associated protein that modulates its behaviour. In the presence of agonist ligands, PR associates with ERα to direct ERα chromatin binding events within breast cancer cells, resulting in a unique gene expression programme that is associated with good clinical outcome. Progesterone inhibited estrogen-mediated growth of ERα+ cell line xenografts and primary ERα+ breast tumour explants and had increased anti-proliferative effects when coupled with an ERα antagonist. Copy number loss of PgR is a common feature in ERα+ breast cancers, explaining lower PR levels in a subset of cases. Our findings indicate that PR functions as a molecular rheostat to control ERα chromatin binding and transcriptional activity, which has important implications for prognosis and therapeutic interventions. PMID:26153859

Diagnosis of inflammatory rheumatic diseases with photon density waves

NASA Astrophysics Data System (ADS)

Beuthan, Juergen; Prapavat, Viravuth; Naber, Rolf-Dieter; Minet, Olaf; Mueller, Gerhard J.

1996-04-01

Rheumatoid arthritis (RA) is a common inflammatory disease of interphalangeal joints. The utilization of conventional imaging systems (e.g. x-rays) for non invasive diagnostics at an early stage of the disease is difficult, since pathologically induced changes do not occur at this stage in hard tissue. Use of MR and ultrasound methods are both methodically problematic and expensive. Therefore investigations for optical diagnostics using photon density waves (PDW) were carried out. The PDW was realized with an intensity modulated laser diode (825 nm, fmod: 110 MHz) and an ac- and phase detection in a 2D transillumination scanner. Measurements of optical properties of synovia and synovialis of healthy and early RA stages were performed and indicated a significant pathological increase of (mu) s. The detected PDW-pictures provided corresponding results. Further investigations regarding the object- variation of the modulation transfer function provide a sufficient spatial resolution in order to assign functional changes to anatomical structures. The results are presented using photos.

Covalent functionalization of monolayered transition metal dichalcogenides by phase engineering.

PubMed

Voiry, Damien; Goswami, Anandarup; Kappera, Rajesh; e Silva, Cecilia de Carvalho Castro; Kaplan, Daniel; Fujita, Takeshi; Chen, Mingwei; Asefa, Tewodros; Chhowalla, Manish

2015-01-01

Chemical functionalization of low-dimensional materials such as nanotubes, nanowires and graphene leads to profound changes in their properties and is essential for solubilizing them in common solvents. Covalent attachment of functional groups is generally achieved at defect sites, which facilitate electron transfer. Here, we describe a simple and general method for covalent functionalization of two-dimensional transition metal dichalcogenide nanosheets (MoS₂, WS₂ and MoSe₂), which does not rely on defect engineering. The functionalization reaction is instead facilitated by electron transfer between the electron-rich metallic 1T phase and an organohalide reactant, resulting in functional groups that are covalently attached to the chalcogen atoms of the transition metal dichalcogenide. The attachment of functional groups leads to dramatic changes in the optoelectronic properties of the material. For example, we show that it renders the metallic 1T phase semiconducting, and gives it strong and tunable photoluminescence and gate modulation in field-effect transistors.

Unconventional binding sites and receptors for VIP and related peptides PACAP and PHI/PHM: an update.

PubMed

Muller, Jean-Marc; Debaigt, Colin; Goursaud, Stéphanie; Montoni, Alicia; Pineau, Nicolas; Meunier, Annie-Claire; Janet, Thierry

2007-09-01

The 28-amino-acid neuropeptide VIP and related peptides PACAP and PHI/PHM modulate virtually all of the vital functions in the body. These peptides are also commonly recognized as major regulators of cell growth and differentiation. Through their trophic and cytoprotective functions, they appear to play major roles in embryonic development, neurogenesis and the progression of a number of cancer types. These peptides bind to three well-characterized subtypes of G-protein coupled receptors: VPAC1 and VPAC2 share a common high affinity in the nanomolar range for VIP and PACAP; a third receptor type, PAC1, has been characterized for its high affinity for PACAP but its low affinity for VIP. Complex effects and pharmacological behaviors of these peptides suggest that multiple subtypes of binding sites may cooperate to mediate their function in target cells and tissues. In this complex response, some of these binding sites correspond to the definition of the conventional receptors cited above, while others display unexpected pharmacological and functional properties. Here we present potential clues that may lead investigators to further characterize the molecular nature and functions of these atypical binding species.

Wavelength locking of single emitters and multi-emitter modules: simulation and experiments

NASA Astrophysics Data System (ADS)

Yanson, Dan; Rappaport, Noam; Peleg, Ophir; Berk, Yuri; Dahan, Nir; Klumel, Genady; Baskin, Ilya; Levy, Moshe

2016-03-01

Wavelength-stabilized high-brightness single emitters are commonly used in fiber-coupled laser diode modules for pumping Yb-doped lasers at 976 nm, and Nd-doped ones at 808 nm. We investigate the spectral behavior of single emitters under wavelength-selective feedback from a volume Bragg (or hologram) grating (VBG) in a multi-emitter module. By integrating a full VBG model as a multi-layer thin film structure with commercial raytracing software, we simulated wavelength locking conditions as a function of beam divergence and angular alignment tolerances. Good correlation between the simulated VBG feedback strength and experimentally measured locking ranges, in both VBG misalignment angle and laser temperature, is demonstrated. The challenges of assembling multi-emitter modules based on beam-stacked optical architectures are specifically addressed, where the wavelength locking conditions must be achieved simultaneously with high fiber coupling efficiency for each emitter in the module. It is shown that angular misorientation between fast and slow-axis collimating optics can have a dramatic effect on the spectral and power performance of the module. We report the development of our NEON-S wavelength-stabilized fiber laser pump module, which uses a VBG to provide wavelength-selective optical feedback in the collimated portion of the beam. Powered by our purpose-developed high-brightness single emitters, the module delivers 47 W output at 11 A from an 0.15 NA fiber and a 0.3 nm linewidth at 976 nm. Preliminary wavelength-locking results at 808 nm are also presented.

Different functional modes of BAR domain proteins in formation and plasticity of mammalian postsynapses.

PubMed

Kessels, Michael M; Qualmann, Britta

2015-09-01

A plethora of cell biological processes involve modulations of cellular membranes. By using extended lipid-binding interfaces, some proteins have the power to shape membranes by attaching to them. Among such membrane shapers, the superfamily of Bin-Amphiphysin-Rvs (BAR) domain proteins has recently taken center stage. Extensive structural work on BAR domains has revealed a common curved fold that can serve as an extended membrane-binding interface to modulate membrane topologies and has allowed the grouping of the BAR domain superfamily into subfamilies with structurally slightly distinct BAR domain subtypes (N-BAR, BAR, F-BAR and I-BAR). Most BAR superfamily members are expressed in the mammalian nervous system. Neurons are elaborately shaped and highly compartmentalized cells. Therefore, analyses of synapse formation and of postsynaptic reorganization processes (synaptic plasticity) - a basis for learning and memory formation - has unveiled important physiological functions of BAR domain superfamily members. These recent advances, furthermore, have revealed that the functions of BAR domain proteins include different aspects. These functions are influenced by the often complex domain organization of BAR domain proteins. In this Commentary, we review these recent insights and propose to classify BAR domain protein functions into (1) membrane shaping, (2) physical integration, (3) action through signaling components, and (4) suppression of other BAR domain functions. © 2015. Published by The Company of Biologists Ltd.

The functional neuroanatomy of bipolar disorder: a consensus model

PubMed Central

Strakowski, Stephen M; Adler, Caleb M; Almeida, Jorge; Altshuler, Lori L; Blumberg, Hilary P; Chang, Kiki D; DelBello, Melissa P; Frangou, Sophia; McIntosh, Andrew; Phillips, Mary L; Sussman, Jessika E; Townsend, Jennifer D

2013-01-01

Objectives Functional neuroimaging methods have proliferated in recent years, such that functional magnetic resonance imaging, in particular, is now widely used to study bipolar disorder. However, discrepant findings are common. A workgroup was organized by the Department of Psychiatry, University of Cincinnati (Cincinnati, OH, USA) to develop a consensus functional neuroanatomic model of bipolar I disorder based upon the participants’ work as well as that of others. Methods Representatives from several leading bipolar disorder neuroimaging groups were organized to present an overview of their areas of expertise as well as focused reviews of existing data. The workgroup then developed a consensus model of the functional neuroanatomy of bipolar disorder based upon these data. Results Among the participants, a general consensus emerged that bipolar I disorder arises from abnormalities in the structure and function of key emotional control networks in the human brain. Namely, disruption in early development (e.g., white matter connectivity, prefrontal pruning) within brain networks that modulate emotional behavior leads to decreased connectivity among ventral prefrontal networks and limbic brain regions, especially amygdala. This developmental failure to establish healthy ventral prefrontal–limbic modulation underlies the onset of mania and ultimately, with progressive changes throughout these networks over time and with affective episodes, a bipolar course of illness. Conclusions This model provides a potential substrate to guide future investigations and areas needing additional focus are identified. PMID:22631617

Age-related commonalities and differences in the relationship between executive functions and intelligence: Analysis of the NAB executive functions module and WAIS-IV scores.

PubMed

Buczylowska, Dorota; Petermann, Franz

2017-01-01

Data from five subtests of the Executive Functions Module of the German Neuropsychological Assessment Battery (NAB) and all ten core subtests of the German Wechsler Adult Intelligence Scale - Fourth Edition (WAIS-IV) were used to examine the relationship between executive functions and intelligence in a comparison of two age groups: individuals aged 18-59 years and individuals aged 60-88 years. The NAB subtests Categories and Word Generation demonstrated a consistent correlation pattern for both age groups. However, the NAB Judgment subtest correlated more strongly with three WAIS-IV indices, the Full Scale IQ (FSIQ), and the General Ability Index (GAI) in the older adult group than in the younger group. Additionally, in the 60-88 age group, the Executive Functions Index (EFI) was more strongly correlated with the Verbal Comprehension Index (VCI) than with the Perceptual Reasoning Index (PRI). Both age groups demonstrated a strong association of the EFI with the FSIQ and the Working Memory Index (WMI). The results imply the potential diagnostic utility of the Judgment subtest and a significant relationship between executive functioning and crystallized intelligence at older ages. Furthermore, it may be concluded that there is a considerable age-independent overlap between the EFI and general intelligence, as well as between the EFI and working memory.

Study of the Inorganic Substitution in a Functionalized UiO-66 Metal-Organic Framework

NASA Astrophysics Data System (ADS)

Yasin, Alhassan Salman

Metal-Organic Frameworks (MOFs) have received considerable attention and fast development in the past few years. These materials have demonstrated a wide range of applications due to their porosity, tailorability of optical properties, and chemical selectivity. This report catalogs common MOF designs based on application and diversity in various fields, as well as conduct an in-depth study of inorganic substitution in a functionalized MOF. This study investigates the band gap modulation in response to inorganic ion substitution within a thermally stable UiO-66 Metal-Organic Framework (MOF). A combination of density functional theory (DFT) predictions in conjunction with experimental predictions were used to map out the complete composition space for three inorganic ions (Zr, Hf, Ti) and three functional groups. The three functional groups include an amino group (NH2), a nitro group (NO2), and a hydrogenated case (H). The smallest determined band gap was for a partially substituted UiO-66(Ti5Zr1)-NH2 resulting in 2.60eV. Theoretical findings sup-port that Ti can be fully substituted within the lattice resulting in a predicted band gap as low as 1.62(2.77)eV. Band gap modulation was reasoned to be a result of a mid gap state introduced through the amino functionalization and HOMO shifting as a result of increased binding of the Ti-O-C bonds.

Treatment strategy and long-term functional outcome of traumatic elbow dislocation in childhood: a single centre study.

PubMed

Nussberger, G; Schädelin, S; Mayr, J; Studer, D; Zimmermann, P

2018-04-01

Traumatic elbow dislocation (TED) is the most common injury of large joints in children. There is an ongoing debate on the optimal treatment for TED. We aimed to assess the functional outcome after operative and nonoperative treatment of TED. We analysed the medical records of patients with TED treated at the University Children's Hospital, Basel, between March 2006 and June 2015. Functional outcome was assessed using the Mayo Elbow Performance Score (MEPS) and Quick Disabilities of the Arm, Shoulder and Hand (QuickDASH) Sport and Music Module score. These scores were compared between nonoperatively and operatively treated patients. A total of 37 patients (mean age 10.2 years, 5.2 to 15.3) were included. Of these, 21 (56.8%) children had undergone nonoperative treatment, with 16 (43.2%) patients having had operative treatment. After a mean follow-up of 5.6 years (1.2 to 5.9), MEPS and QuickDASH Sport and Music Module scores in the nonoperative group and operative group were similar: MEPS: 97.1 points (SD 4.6) versus 97.2 points (SD 2.6); 95% confidence interval (CI)-2.56 to 2.03); p = 0.53; QuickDASH Sport and Music Module score: 3.9 points (SD 6.1) versus 3.1 points (SD 4.6); 95% CI 2.60 to 4.17; p = 0.94. We noted no significant differences regarding the long-term functional outcome between the subgroup of children treated operatively versus those treated nonoperatively for TED with accompanying fractures of the medial epicondyle and medial condyle. Functional outcome after TED was excellent, independent of the treatment strategy. If clear indications for surgery are absent, a nonoperative approach for TED should be considered. Level III - therapeutic, retrospective, comparative study.

Specifying Software Behavior for Requirements and Design

DTIC Science & Technology

2013-01-01

e.g., Behavior Hiding is comprised of the Function Driver and Shared Services modules. Blacked-out modules, which are concerned with mechanisms for...and Shared Services modules. “The Func- tion Driver Module consists of a set of modules called Func- tion Drivers; each Function Driver is the sole...system environment. Functions that capture the rules determining these output values specify that behavior. The Shared Services module concerns aspects of

Coordination of intrinsic and extrinsic hand muscle activity as a function of wrist joint angle during two-digit grasping.

PubMed

Johnston, Jamie A; Bobich, Lisa R; Santello, Marco

2010-04-26

Fingertip forces result from the activation of muscles that cross the wrist and muscles whose origins and insertions reside within the hand (extrinsic and intrinsic hand muscles, respectively). Thus, tasks that involve changes in wrist angle affect the moment arm and length, hence the force-producing capabilities, of extrinsic muscles only. If a grasping task requires the exertion of constant fingertip forces, the Central Nervous System (CNS) may respond to changes in wrist angle by modulating the neural drive to extrinsic or intrinsic muscles only or by co-activating both sets of muscles. To distinguish between these scenarios, we recorded electromyographic (EMG) activity of intrinsic and extrinsic muscles of the thumb and index finger as a function of wrist angle during a two-digit object hold task. We hypothesized that changes in wrist angle would elicit EMG amplitude modulation of the extrinsic and intrinsic hand muscles. In one experimental condition we asked subjects to exert the same digit forces at each wrist angle, whereas in a second condition subjects could choose digit forces for holding the object. EMG activity was significantly modulated in both extrinsic and intrinsic muscles as a function of wrist angle (both p<0.05) but only for the constant force condition. Furthermore, EMG modulation resulted from uniform scaling of EMG amplitude across all muscles. We conclude that the CNS controlled both extrinsic and intrinsic muscles as a muscle synergy. These findings are discussed within the theoretical frameworks of synergies and common neural input across motor nuclei of hand muscles. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

Electro-optic architecture (EOA) for sensors and actuators in aircraft propulsion systems

NASA Technical Reports Server (NTRS)

Glomb, W. L., Jr.

1989-01-01

Results of a study to design an optimal architecture for electro-optical sensing and control in advanced aircraft and space systems are described. The propulsion full authority digital Electronic Engine Control (EEC) was the focus for the study. The recommended architecture is an on-engine EEC which contains electro-optic interface circuits for fiber-optic sensors on the engine. Size and weight are reduced by multiplexing arrays of functionally similar sensors on a pair of optical fibers to common electro-optical interfaces. The architecture contains common, multiplex interfaces to seven sensor groups: (1) self luminous sensors; (2) high temperatures; (3) low temperatures; (4) speeds and flows; (5) vibration; (6) pressures; and (7) mechanical positions. Nine distinct fiber-optic sensor types were found to provide these sensing functions: (1) continuous wave (CW) intensity modulators; (2) time division multiplexing (TDM) digital optic codeplates; (3) time division multiplexing (TDM) analog self-referenced sensors; (4) wavelength division multiplexing (WDM) digital optic code plates; (5) wavelength division multiplexing (WDM) analog self-referenced intensity modulators; (6) analog optical spectral shifters; (7) self-luminous bodies; (8) coherent optical interferometers; and (9) remote electrical sensors. The report includes the results of a trade study including engine sensor requirements, environment, the basic sensor types, and relevant evaluation criteria. These figures of merit for the candidate interface types were calculated from the data supplied by leading manufacturers of fiber-optic sensors.

Encoding and decoding amplitude-modulated cochlear implant stimuli—a point process analysis

PubMed Central

Shea-Brown, Eric; Rubinstein, Jay T.

2010-01-01

Cochlear implant speech processors stimulate the auditory nerve by delivering amplitude-modulated electrical pulse trains to intracochlear electrodes. Studying how auditory nerve cells encode modulation information is of fundamental importance, therefore, to understanding cochlear implant function and improving speech perception in cochlear implant users. In this paper, we analyze simulated responses of the auditory nerve to amplitude-modulated cochlear implant stimuli using a point process model. First, we quantify the information encoded in the spike trains by testing an ideal observer’s ability to detect amplitude modulation in a two-alternative forced-choice task. We vary the amount of information available to the observer to probe how spike timing and averaged firing rate encode modulation. Second, we construct a neural decoding method that predicts several qualitative trends observed in psychophysical tests of amplitude modulation detection in cochlear implant listeners. We find that modulation information is primarily available in the sequence of spike times. The performance of an ideal observer, however, is inconsistent with observed trends in psychophysical data. Using a neural decoding method that jitters spike times to degrade its temporal resolution and then computes a common measure of phase locking from spike trains of a heterogeneous population of model nerve cells, we predict the correct qualitative dependence of modulation detection thresholds on modulation frequency and stimulus level. The decoder does not predict the observed loss of modulation sensitivity at high carrier pulse rates, but this framework can be applied to future models that better represent auditory nerve responses to high carrier pulse rate stimuli. The supplemental material of this article contains the article’s data in an active, re-usable format. PMID:20177761

Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis.

PubMed

Challa, Krishna Reddy; Aggarwal, Pooja; Nath, Utpal

2016-09-05

Cell expansion is an essential process in plant morphogenesis and is regulated by the coordinated action of environmental stimuli and endogenous factors, such as the phytohormones auxin and brassinosteroid. Although the biosynthetic pathways that generate these hormones and their downstream signaling mechanisms have been extensively studied, the upstream transcriptional network that modulates their levels and connects their action to cell morphogenesis is less clear. Here we show that the miR319-regulated TCP (TEOSINTE BRANCHED 1, CYCLODEA, PROLIFERATING CELL FACTORS) transcription factors, notably TCP4, directly activate YUCCA5 transcription and integrate the auxin response to a brassinosteroid-dependent molecular circuit that promotes cell elongation in Arabidopsis hypocotyls. Further, TCP4 modulates the common transcriptional network downstream to auxin-BR signaling, which is also triggered by environmental cues, such as light, to promote cell expansion. Our study links TCP function with the hormone response during cell morphogenesis and shows that developmental and environmental signals converge on a common transcriptional network to promote cell elongation. {copyright, serif} 2016 American Society of Plant Biologists. All rights reserved.

LRP5 regulates human body fat distribution by modulating adipose progenitor biology in a dose- and depot-specific fashion.

PubMed

Loh, Nellie Y; Neville, Matt J; Marinou, Kyriakoula; Hardcastle, Sarah A; Fielding, Barbara A; Duncan, Emma L; McCarthy, Mark I; Tobias, Jonathan H; Gregson, Celia L; Karpe, Fredrik; Christodoulides, Constantinos

2015-02-03

Common variants in WNT pathway genes have been associated with bone mass and fat distribution, the latter predicting diabetes and cardiovascular disease risk. Rare mutations in the WNT co-receptors LRP5 and LRP6 are similarly associated with bone and cardiometabolic disorders. We investigated the role of LRP5 in human adipose tissue. Subjects with gain-of-function LRP5 mutations and high bone mass had enhanced lower-body fat accumulation. Reciprocally, a low bone mineral density-associated common LRP5 allele correlated with increased abdominal adiposity. Ex vivo LRP5 expression was higher in abdominal versus gluteal adipocyte progenitors. Equivalent knockdown of LRP5 in both progenitor types dose-dependently impaired β-catenin signaling and led to distinct biological outcomes: diminished gluteal and enhanced abdominal adipogenesis. These data highlight how depot differences in WNT/β-catenin pathway activity modulate human fat distribution via effects on adipocyte progenitor biology. They also identify LRP5 as a potential pharmacologic target for the treatment of cardiometabolic disorders. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

LRP5 Regulates Human Body Fat Distribution by Modulating Adipose Progenitor Biology in a Dose- and Depot-Specific Fashion

PubMed Central

Loh, Nellie Y.; Neville, Matt J.; Marinou, Kyriakoula; Hardcastle, Sarah A.; Fielding, Barbara A.; Duncan, Emma L.; McCarthy, Mark I.; Tobias, Jonathan H.; Gregson, Celia L.; Karpe, Fredrik; Christodoulides, Constantinos

2015-01-01

Summary Common variants in WNT pathway genes have been associated with bone mass and fat distribution, the latter predicting diabetes and cardiovascular disease risk. Rare mutations in the WNT co-receptors LRP5 and LRP6 are similarly associated with bone and cardiometabolic disorders. We investigated the role of LRP5 in human adipose tissue. Subjects with gain-of-function LRP5 mutations and high bone mass had enhanced lower-body fat accumulation. Reciprocally, a low bone mineral density-associated common LRP5 allele correlated with increased abdominal adiposity. Ex vivo LRP5 expression was higher in abdominal versus gluteal adipocyte progenitors. Equivalent knockdown of LRP5 in both progenitor types dose-dependently impaired β-catenin signaling and led to distinct biological outcomes: diminished gluteal and enhanced abdominal adipogenesis. These data highlight how depot differences in WNT/β-catenin pathway activity modulate human fat distribution via effects on adipocyte progenitor biology. They also identify LRP5 as a potential pharmacologic target for the treatment of cardiometabolic disorders. PMID:25651180

Programmable logic controller optical fibre sensor interface module

NASA Astrophysics Data System (ADS)

Allwood, Gary; Wild, Graham; Hinckley, Steven

2011-12-01

Most automated industrial processes use Distributed Control Systems (DCSs) or Programmable Logic Controllers (PLCs) for automated control. PLCs tend to be more common as they have much of the functionality of DCSs, although they are generally cheaper to install and maintain. PLCs in conjunction with a human machine interface form the basis of Supervisory Control And Data Acquisition (SCADA) systems, combined with communication infrastructure and Remote Terminal Units (RTUs). RTU's basically convert different sensor measurands in to digital data that is sent back to the PLC or supervisory system. Optical fibre sensors are becoming more common in industrial processes because of their many advantageous properties. Being small, lightweight, highly sensitive, and immune to electromagnetic interference, means they are an ideal solution for a variety of diverse sensing applications. Here, we have developed a PLC Optical Fibre Sensor Interface Module (OFSIM), in which an optical fibre is connected directly to the OFSIM located next to the PLC. The embedded fibre Bragg grating sensors, are highly sensitive and can detect a number of different measurands such as temperature, pressure and strain without the need for a power supply.

Common and distinct modulation of electrophysiological indices of feedback processing by autistic and psychopathic traits.

PubMed

Carter Leno, Virginia; Naples, Adam; Cox, Anthony; Rutherford, Helena; McPartland, James C

2016-01-01

Both autism spectrum disorder (ASD) and psychopathy are primarily characterized by social dysfunction; overlapping phenotypic features may reflect altered function in common brain mechanisms. The current study examined the degree to which neural response to social and nonsocial feedback is modulated by autistic versus psychopathic traits in a sample of typically developing adults (N = 31, 11 males, 18-52 years). Event-related potentials were recorded whilst participants completed a behavioral task and received feedback on task performance. Both autistic and psychopathic traits were associated with alterations in the neural correlates of feedback processing. Sensitivity to specific forms of feedback (social, nonsocial, positively valenced, negatively valenced) differed between the two traits. Autistic traits were associated with decreased sensitivity to social feedback. In contrast, the antisocial domain of psychopathic traits was associated with an overall decrease in sensitivity to feedback, and the interpersonal manipulation domain was associated with preserved processing of positively valenced feedback. Results suggest distinct alterations within specific mechanisms of feedback processing may underlie similar difficulties in social behavior.

Effects of Insecticidal Ketones Present in Mint Plants on GABAA Receptor from Mammalian Neurons

PubMed Central

Sánchez-Borzone, Mariela Eugenia; Marin, Leticia Delgado; García, Daniel Asmed

2017-01-01

Background: The genus Mentha, an important member of the Lamiaceae family, is represented by many species commonly known as mint. The insecticidal activity of Mentha oil and its main components has been tested and established against various insects/pests. Among these, the ketone monoterpenes that are most common in different Mentha species demonstrated insect toxicity, with pulegone being the most active, followed by carvone and menthone. Considering that the GABAA receptor (GABAA-R) is one of the main insecticide targets on neurons, and that pulegone would modulate the insect GABA system, it may be expected that the insecticidal properties of Mentha ketones are mediated by their interaction with this receptor. Objective: In order to discern the pharmacological actions of these products when used as insecticides on mammalian organisms, we evaluated the pharmacologic activity of ketones, commonly present in Mentha plants, on native GABAA-R from rats. Materials and Methods: Determination of ketones effects on allosterically enhanced benzodiazepine binding, using primary cultures of cortical neurons, which express functional receptors and MTT assay to evaluate their cell toxicity. Results: Our results seem to indicate that ketone components of Mentha, with proven repellent or insecticide activity, were able to behave as GABAA-R negative allosteric modulators in murine cells and consequently could exhibit convulsant activity in mammalians. Only pulegone at the highest assayed concentration (2 mM) showed a significant reduction in cell viability after exposure for 24 hr. Conclusion: The present results strongly suggest that the ketone components of Mentha are able to exhibit convulsant activity in mammalian organisms, but functional assays and in vivo experiments would be necessary to corroborate this proposed action. SUMMARY The pharmacological activity of insecticide ketones, commonly present in Mentha plants, was evaluated on native GABAA receptor from mammalian neurons.All studied compounds: pulegone, menthone and dihydrocarvone, were able to behave as negative allosteric modulators and could exhibit convulsant activity in mammalian organisms.Citotoxicity assays demonstrated that only pulegone affected the cell viability. Abbreviations used: GABA: gamma aminobutyric acid, GABAA-R: GABAA receptor, MTT: 1-(4,5-dimethylthiazol-2-yl)-3,5-diphenylformazam, DMEM: Dulbecco's modified minimum essential mèdium, [3H]TBOB: [3H] t-Butylbicycloorthobenzoate PMID:28216893

L-Arginine and Alzheimer's Disease

PubMed Central

Yi, Jing; Horky, Laura L.; Friedlich, Avi L.; Shi, Ying; Rogers, Jack T.; Huang, Xudong

2009-01-01

Alzheimer's disease (AD), the most common form of dementia, is characterized by progressive neurodegeneration and loss of cognitive and memory functions. Although the exact causes of AD are still unclear, evidence suggests that atherosclerosis, redox stress, inflammation, neurotransmitter dysregulation, and impaired brain energy metabolism may all be associated with AD pathogenesis. Herein, we explore a possible role for L-arginine (L-arg) in AD, taking into consideration known functions for L-arg in atherosclerosis, redox stress and the inflammatory process, regulation of synaptic plasticity and neurogenesis, and modulation of glucose metabolism and insulin activity. L-arg, a precursor of nitric oxide and polyamine, exhibits multiple functions in human health and may play a prominent role in age-related degenerative diseases such as AD. PMID:19079617

Virtual Sensor Test Instrumentation

NASA Technical Reports Server (NTRS)

Wang, Roy

2011-01-01

Virtual Sensor Test Instrumentation is based on the concept of smart sensor technology for testing with intelligence needed to perform sell-diagnosis of health, and to participate in a hierarchy of health determination at sensor, process, and system levels. A virtual sensor test instrumentation consists of five elements: (1) a common sensor interface, (2) microprocessor, (3) wireless interface, (4) signal conditioning and ADC/DAC (analog-to-digital conversion/ digital-to-analog conversion), and (5) onboard EEPROM (electrically erasable programmable read-only memory) for metadata storage and executable software to create powerful, scalable, reconfigurable, and reliable embedded and distributed test instruments. In order to maximize the efficient data conversion through the smart sensor node, plug-and-play functionality is required to interface with traditional sensors to enhance their identity and capabilities for data processing and communications. Virtual sensor test instrumentation can be accessible wirelessly via a Network Capable Application Processor (NCAP) or a Smart Transducer Interlace Module (STIM) that may be managed under real-time rule engines for mission-critical applications. The transducer senses the physical quantity being measured and converts it into an electrical signal. The signal is fed to an A/D converter, and is ready for use by the processor to execute functional transformation based on the sensor characteristics stored in a Transducer Electronic Data Sheet (TEDS). Virtual sensor test instrumentation is built upon an open-system architecture with standardized protocol modules/stacks to interface with industry standards and commonly used software. One major benefit for deploying the virtual sensor test instrumentation is the ability, through a plug-and-play common interface, to convert raw sensor data in either analog or digital form, to an IEEE 1451 standard-based smart sensor, which has instructions to program sensors for a wide variety of functions. The sensor data is processed in a distributed fashion across the network, providing a large pool of resources in real time to meet stringent latency requirements.

Impact of Cigarette Smoke on the Human and Mouse Lungs: A Gene-Expression Comparison Study

PubMed Central

Morissette, Mathieu C.; Lamontagne, Maxime; Bérubé, Jean-Christophe; Gaschler, Gordon; Williams, Andrew; Yauk, Carole; Couture, Christian; Laviolette, Michel; Hogg, James C.; Timens, Wim; Halappanavar, Sabina; Stampfli, Martin R.; Bossé, Yohan

2014-01-01

Cigarette smoke is well known for its adverse effects on human health, especially on the lungs. Basic research is essential to identify the mechanisms involved in the development of cigarette smoke-related diseases, but translation of new findings from pre-clinical models to the clinic remains difficult. In the present study, we aimed at comparing the gene expression signature between the lungs of human smokers and mice exposed to cigarette smoke to identify the similarities and differences. Using human and mouse whole-genome gene expression arrays, changes in gene expression, signaling pathways and biological functions were assessed. We found that genes significantly modulated by cigarette smoke in humans were enriched for genes modulated by cigarette smoke in mice, suggesting a similar response of both species. Sixteen smoking-induced genes were in common between humans and mice including six newly reported to be modulated by cigarette smoke. In addition, we identified a new conserved pulmonary response to cigarette smoke in the induction of phospholipid metabolism/degradation pathways. Finally, the majority of biological functions modulated by cigarette smoke in humans were also affected in mice. Altogether, the present study provides information on similarities and differences in lung gene expression response to cigarette smoke that exist between human and mouse. Our results foster the idea that animal models should be used to study the involvement of pathways rather than single genes in human diseases. PMID:24663285

G-protein signaling modulator 1 deficiency accelerates cystic disease in an orthologous mouse model of autosomal dominant polycystic kidney disease

PubMed Central

Kwon, Michelle; Pavlov, Tengis S.; Nozu, Kandai; Rasmussen, Shauna A.; Ilatovskaya, Daria V.; Lerch-Gaggl, Alexandra; North, Lauren M.; Kim, Hyunho; Qian, Feng; Sweeney, William E.; Avner, Ellis D.; Blumer, Joe B.; Staruschenko, Alexander; Park, Frank

2012-01-01

Polycystic kidney diseases are the most common genetic diseases that affect the kidney. There remains a paucity of information regarding mechanisms by which G proteins are regulated in the context of polycystic kidney disease to promote abnormal epithelial cell expansion and cystogenesis. In this study, we describe a functional role for the accessory protein, G-protein signaling modulator 1 (GPSM1), also known as activator of G-protein signaling 3, to act as a modulator of cyst progression in an orthologous mouse model of autosomal dominant polycystic kidney disease (ADPKD). A complete loss of Gpsm1 in the Pkd1V/V mouse model of ADPKD, which displays a hypomorphic phenotype of polycystin-1, demonstrated increased cyst progression and reduced renal function compared with age-matched cystic Gpsm1+/+ and Gpsm1+/− mice. Electrophysiological studies identified a role by which GPSM1 increased heteromeric polycystin-1/polycystin-2 ion channel activity via Gβγ subunits. In summary, the present study demonstrates an important role for GPSM1 in controlling the dynamics of cyst progression in an orthologous mouse model of ADPKD and presents a therapeutic target for drug development in the treatment of this costly disease. PMID:23236168

A General Water Resources Regulation Software System in China

NASA Astrophysics Data System (ADS)

LEI, X.

2017-12-01

To avoid iterative development of core modules in water resource normal regulation and emergency regulation and improve the capability of maintenance and optimization upgrading of regulation models and business logics, a general water resources regulation software framework was developed based on the collection and analysis of common demands for water resources regulation and emergency management. It can provide a customizable, secondary developed and extensible software framework for the three-level platform "MWR-Basin-Province". Meanwhile, this general software system can realize business collaboration and information sharing of water resources regulation schemes among the three-level platforms, so as to improve the decision-making ability of national water resources regulation. There are four main modules involved in the general software system: 1) A complete set of general water resources regulation modules allows secondary developer to custom-develop water resources regulation decision-making systems; 2) A complete set of model base and model computing software released in the form of Cloud services; 3) A complete set of tools to build the concept map and model system of basin water resources regulation, as well as a model management system to calibrate and configure model parameters; 4) A database which satisfies business functions and functional requirements of general water resources regulation software can finally provide technical support for building basin or regional water resources regulation models.

A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity

PubMed Central

Humphry, Matt; Bednarek, Paweł; Kemmerling, Birgit; Koh, Serry; Stein, Mónica; Göbel, Ulrike; Stüber, Kurt; Piślewska-Bednarek, Mariola; Loraine, Ann; Schulze-Lefert, Paul; Somerville, Shauna; Panstruga, Ralph

2010-01-01

At least two components that modulate plant resistance against the fungal powdery mildew disease are ancient and have been conserved since the time of the monocot–dicot split (≈200 Mya). These components are the seven transmembrane domain containing MLO/MLO2 protein and the syntaxin ROR2/PEN1, which act antagonistically and have been identified in the monocot barley (Hordeum vulgare) and the dicot Arabidopsis thaliana, respectively. Additionally, syntaxin-interacting N-ethylmaleimide sensitive factor adaptor protein receptor proteins (VAMP721/722 and SNAP33/34) as well as a myrosinase (PEN2) and an ABC transporter (PEN3) contribute to antifungal resistance in both barley and/or Arabidopsis. Here, we show that these genetically defined defense components share a similar set of coexpressed genes in the two plant species, comprising a statistically significant overrepresentation of gene products involved in regulation of transcription, posttranslational modification, and signaling. Most of the coexpressed Arabidopsis genes possess a common cis-regulatory element that may dictate their coordinated expression. We exploited gene coexpression to uncover numerous components in Arabidopsis involved in antifungal defense. Together, our data provide evidence for an evolutionarily conserved regulon composed of core components and clade/species-specific innovations that functions as a module in plant innate immunity. PMID:21098265

Comparison between the protective effects of vitamin K and vitamin A on the modulation of hypervitaminosis D3 short-term toxicity in adult albino rats.

PubMed

Elshama, Said Said; Osman, Hosam-Eldin Hussein; El-Kenawy, Ayman El-Meghawry; Youseef, Hamdi Mohamed

2016-02-17

Vitamin D3 has increased risk of toxicity due to its common use in multivitamin preparations. Vitamin K and vitamin A play an important role in vitamin D action. The goal of the current study was to compare the protective effects of vitamin K and vitamin A on the modulation of hypervitaminosis D3 toxicity in rats by assessing serum calcium, renal function tests, cardiac enzymes, and related histopathological changes. Eighty adult albino rats were divided into four groups; each group consisted of 20 rats. The first group received water; the second received a toxic dose of vitamin D3; the third received a toxic dose of vitamin D3 with vitamin A; and the fourth received a toxic dose of vitamin D3 with vitamin K. Vitamin D3 toxicity led to significant abnormalities of cardiac enzymes, renal function tests, and serum calcium associated with histopathological changes in the kidney, heart, lung, adrenal gland, and aorta. Individual administration of vitamin A or vitamin K with a toxic dose of vitamin D improved the biochemical and histopathological abnormalities of hypervitaminosis D3. Vitamins A and K showed the same protective effects in the modulation of hypervitaminosis D3 short-term toxicity.

Serotonergic and dopaminergic modulation of attentional processes.

PubMed

Boulougouris, Vasileios; Tsaltas, Eleftheria

2008-01-01

Disturbances in attentional processes are a common feature of several psychiatric disorders such as schizophrenia, attention deficit/hyperactivity disorder and Huntington's disease. The use of animal models has been useful in defining various candidate neural systems thus enabling us to translate basic laboratory science to the clinic and vice-versa. In this chapter, a comparative and integrated account is provided on the neuroanatomical and neurochemical modulation of basic behavioural operations such as selective attention, vigilance, set-shifting and executive control focusing on the comparative functions of the serotonin and dopamine systems in the cognitive control exerted by the prefrontal cortex. Specifically, we have reviewed evidence emerging from several behavioural paradigms in experimental animals and humans each of which centres on a different aspect of the attentional function. These paradigms offering both human and animal variants include the five-choice serial reaction time task (5CSRTT), attentional set-shifting and stop-signal reaction time task. In each case, the types of operation that are measured by the given paradigm and their neural correlates are defined. Then, the role of the ascending dopaminergic and serotonergic systems in the neurochemical modulation of its behavioural output are examined, and reference is made to clinical implications for neurological and neuropsychiatric disorders which exhibit deficits in these cognitive tests.

Galanin and addiction.

PubMed

Picciotto, M R

2008-06-01

There has been increasing interest in the ability of neuropeptides involved in feeding to modulate circuits important for responses to drugs of abuse. A number of peptides with effects on hypothalamic function also modulate the mesolimbic dopamine system (ventral tegmental area and nucleus accumbens). Similarly, common stress-related pathways can modulate food intake, drug reward and symptoms of drug withdrawal. Galanin promotes food intake and the analgesic properties of opiates; thus it initially seemed possible that galanin might potentiate opiate reinforcement. Instead, galanin agonists decrease opiate reward, measured by conditioned place preference, and opiate withdrawal signs, whereas opiate reward and withdrawal are increased in knock-out mice lacking galanin. This is consistent with studies showing that galanin decreases activity-evoked dopamine release in striatal slices and decreases the firing rate of noradrenergic neurons in locus coeruleus, areas involved in drug reward and withdrawal, respectively. These data suggest that polymorphisms in genes encoding galanin or galanin receptors might be associated with susceptibility to opiate abuse. Further, galanin receptors might be potential targets for development of novel treatments for addiction.

The tongue and its control by sleep state-dependent modulators.

PubMed

Horner, R L

2011-12-01

The neural networks controlling vital functions such as breathing are embedded in the brain, the neural and chemical environment of which changes with state, i.e., wakefulness, non-rapid eye movement (non-REM) sleep and REM sleep, and with commonly administered drugs such as anaesthetics, sedatives and ethanol. One particular output from the state-dependent chemical brain is the focus of attention in this paper; the motor output to the muscles of the tongue, specifically the actions of state-dependent modulators acting at the hypoglossal motor pool. Determining the mechanisms underlying the modulation of the hypoglossal motor output during sleep is relevant to understanding the spectrum of increased upper airway resistance, airflow limitation, hypoventilation and airway obstructions that occur during natural and drug-influenced sleep in humans. Understanding the mechanisms underlying upper airway dysfunction in sleep-disordered breathing is also important given the large and growing prevalence of obstructive sleep apnea syndrome which constitutes a major public health problem with serious clinical, social and economic consequences.

Generalized hamming networks and applications.

PubMed

Koutroumbas, Konstantinos; Kalouptsidis, Nicholas

2005-09-01

In this paper the classical Hamming network is generalized in various ways. First, for the Hamming maxnet, a generalized model is proposed, which covers under its umbrella most of the existing versions of the Hamming Maxnet. The network dynamics are time varying while the commonly used ramp function may be replaced by a much more general non-linear function. Also, the weight parameters of the network are time varying. A detailed convergence analysis is provided. A bound on the number of iterations required for convergence is derived and its distribution functions are given for the cases where the initial values of the nodes of the Hamming maxnet stem from the uniform and the peak distributions. Stabilization mechanisms aiming to prevent the node(s) with the maximum initial value diverging to infinity or decaying to zero are described. Simulations demonstrate the advantages of the proposed extension. Also, a rough comparison between the proposed generalized scheme as well as the original Hamming maxnet and its variants is carried out in terms of the time required for convergence, in hardware implementations. Finally, the other two parts of the Hamming network, namely the competitors generating module and the decoding module, are briefly considered in the framework of various applications such as classification/clustering, vector quantization and function optimization.

The regulatory network analysis of long noncoding RNAs in human colorectal cancer.

PubMed

Zhang, Yuwei; Tao, Yang; Li, Yang; Zhao, Jinshun; Zhang, Lina; Zhang, Xiaohong; Dong, Changzheng; Xie, Yangyang; Dai, Xiaoyu; Zhang, Xinjun; Liao, Qi

2018-05-01

Colorectal cancer (CRC) is among one of the most prevalent and lethiferous diseases worldwide. Long noncoding RNAs (lncRNAs) are commonly accepted to function as a key regulatory factor in human cancer, but the potential regulatory mechanisms of CRC-associated lncRNA are largely obscure. Here, we integrated several expression profiles to obtain 55 differentially expressed (DE) lncRNAs. We first detected lncRNA interactions with transcription factors, microRNAs, mRNAs, and RNA-binding proteins to construct a regulatory network and then create functional enrichment analyses for them using bioinformatics approaches. We found the upregulated genes in the regulatory network are enriched in cell cycle and DNA damage response, while the downregulated genes are enriched in cell differentiation, cellular response, and cell signaling. We then employed module-based methods to mine several intriguing modules from the overall network, which helps to classify the functions of genes more specifically. Next, we confirmed the validity of our network by comparisons with a randomized network using computational method. Finally, we attempted to annotate lncRNA functions based on the regulatory network, which indicated its potential application. Our study of the lncRNA regulatory network provided significant clues to unveil lncRNAs potential regulatory mechanisms in CRC and laid a foundation for further experimental investigation.

Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.

PubMed

Kweon, Ohgew; Kim, Seong-Jae; Holland, Ricky D; Chen, Hongyan; Kim, Dae-Wi; Gao, Yuan; Yu, Li-Rong; Baek, Songjoon; Baek, Dong-Heon; Ahn, Hongsik; Cerniglia, Carl E

2011-09-01

This study investigated a metabolic network (MN) from Mycobacterium vanbaalenii PYR-1 for polycyclic aromatic hydrocarbons (PAHs) from the perspective of structure, behavior, and evolution, in which multilayer omics data are integrated. Initially, we utilized a high-throughput proteomic analysis to assess the protein expression response of M. vanbaalenii PYR-1 to seven different aromatic compounds. A total of 3,431 proteins (57.38% of the genome-predicted proteins) were identified, which included 160 proteins that seemed to be involved in the degradation of aromatic hydrocarbons. Based on the proteomic data and the previous metabolic, biochemical, physiological, and genomic information, we reconstructed an experiment-based system-level PAH-MN. The structure of PAH-MN, with 183 metabolic compounds and 224 chemical reactions, has a typical scale-free nature. The behavior and evolution of the PAH-MN reveals a hierarchical modularity with funnel effects in structure/function and intimate association with evolutionary modules of the functional modules, which are the ring cleavage process (RCP), side chain process (SCP), and central aromatic process (CAP). The 189 commonly upregulated proteins in all aromatic hydrocarbon treatments provide insights into the global adaptation to facilitate the PAH metabolism. Taken together, the findings of our study provide the hierarchical viewpoint from genes/proteins/metabolites to the network via functional modules of the PAH-MN equipped with the engineering-driven approaches of modularization and rationalization, which may expand our understanding of the metabolic potential of M. vanbaalenii PYR-1 for bioremediation applications.

Dopamine modulation of emotional processing in cortical and subcortical neural circuits: evidence for a final common pathway in schizophrenia?

PubMed

Laviolette, Steven R

2007-07-01

The neural regulation of emotional perception, learning, and memory is essential for normal behavioral and cognitive functioning. Many of the symptoms displayed by individuals with schizophrenia may arise from fundamental disturbances in the ability to accurately process emotionally salient sensory information. The neurotransmitter dopamine (DA) and its ability to modulate neural regions involved in emotional learning, perception, and memory formation has received considerable research attention as a potential final common pathway to account for the aberrant emotional regulation and psychosis present in the schizophrenic syndrome. Evidence from both human neuroimaging studies and animal-based research using neurodevelopmental, behavioral, and electrophysiological techniques have implicated the mesocorticolimbic DA circuit as a crucial system for the encoding and expression of emotionally salient learning and memory formation. While many theories have examined the cortical-subcortical interactions between prefrontal cortical regions and subcortical DA substrates, many questions remain as to how DA may control emotional perception and learning and how disturbances linked to DA abnormalities may underlie the disturbed emotional processing in schizophrenia. Beyond the mesolimbic DA system, increasing evidence points to the amygdala-prefrontal cortical circuit as an important processor of emotionally salient information and how neurodevelopmental perturbances within this circuitry may lead to dysregulation of DAergic modulation of emotional processing and learning along this cortical-subcortical emotional processing circuit.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Identification of Modules in Protein-Protein Interaction Networks

NASA Astrophysics Data System (ADS)

Erten, Sinan; Koyutürk, Mehmet

In biological systems, most processes are carried out through orchestration of multiple interacting molecules. These interactions are often abstracted using network models. A key feature of cellular networks is their modularity, which contributes significantly to the robustness, as well as adaptability of biological systems. Therefore, modularization of cellular networks is likely to be useful in obtaining insights into the working principles of cellular systems, as well as building tractable models of cellular organization and dynamics. A common, high-throughput source of data on molecular interactions is in the form of physical interactions between proteins, which are organized into protein-protein interaction (PPI) networks. This chapter provides an overview on identification and analysis of functional modules in PPI networks, which has been an active area of research in the last decade.

Space station automation of common module power management and distribution

NASA Technical Reports Server (NTRS)

Miller, W.; Jones, E.; Ashworth, B.; Riedesel, J.; Myers, C.; Freeman, K.; Steele, D.; Palmer, R.; Walsh, R.; Gohring, J.

1989-01-01

The purpose is to automate a breadboard level Power Management and Distribution (PMAD) system which possesses many functional characteristics of a specified Space Station power system. The automation system was built upon 20 kHz ac source with redundancy of the power buses. There are two power distribution control units which furnish power to six load centers which in turn enable load circuits based upon a system generated schedule. The progress in building this specified autonomous system is described. Automation of Space Station Module PMAD was accomplished by segmenting the complete task in the following four independent tasks: (1) develop a detailed approach for PMAD automation; (2) define the software and hardware elements of automation; (3) develop the automation system for the PMAD breadboard; and (4) select an appropriate host processing environment.

Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro.

PubMed

Johnson, Laura P; Walton, Gemma E; Psichas, Arianna; Frost, Gary S; Gibson, Glenn R; Barraclough, Timothy G

2015-06-04

Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs), which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation--another method used to modulate gut composition and function--could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre), inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria) or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

S187. SEARCHING FOR BRAIN CO-EXPRESSION MODULES THAT CONTRIBUTE DISPROPORTIONATELY TO THE COMMON POLYGENIC RISK FOR SCHIZOPHRENIA

PubMed Central

Costas, Javier; Paramo, Mario; Arrojo, Manuel

2018-01-01

Abstract Background Genomic research has revealed that schizophrenia is a highly polygenic disease. Recent estimates indicate that at least 71% of genomic segments of 1 Mb include one or more risk loci for schizophrenia (Loh et al., Nature Genet 2015). This extremely high polygenicity represents a challenge to decipher the biological basis of schizophrenia, as it is expected that any set of SNPs with enough size will be associated with the disorder. Among the different gene sets available for study (such as those from Gene Ontology, KEGG pathway, Reactome pathways or protein protein interaction datasets), those based on brain co-expression networks represent putative functional relationships in the relevant tissue. The aim of this work was to identify brain co-expression networks that contribute disproportionately to the common polygenic risk for schizophrenia to get more insight on schizophrenia etiopathology. Methods We analyzed a case -control dataset consisting of 582 schizophrenia patients from Galicia, NW Spain, and 591 ancestrally matched controls, genotyped with the Illumina PsychArray. Using as discovery sample the summary results from the largest GWAS of schizophrenia to date (Psychiatric Genomics Consortium, SCZ2), we generated polygenic risk scores (PRS) in our sample based on SNPs located at genes belonging to brain co-expression modules determined by the CommonMind Consortium (Fromer et al., Nature Neurosci 2016). PRS were generated using the clumping procedure of PLINK, considering several different thresholds to select SNPs from the discovery sample. In order to test if any specific module increased risk to schizophrenia more than expected by their size, we generated up to 10,000 random permutations of the same number of SNPs, matched by frequency, distance to nearest gene, number of SNPs in LD and gene density, using SNPsnap. Results As expected, most modules with enough number of independent SNPs belonging to them showed a significant increase in Nagelkerke’s R2 in our case-control sample after the addition of the module-specific PRS in a logistic regression model. Our permutation strategy revealed that most modules did not show an excess of risk, measured by increase in Nagelkerke’s R2, in comparison to equal number of SNPs with similar characteristics. But one module, M2c from Fromer et al., remained highly significant after multiple tests’ correction. Reactome pathways analysis revealed an over-representation of genes involved in “Neuronal System” and “Axon guidance” among genes from this module. Using the same protocol, we detected that the 84 genes from the neuronal system pathway at this module, representing less than 6% of the genes from the module, explained a higher level of risk than expected. “Voltage-gated Potassium channels” and “Neurexins and neuroligins” are overrepresented among the Neuronal System genes from module M2c. Discussion Here, we show that, in spite of the high polygenicity of schizophrenia, it is possible to identify gene sets contributing disproportionately to total risk, as it was the case for the M2c module from Fromer et al. These authors have previously reported that the M2c module was enriched in GWAS signals, as well as CNVs and rare variants associated with schizophrenia. Therefore, this module shows a disproportionately contribution to schizophrenia risk. Study supported by Grant PI14/01020 from Instituto de Salud Carlos III, Ministry of Health, Spanish Government.

Space Station Furnace Facility. Experiment/Facility Requirements Document (E/FRD), volume 2, appendix 5

NASA Technical Reports Server (NTRS)

Kephart, Nancy

1992-01-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidifcation conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment, and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace.

Purification of complex samples: Implementation of a modular and reconfigurable droplet-based microfluidic platform with cascaded deterministic lateral displacement separation modules

PubMed Central

Pudda, Catherine; Boizot, François; Verplanck, Nicolas; Revol-Cavalier, Frédéric; Berthier, Jean; Thuaire, Aurélie

2018-01-01

Particle separation in microfluidic devices is a common problematic for sample preparation in biology. Deterministic lateral displacement (DLD) is efficiently implemented as a size-based fractionation technique to separate two populations of particles around a specific size. However, real biological samples contain components of many different sizes and a single DLD separation step is not sufficient to purify these complex samples. When connecting several DLD modules in series, pressure balancing at the DLD outlets of each step becomes critical to ensure an optimal separation efficiency. A generic microfluidic platform is presented in this paper to optimize pressure balancing, when DLD separation is connected either to another DLD module or to a different microfluidic function. This is made possible by generating droplets at T-junctions connected to the DLD outlets. Droplets act as pressure controllers, which perform at the same time the encapsulation of DLD sorted particles and the balance of output pressures. The optimized pressures to apply on DLD modules and on T-junctions are determined by a general model that ensures the equilibrium of the entire platform. The proposed separation platform is completely modular and reconfigurable since the same predictive model applies to any cascaded DLD modules of the droplet-based cartridge. PMID:29768490

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen-specific modulation of immune reactivity.

PubMed

Hinz, D; Seumois, G; Gholami, A M; Greenbaum, J A; Lane, J; White, B; Broide, D H; Schulten, V; Sidney, J; Bakhru, P; Oseroff, C; Wambre, E; James, E A; Kwok, W W; Peters, B; Vijayanand, P; Sette, A

2016-05-01

Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging from mild rhinitis to severe asthma. The aim of this study was to characterize changes in TG-specific T cell responses as a function of seasonality. Peripheral blood mononuclear cells (PBMCs) obtained from allergic individuals and non-allergic controls, either during the pollen season or out of season, were stimulated with either TG extract or a pool of previously identified immunodominant antigenic regions. PBMCs from allergic subjects exhibit higher IL-5 and IL-10 responses in season than when collected out of season. In the case of non-allergic subjects, as expected we observed lower IL-5 responses and robust production of IFN-γ compared to allergic individuals. Strikingly, non-allergic donors exhibited an opposing pattern, with decreased immune reactivity in season. The broad down-regulation in non-allergic donors indicates that healthy individuals are not oblivious to allergen exposure, but rather react with an active modulation of responses following the antigenic stimulus provided during the pollen season. Transcriptomic analysis of allergen-specific T cells defined genes modulated in concomitance with the allergen exposure and inhibition of responses in non-allergic donors. Magnitude and functionality of T helper cell responses differ substantially in season vs. out of season in allergic and non-allergic subjects. The results indicate the specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programmes associated with health and allergic disease. © 2015 John Wiley & Sons Ltd.

Components of cross-frequency modulation in health and disease.

PubMed

Allen, Elena A; Liu, Jingyu; Kiehl, Kent A; Gelernter, Joel; Pearlson, Godfrey D; Perrone-Bizzozero, Nora I; Calhoun, Vince D

2011-01-01

The cognitive deficits associated with schizophrenia are commonly believed to arise from the abnormal temporal integration of information, however a quantitative approach to assess network coordination is lacking. Here, we propose to use cross-frequency modulation (cfM), the dependence of local high-frequency activity on the phase of widespread low-frequency oscillations, as an indicator of network coordination and functional integration. In an exploratory analysis based on pre-existing data, we measured cfM from multi-channel EEG recordings acquired while schizophrenia patients (n = 47) and healthy controls (n = 130) performed an auditory oddball task. Novel application of independent component analysis (ICA) to modulation data delineated components with specific spatial and spectral profiles, the weights of which showed covariation with diagnosis. Global cfM was significantly greater in healthy controls (F(1,175) = 9.25, P < 0.005), while modulation at fronto-temporal electrodes was greater in patients (F(1,175) = 17.5, P < 0.0001). We further found that the weights of schizophrenia-relevant components were associated with genetic polymorphisms at previously identified risk loci. Global cfM decreased with copies of 957C allele in the gene for the dopamine D2 receptor (r = -0.20, P < 0.01) across all subjects. Additionally, greater "aberrant" fronto-temporal modulation in schizophrenia patients was correlated with several polymorphisms in the gene for the α2-subunit of the GABA(A) receptor (GABRA2) as well as the total number of risk alleles in GABRA2 (r = 0.45, P < 0.01). Overall, our results indicate great promise for this approach in establishing patterns of cfM in health and disease and elucidating the roles of oscillatory interactions in functional connectivity.

Modular Multi-Function Multi-Band Airborne Radio System (MFBARS). Volume II. Detailed Report.

DTIC Science & Technology

1981-06-01

Three Platforms in a Field of Hyperbolic LOP’s.......................... 187 76 Comparison, MFBARS Versus Baseline .......... 190 77 Program Flow Chart...configure, from a set of common modules, a given total CNI capability on specific platforms for a given mission " the ability to take advantage of...X Comm/Nav GPS L-Band; Spread Spectrum Nay X X SEEK TALK UHF Spread; Spectrum Comm X X SINCGARS VHF; Freq. Hop Comm (some platforms ) AFSATCOM UHF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Shunmin; Tian, Chengcheng; Zhu, Xiang

Transition-metal-catalyzed cyanation of aryl halides is a common route to benzonitriles, which are integral to many industrial procedures. However, traditional homogeneous catalysts for such processes are expensive and suffer poor recyclability, so a heterogeneous analogue is highly desired. A novel spatial modulation approach has been developed in this paper to fabricate a heterogeneous Pd-metalated nanoporous polymer, which catalyzes the cyanation of aryl halides without need for ligands. Finally, the catalyst displays high activity in the synthesis of benzonitriles, including high product yields, excellent stability and recycling, and broad functional-group tolerance.

System and method for radiation dose calculation within sub-volumes of a monte carlo based particle transport grid

DOEpatents

Bergstrom, Paul M.; Daly, Thomas P.; Moses, Edward I.; Patterson, Jr., Ralph W.; Schach von Wittenau, Alexis E.; Garrett, Dewey N.; House, Ronald K.; Hartmann-Siantar, Christine L.; Cox, Lawrence J.; Fujino, Donald H.

2000-01-01

A system and method is disclosed for radiation dose calculation within sub-volumes of a particle transport grid. In a first step of the method voxel volumes enclosing a first portion of the target mass are received. A second step in the method defines dosel volumes which enclose a second portion of the target mass and overlap the first portion. A third step in the method calculates common volumes between the dosel volumes and the voxel volumes. A fourth step in the method identifies locations in the target mass of energy deposits. And, a fifth step in the method calculates radiation doses received by the target mass within the dosel volumes. A common volume calculation module inputs voxel volumes enclosing a first portion of the target mass, inputs voxel mass densities corresponding to a density of the target mass within each of the voxel volumes, defines dosel volumes which enclose a second portion of the target mass and overlap the first portion, and calculates common volumes between the dosel volumes and the voxel volumes. A dosel mass module, multiplies the common volumes by corresponding voxel mass densities to obtain incremental dosel masses, and adds the incremental dosel masses corresponding to the dosel volumes to obtain dosel masses. A radiation transport module identifies locations in the target mass of energy deposits. And, a dose calculation module, coupled to the common volume calculation module and the radiation transport module, for calculating radiation doses received by the target mass within the dosel volumes.

Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis.

PubMed

Chen, Wei; Zhao, Wenshan; Yang, Aiting; Xu, Anjian; Wang, Huan; Cong, Min; Liu, Tianhui; Wang, Ping; You, Hong

2017-12-15

Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis. Differentially expressed miRNAs (DEMs) and genes (DEGs) were identified using GEO2R web tool. Putative target gene prediction of DEMs was carried out using the intersection of five major algorithms: DIANA-microT, TargetScan, miRanda, PICTAR5 and miRWalk. Functional miRNA-gene regulatory network (FMGRN) was constructed based on the computational target predictions at the sequence level and the inverse expression relationships between DEMs and DEGs. DAVID web server was selected to perform KEGG pathway enrichment analysis. Functional miRNA-gene regulatory module was generated based on the biological interpretation. Internal connections among genes in liver fibrosis-related module were determined using String database. MiRNA-gene regulatory modules related to liver fibrosis were experimentally verified in recombinant human TGFβ1 stimulated and specific miRNA inhibitor treated LX-2 cells. We totally identified 85 and 923 dysregulated miRNAs and genes in liver cirrhosis biopsy samples compared to their normal controls. All evident miRNA-gene pairs were identified and assembled into FMGRN which consisted of 990 regulations between 51 miRNAs and 275 genes, forming two big sub-networks that were defined as down-network and up-network, respectively. KEGG pathway enrichment analysis revealed that up-network was prominently involved in several KEGG pathways, in which "Focal adhesion", "PI3K-Akt signaling pathway" and "ECM-receptor interaction" were remarked significant (adjusted p<0.001). Genes enriched in these pathways coupled with their regulatory miRNAs formed a functional miRNA-gene regulatory module that contains 7 miRNAs, 22 genes and 42 miRNA-gene connections. Gene interaction analysis based on String database revealed that 8 out of 22 genes were highly clustered. Finally, we experimentally confirmed a functional regulatory module containing 5 miRNAs (miR-130b-3p, miR-148a-3p, miR-345-5p, miR-378a-3p, and miR-422a) and 6 genes (COL6A1, COL6A2, COL6A3, PIK3R3, COL1A1, CCND2) associated with liver fibrosis. Our integrated analysis of miRNA and gene expression profiles highlighted a functional miRNA-gene regulatory module associated with liver fibrosis, which, to some extent, may provide important clues to better understand the underlying pathogenesis of liver fibrosis. Copyright © 2017. Published by Elsevier B.V.

Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris)

PubMed Central

Villordo-Pineda, Emiliano; González-Chavira, Mario M.; Giraldo-Carbajo, Patricia; Acosta-Gallegos, Jorge A.; Caballero-Pérez, Juan

2015-01-01

Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector. PMID:26257755

Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris).

PubMed

Villordo-Pineda, Emiliano; González-Chavira, Mario M; Giraldo-Carbajo, Patricia; Acosta-Gallegos, Jorge A; Caballero-Pérez, Juan

2015-01-01

Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector.

Experiment module concepts study. Volume 1: Management summary

NASA Technical Reports Server (NTRS)

1970-01-01

The minimum number of standardized (common) module concepts that will satisfy the experiment program for manned space stations at least cost is investigated. The module interfaces with other elements such as the space shuttle, ground stations, and the experiments themselves are defined. The total experiment module program resource and test requirements are also considered. The minimum number of common module concepts that will satisfy the program at least cost is found to be three, plus a propulsion slice and certain experiment-peculiar integration hardware. The experiment modules rely on the space station for operational, maintenance, and logistic support. They are compatible with both expendable and shuttle launch vehicles, and with servicing by shuttle, tug, or directly from the space station. A total experiment module program cost of approximately $2319M under the study assumptions is indicated. This total is made up of $838M for experiment module development and production, $806M for experiment equipment, and $675M for interface hardware, experiment integration, launch and flight operations, and program management and support.

The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives.

PubMed

Leal, Rodolfo Oliveira; Gil, Solange

2016-10-27

Type I interferons (IFNs) are well-known cytokines that, among their main functions, are key components of the host immune response against viral infections. Due to its immune modulation properties, they are commonly used in the therapeutic approach of various retroviral infections, namely human immunodeficiency virus (HIV) and feline immunodeficiency virus (FIV). In HIV infection, it has been shown that IFN therapy limits early viral replication, particularly useful on post-exposure prophylaxis. In veterinary medicine, recombinant feline interferon omega (rFeIFN-ω) was the first interferon licensed for use in cats. Several studies have recently shown that this compound seems to stimulate the innate immunity, decreasing clinical signs and co-infections in naturally FIV-infected cats. More than summarizing the main conclusions about rFeIFN-ω in cats, this review emphasizes the immune-modulation properties of IFN therapy, opening new perspectives for its use in retroviral infections. Either in FIV-infected cats or in HIV individuals, type I IFNs seem to induce an innate immune-modulation and should not be overlooked as a therapeutic option in retroviral infections.

Opening a Window on ICME-driven GCR Modulation in the Inner Solar System

NASA Astrophysics Data System (ADS)

Winslow, Reka M.; Schwadron, Nathan A.; Lugaz, Noé; Guo, Jingnan; Joyce, Colin J.; Jordan, Andrew P.; Wilson, Jody K.; Spence, Harlan E.; Lawrence, David J.; Wimmer-Schweingruber, Robert F.; Mays, M. Leila

2018-04-01

Interplanetary coronal mass ejections (ICMEs) often cause Forbush decreases (Fds) in the flux of galactic cosmic rays (GCRs). We investigate how a single ICME, launched from the Sun on 2014 February 12, affected GCR fluxes at Mercury, Earth, and Mars. We use GCR observations from MESSENGER at Mercury, ACE/LRO at the Earth/Moon, and MSL at Mars. We find that Fds are steeper and deeper closer to the Sun, and that the magnitude of the magnetic field in the ICME magnetic ejecta as well as the “strength” of the ICME sheath both play a large role in modulating the depth of the Fd. Based on our results, we hypothesize that (1) the Fd size decreases exponentially with heliocentric distance, and (2) that two-step Fds are more common closer to the Sun. Both hypotheses will be directly verifiable by the upcoming Parker Solar Probe and Solar Orbiter missions. This investigation provides the first systematic study of the changes in GCR modulation as a function of distance from the Sun using nearly contemporaneous observations at Mercury, Earth/Moon, and Mars, which will be critical for validating our physical understanding of the modulation process throughout the heliosphere.

Motivational salience and genetic variability of dopamine D2 receptor expression interact in the modulation of interference processing

PubMed Central

Richter, Anni; Richter, Sylvia; Barman, Adriana; Soch, Joram; Klein, Marieke; Assmann, Anne; Libeau, Catherine; Behnisch, Gusalija; Wüstenberg, Torsten; Seidenbecher, Constanze I.; Schott, Björn H.

2013-01-01

Dopamine has been implicated in the fine-tuning of complex cognitive and motor function and also in the anticipation of future rewards. This dual function of dopamine suggests that dopamine might be involved in the generation of active motivated behavior. The DRD2 TaqIA polymorphism of the dopamine D2 receptor gene (rs1800497) has previously been suggested to affect striatal function with carriers of the less common A1 allele exhibiting reduced striatal D2 receptor density and increased risk for addiction. Here we aimed to investigate the influences of DRD2 TaqIA genotype on the modulation of interference processing by reward and punishment. Forty-six young, healthy volunteers participated in a behavioral experiment, and 32 underwent functional magnetic resonance imaging (fMRI). Participants performed a flanker task with a motivation manipulation (monetary reward, monetary loss, neither, or both). Reaction times (RTs) were shorter in motivated flanker trials, irrespective of congruency. In the fMRI experiment motivation was associated with reduced prefrontal activation during incongruent vs. congruent flanker trials, possibly reflecting increased processing efficiency. DRD2 TaqIA genotype did not affect overall RTs, but interacted with motivation on the congruency-related RT differences, with A1 carriers showing smaller interference effects to reward alone and A2 homozygotes exhibiting a specific interference reduction during combined reward (REW) and punishment trials (PUN). In fMRI, anterior cingulate activity showed a similar pattern of genotype-related modulation. Additionally, A1 carriers showed increased anterior insula activation relative to A2 homozygotes. Our results point to a role for genetic variations of the dopaminergic system in individual differences of cognition-motivation interaction. PMID:23760450

Phytochemicals perturb membranes and promiscuously alter protein function.

PubMed

Ingólfsson, Helgi I; Thakur, Pratima; Herold, Karl F; Hobart, E Ashley; Ramsey, Nicole B; Periole, Xavier; de Jong, Djurre H; Zwama, Martijn; Yilmaz, Duygu; Hall, Katherine; Maretzky, Thorsten; Hemmings, Hugh C; Blobel, Carl; Marrink, Siewert J; Koçer, Armağan; Sack, Jon T; Andersen, Olaf S

2014-08-15

A wide variety of phytochemicals are consumed for their perceived health benefits. Many of these phytochemicals have been found to alter numerous cell functions, but the mechanisms underlying their biological activity tend to be poorly understood. Phenolic phytochemicals are particularly promiscuous modifiers of membrane protein function, suggesting that some of their actions may be due to a common, membrane bilayer-mediated mechanism. To test whether bilayer perturbation may underlie this diversity of actions, we examined five bioactive phenols reported to have medicinal value: capsaicin from chili peppers, curcumin from turmeric, EGCG from green tea, genistein from soybeans, and resveratrol from grapes. We find that each of these widely consumed phytochemicals alters lipid bilayer properties and the function of diverse membrane proteins. Molecular dynamics simulations show that these phytochemicals modify bilayer properties by localizing to the bilayer/solution interface. Bilayer-modifying propensity was verified using a gramicidin-based assay, and indiscriminate modulation of membrane protein function was demonstrated using four proteins: membrane-anchored metalloproteases, mechanosensitive ion channels, and voltage-dependent potassium and sodium channels. Each protein exhibited similar responses to multiple phytochemicals, consistent with a common, bilayer-mediated mechanism. Our results suggest that many effects of amphiphilic phytochemicals are due to cell membrane perturbations, rather than specific protein binding.

Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function

PubMed Central

2015-01-01

A wide variety of phytochemicals are consumed for their perceived health benefits. Many of these phytochemicals have been found to alter numerous cell functions, but the mechanisms underlying their biological activity tend to be poorly understood. Phenolic phytochemicals are particularly promiscuous modifiers of membrane protein function, suggesting that some of their actions may be due to a common, membrane bilayer-mediated mechanism. To test whether bilayer perturbation may underlie this diversity of actions, we examined five bioactive phenols reported to have medicinal value: capsaicin from chili peppers, curcumin from turmeric, EGCG from green tea, genistein from soybeans, and resveratrol from grapes. We find that each of these widely consumed phytochemicals alters lipid bilayer properties and the function of diverse membrane proteins. Molecular dynamics simulations show that these phytochemicals modify bilayer properties by localizing to the bilayer/solution interface. Bilayer-modifying propensity was verified using a gramicidin-based assay, and indiscriminate modulation of membrane protein function was demonstrated using four proteins: membrane-anchored metalloproteases, mechanosensitive ion channels, and voltage-dependent potassium and sodium channels. Each protein exhibited similar responses to multiple phytochemicals, consistent with a common, bilayer-mediated mechanism. Our results suggest that many effects of amphiphilic phytochemicals are due to cell membrane perturbations, rather than specific protein binding. PMID:24901212

International Space Station Powered Bolt Nut Anomaly and Failure Analysis Summary

NASA Technical Reports Server (NTRS)

Sievers, Daniel E.; Warden, Harry K.

2010-01-01

A key mechanism used in the on-orbit assembly of the International Space Station (ISS) pressurized elements is the Common Berthing Mechanism. The mechanism that effects the structural connection of the Common Berthing Mechanism halves is the Powered Bolt Assembly. There are sixteen Powered Bolt Assemblies per Common Berthing Mechanism. The Common Berthing Mechanism has a bolt which engages a self aligning Powered Bolt Nut (PBN) on the mating interface (Figure 1). The Powered Bolt Assemblies are preloaded to approximately 84.5 kN (19000 lb) prior to pressurization of the CBM. The PBNs mentioned below, manufactured in 2009, will be used on ISS future missions. An on orbit functional failure of this hardware would be unacceptable and in some instances catastrophic due to the failure of modules to mate and seal the atmosphere, risking loss of crew and ISS functions. The manufacturing processes that create the PBNs need to be strictly controlled. Functional (torque vs. tension) acceptance test failures will be the result of processes not being strictly followed. Without the proper knowledge of thread tolerances, fabrication techniques, and dry film lubricant application processes, PBNs will be, and have been manufactured improperly. The knowledge gained from acceptance test failures and the resolution of those failures, thread fabrication techniques and thread dry film lubrication processes can be applied to many aerospace mechanisms to enhance their performance. Test data and manufactured PBN thread geometry will be discussed for both failed and successfully accepted PBNs.

TRANSFORM - TRANsient Simulation Framework of Reconfigurable Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greenwood, Michael S; Cetiner, Mustafa S; Fugate, David L

Existing development tools for early stage design and scoping of energy systems are often time consuming to use, proprietary, and do not contain the necessary function to model complete systems (i.e., controls, primary, and secondary systems) in a common platform. The Modelica programming language based TRANSFORM tool (1) provides a standardized, common simulation environment for early design of energy systems (i.e., power plants), (2) provides a library of baseline component modules to be assembled into full plant models using available geometry, design, and thermal-hydraulic data, (3) defines modeling conventions for interconnecting component models, and (4) establishes user interfaces and supportmore » tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.« less

Low profile, highly configurable, current sharing paralleled wide band gap power device power module

DOEpatents

McPherson, Brice; Killeen, Peter D.; Lostetter, Alex; Shaw, Robert; Passmore, Brandon; Hornberger, Jared; Berry, Tony M

2016-08-23

A power module with multiple equalized parallel power paths supporting multiple parallel bare die power devices constructed with low inductance equalized current paths for even current sharing and clean switching events. Wide low profile power contacts provide low inductance, short current paths, and large conductor cross section area provides for massive current carrying. An internal gate & source kelvin interconnection substrate is provided with individual ballast resistors and simple bolted construction. Gate drive connectors are provided on either left or right size of the module. The module is configurable as half bridge, full bridge, common source, and common drain topologies.

Motor Recovery After Subcortical Stroke Depends on Modulation of Extant Motor Networks.

PubMed

Sharma, Nikhil; Baron, Jean-Claude

2015-01-01

Stroke is the leading cause of long-term disability. Functional imaging studies report widespread changes in movement-related cortical networks after stroke. Whether these are a result of stroke-specific cognitive processes or reflect modulation of existing movement-related networks is unknown. Understanding this distinction is critical in establishing more effective restorative therapies after stroke. Using multivariate analysis (tensor-independent component analysis - TICA), we map the neural networks involved during motor imagery (MI) and executed movement (EM) in subcortical stroke patients and age-matched controls. Twenty subcortical stroke patients and 17 age-matched controls were recruited. They were screened for their ability to carry out MI (Chaotic MI Assessment). The fMRI task was a right-hand finger-thumb opposition sequence (auditory-paced 1 Hz; 2, 3, 4, 5, 2…). Two separate runs were acquired (MI and rest and EM and rest; block design). There was no distinction between groups or tasks until the last stage of analysis, which allowed TICA to identify independent components (ICs) that were common or distinct to each group or task with no prior assumptions. TICA defined 28 ICs. ICs representing artifacts were excluded. ICs were only included if the subject scores were significant (for either EM or MI). Seven ICs remained that involved the primary and secondary motor networks. All ICs were shared between the stroke and age-matched controls. Five ICs were common to both tasks and three were exclusive to EM. Two ICs were related to motor recovery and one with time since stroke onset, but all were shared with age-matched controls. No IC was exclusive to stroke patients. We report that the cortical networks in stroke patients that relate to recovery of motor function represent modulation of existing cortical networks present in age-matched controls. The absence of cortical networks specific to stroke patients suggests that motor adaptation and other potential confounders (e.g., effort and additional muscle use) are not responsible for the changes in the cortical networks reported after stroke. This highlights that recovery of motor function after subcortical stroke involves preexisting cortical networks that could help identify more effective restorative therapies.

Salivary enhancement: current status and future therapies.

PubMed

Atkinson, J C; Baum, B J

2001-10-01

Saliva provides the principal protective milieu for teeth by modulating oral microbial ecosystems and reversing the initial phases of caries development. Patients with inadequate salivary function are at increased risk for dental decay. Therefore, it is likely that therapies that increase overall fluid output of these individuals will reverse early carious lesions. The most common causes of salivary dysfunction are medication usage, Sjögren's syndrome, and damage of salivary parenchyma during therapeutic irradiation. For patients with remaining functional acinar tissue, treatment with the parasypathomimetic secretogogues pilocarpine and Cevimeline may provide relief. However, these medications do not benefit all patients. The possibilities of using gene therapy and tissue engineering to develop treatments for those with severe salivary dysfunction are discussed.

Limb deficiency and prosthetic management. 2. Aging with limb loss.

PubMed

Flood, Katherine M; Huang, Mark E; Roberts, Toni L; Pasquina, Paul F; Nelson, Virginia S; Bryant, Phillip R

2006-03-01

This self-directed learning module highlights the issues faced by people aging with limb loss. It is part of the study guide on limb deficiency and vascular rehabilitation in the Self-Directed Physiatric Education Program for practitioners and trainees in physical medicine and rehabilitation. This article specifically focuses on the impact that limb loss has on health and physical function throughout the life span. Case examples are used to illustrate what effect limb loss in childhood or young adulthood has on the incidence and management of new impairments or disease processes commonly associated with aging. To discuss the impact of early-life limb loss on the incidence and management of physiologic and functional changes associated with aging.

A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

NASA Astrophysics Data System (ADS)

Lee, Yen-Chun; Patil, Sumersing; Golz, Christopher; Strohmann, Carsten; Ziegler, Slava; Kumar, Kamal; Waldmann, Herbert

2017-02-01

The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

Novel Insights into the Role of Neurospora crassa NDUFAF2, an Evolutionarily Conserved Mitochondrial Complex I Assembly Factor

PubMed Central

Pereira, Bruno; Videira, Arnaldo

2013-01-01

Complex I deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. Mutations in nuclear genes encoding structural subunits or assembly factors of complex I have been increasingly identified as the cause of the diseases. One such factor, NDUFAF2, is a paralog of the NDUFA12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. Herein, we demonstrate that the Neurospora crassa NDUFAF2 homologue, the 13.4L protein, is a late assembly factor that associates with complex I assembly intermediates containing the membrane arm and the connecting part but lacking the N module of the enzyme. Furthermore, we provide evidence that dissociation of the assembly factor is dependent on the incorporation of the putative regulatory module composed of the subunits of 13.4 (NDUFA12), 18.4 (NDUFS6), and 21 (NDUFS4) kDa. Our results demonstrate that the 13.4L protein is a complex I assembly factor functionally conserved from fungi to mammals. PMID:23648483

Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity

PubMed Central

Raj, Prithvi; Rai, Ekta; Song, Ran; Khan, Shaheen; Wakeland, Benjamin E; Viswanathan, Kasthuribai; Arana, Carlos; Liang, Chaoying; Zhang, Bo; Dozmorov, Igor; Carr-Johnson, Ferdicia; Mitrovic, Mitja; Wiley, Graham B; Kelly, Jennifer A; Lauwerys, Bernard R; Olsen, Nancy J; Cotsapas, Chris; Garcia, Christine K; Wise, Carol A; Harley, John B; Nath, Swapan K; James, Judith A; Jacob, Chaim O; Tsao, Betty P; Pasare, Chandrashekhar; Karp, David R; Li, Quan Zhen; Gaffney, Patrick M; Wakeland, Edward K

2016-01-01

Targeted sequencing of sixteen SLE risk loci among 1349 Caucasian cases and controls produced a comprehensive dataset of the variations causing susceptibility to systemic lupus erythematosus (SLE). Two independent disease association signals in the HLA-D region identified two regulatory regions containing 3562 polymorphisms that modified thirty-seven transcription factor binding sites. These extensive functional variations are a new and potent facet of HLA polymorphism. Variations modifying the consensus binding motifs of IRF4 and CTCF in the XL9 regulatory complex modified the transcription of HLA-DRB1, HLA-DQA1 and HLA-DQB1 in a chromosome-specific manner, resulting in a 2.5-fold increase in the surface expression of HLA-DR and DQ molecules on dendritic cells with SLE risk genotypes, which increases to over 4-fold after stimulation. Similar analyses of fifteen other SLE risk loci identified 1206 functional variants tightly linked with disease-associated SNPs and demonstrated that common disease alleles contain multiple causal variants modulating multiple immune system genes. DOI: http://dx.doi.org/10.7554/eLife.12089.001 PMID:26880555

Early Childhood Development Cultural Considerations--Commonalities, Variables, and Local Community Determinants for Program Modules.

ERIC Educational Resources Information Center

Taylor, Anne P.; Warren, Dave

The paper discusses cultural commonality and variability considerations of the Native American populations served by the Federation of Rocky Mountain States Educational Technical Development (ETD) Project. Section I explores important factors to consider when setting up an Early Childhood Development program module for Indian people, such as…

77 FR 35691 - Update to Electronic Common Technical Document Module 1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-14

... Electronic Common Technical Document (eCTD) Module 1, which is used for electronic submission of... they are received with a limit of 350. SUPPLEMENTARY INFORMATION: The eCTD is an International... Research (CBER) have been receiving submissions in the eCTD format since 2003, and the eCTD has been the...

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

PubMed

Sanderson, Lacey-Anne; Ficklin, Stephen P; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A; Bett, Kirstin E; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

PubMed Central

Sanderson, Lacey-Anne; Ficklin, Stephen P.; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A.; Bett, Kirstin E.; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map’, ‘Genetic’, ‘Publication’, ‘Project’, ‘Contact’ and the ‘Natural Diversity’ modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. Database URL: http://tripal.info/ PMID:24163125

Single-trial EEG-informed fMRI reveals spatial dependency of BOLD signal on early and late IC-ERP amplitudes during face recognition.

PubMed

Wirsich, Jonathan; Bénar, Christian; Ranjeva, Jean-Philippe; Descoins, Médéric; Soulier, Elisabeth; Le Troter, Arnaud; Confort-Gouny, Sylviane; Liégeois-Chauvel, Catherine; Guye, Maxime

2014-10-15

Simultaneous EEG-fMRI has opened up new avenues for improving the spatio-temporal resolution of functional brain studies. However, this method usually suffers from poor EEG quality, especially for evoked potentials (ERPs), due to specific artifacts. As such, the use of EEG-informed fMRI analysis in the context of cognitive studies has particularly focused on optimizing narrow ERP time windows of interest, which ignores the rich diverse temporal information of the EEG signal. Here, we propose to use simultaneous EEG-fMRI to investigate the neural cascade occurring during face recognition in 14 healthy volunteers by using the successive ERP peaks recorded during the cognitive part of this process. N170, N400 and P600 peaks, commonly associated with face recognition, were successfully and reproducibly identified for each trial and each subject by using a group independent component analysis (ICA). For the first time we use this group ICA to extract several independent components (IC) corresponding to the sequence of activation and used single-trial peaks as modulation parameters in a general linear model (GLM) of fMRI data. We obtained an occipital-temporal-frontal stream of BOLD signal modulation, in accordance with the three successive IC-ERPs providing an unprecedented spatio-temporal characterization of the whole cognitive process as defined by BOLD signal modulation. By using this approach, the pattern of EEG-informed BOLD modulation provided improved characterization of the network involved than the fMRI-only analysis or the source reconstruction of the three ERPs; the latter techniques showing only two regions in common localized in the occipital lobe. Copyright © 2014 Elsevier Inc. All rights reserved.

Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis.

PubMed

Hwang, Sun-Goo; Kim, Dong Sub; Hwang, Jung Eun; Han, A-Reum; Jang, Cheol Seong

2014-05-15

In order to better understand the biological systems that are affected in response to cosmic ray (CR), we conducted weighted gene co-expression network analysis using the module detection method. By using the Pearson's correlation coefficient (PCC) value, we evaluated complex gene-gene functional interactions between 680 CR-responsive probes from integrated microarray data sets, which included large-scale transcriptional profiling of 1000 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched gene ontology (GO) functions, such as oxidoreductase activity, hydrolase activity, and response to stimulus and stress. In particular, modules 1 and 2 commonly showed enriched annotation categories such as oxidoreductase activity, including enriched cis-regulatory elements known as ROS-specific regulators. These results suggest that the ROS-mediated irradiation response pathway is affected by CR in modules 1 and 2. We found 243 ionizing radiation (IR)-responsive probes that exhibited similarities in expression patterns in various irradiation microarray data sets. The expression patterns of 6 randomly selected IR-responsive genes were evaluated by quantitative reverse transcription polymerase chain reaction following treatment with CR, gamma rays (GR), and ion beam (IB); similar patterns were observed among these genes under these 3 treatments. Moreover, we constructed subnetworks of IR-responsive genes and evaluated the expression levels of their neighboring genes following GR treatment; similar patterns were observed among them. These results of network-based analyses might provide a clue to understanding the complex biological system related to the CR response in plants. Copyright © 2014 Elsevier B.V. All rights reserved.

TkPl_SU: An Open-source Perl Script Builder for Seismic Unix

NASA Astrophysics Data System (ADS)

Lorenzo, J. M.

2017-12-01

TkPl_SU (beta) is a graphical user interface (GUI) to select parameters for Seismic Unix (SU) modules. Seismic Unix (Stockwell, 1999) is a widely distributed free software package for processing seismic reflection and signal processing. Perl/Tk is a mature, well-documented and free object-oriented graphical user interface for Perl. In a classroom environment, shell scripting of SU modules engages students and helps focus on the theoretical limitations and strengths of signal processing. However, complex interactive processing stages, e.g., selection of optimal stacking velocities, killing bad data traces, or spectral analysis requires advanced flows beyond the scope of introductory classes. In a research setting, special functionality from other free seismic processing software such as SioSeis (UCSD-NSF) can be incorporated readily via an object-oriented style to programming. An object oriented approach is a first step toward efficient extensible programming of multi-step processes, and a simple GUI simplifies parameter selection and decision making. Currently, in TkPl_SU, Perl 5 packages wrap 19 of the most common SU modules that are used in teaching undergraduate and first-year graduate student classes (e.g., filtering, display, velocity analysis and stacking). Perl packages (classes) can advantageously add new functionality around each module and clarify parameter names for easier usage. For example, through the use of methods, packages can isolate the user from repetitive control structures, as well as replace the names of abbreviated parameters with self-describing names. Moose, an extension of the Perl 5 object system, greatly facilitates an object-oriented style. Perl wrappers are self-documenting via Perl programming document markup language.

Smartphone-coupled rhinolaryngoscopy at the point of care

NASA Astrophysics Data System (ADS)

Mink, Jonah; Bolton, Frank J.; Sebag, Cathy M.; Peterson, Curtis W.; Assia, Shai; Levitz, David

2018-02-01

Rhinolaryngoscopy remains difficult to perform in resource-limited settings due to the high cost of purchasing and maintaining equipment as well as the need for specialists to interpret exam findings. While the lack of expertise can be obviated by adopting telemedicine-based approaches, the capture, storage, and sharing of images/video is not a common native functionality of medical devices. Most rhinolaryngoscopy systems consist of an endoscope that interfaces with the patient's naso/oropharynx, and a tower of modules that record video/images. However, these expensive and bulky modules can be replaced by a smartphone that can fulfill the same functions but at a lower cost. To demonstrate this, a commercially available rhinolaryngoscope was coupled to a smartphone using a 3D-printed adapter. Software developed for other clinical applications was repurposed for ENT use, including an application that controls image and video capture, a HIPAA-compliant image/video storage and transfer cloud database, and customized software features developed to improve practitioner competency. Audio recording capabilities to assess speech pathology were also integrated into the smartphone rhinolaryngoscope system. The illumination module coupled onto the endoscope remained unchanged. The spatial resolution of the rhinolaryngoscope system was defined by the fiber diameter of endoscope fiber bundle, rather than the smartphone camera. The mobile rhinolaryngoscope system was used with appropriate patients by a general practitioner in an office setting. The general practitioner then consulted with an ENT specialist via the HIPAA compliant cloud database and workflow modules on difficult cases. These results suggest the smartphone-based rhinolaryngoscope holds promise for use in low-resource settings.

Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

NASA Astrophysics Data System (ADS)

Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella

2015-07-01

Small-molecule inhibitors of Tumor Necrosis Factor α Converting Enzyme (TACE) are a promising therapeutic tool for Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. Here we report on an extensive chemical-physical analysis of the media effects in modulating the conformational landscape of MBET306, the common scaffold and a synthetic precursor of a family of recently discovered tartrate-based TACE inhibitors. The structural features of this molecule with potential pharmaceutical applications have been disclosed by interpreting extensive photophysical measurements in various solvents with the aid of enhanced sampling molecular dynamics simulations and time dependent density functional calculations. Using a combination of experimental and computational techniques, the paper provides a general protocol for studying the structure in solution of molecular systems characterized by the existence of conformational metastable states.

Crosstalk between poly(ADP-ribose) polymerase and sirtuin enzymes

PubMed Central

Cantó, Carles; Sauve, Anthony A.; Bai, Peter

2013-01-01

Poly(ADP-ribose) polymerases (PARPs) are NAD+ dependent enzymes that were identified as DNA repair proteins, however, today it seems clear that PARPs are responsible for a plethora of biological functions. Sirtuins (SIRTs) are NAD+-dependent deacetylase enzymes involved in the same biological processes as PARPs raising the question whether PARP and SIRT enzymes may interact with each other in physiological and pathophysiological conditions. Hereby we review the current understanding of the SIRT-PARP interplay in regard to the biochemical nature of the interaction (competition for the common NAD+ substrate, mutual posttranslational modifications and direct transcriptional effects) and the physiological, or pathophysiological consequences of the interactions (metabolic events, oxidative stress response, genomic stability and ageing). Finally, we give an overview of the possibilities of pharmacological intervention to modulate PARP and SIRT enzymes either directly, or through modulating NAD+ homeostasis. PMID:23357756

The neurobiological basis of orientation in insects: insights from the silkmoth mating dance.

PubMed

Namiki, Shigehiro; Kanzaki, Ryohei

2016-06-01

Counterturning is a common movement pattern during orientation behavior in insects. Once male moths sense sex pheromones and then lose the input, they demonstrate zigzag movements, alternating between left and right turns, to increase the probability to contact with the pheromone plume. We summarize the anatomy and function of the neural circuit involved in pheromone orientation in the silkmoth. A neural circuit, the lateral accessory lobe (LAL), serves a role as the circuit module for zigzag movements and controls this operation using a flip-flop neural switch. Circuit design of the LAL is well conserved across species. We hypothesize that this zigzag module is utilized in a wide range of insect behavior. We introduce two examples of the potential use: orientation flight and the waggle dance in bees. Copyright © 2016 Elsevier Inc. All rights reserved.

Modularity of a leaf moth-wing pattern and a versatile characteristic of the wing-pattern ground plan

PubMed Central

2013-01-01

Background One of the most intriguing questions in evolutionary developmental biology is how an insect acquires a mimicry pattern within its body parts. A striking example of pattern mimicry is found in the pattern diversity of moth and butterfly wings, which is thought to evolve from preexisting elements illustrated by the nymphalid ground plan (NGP). Previous studies demonstrated that individuality of the NGP facilitates the decoupling of associated common elements, leading to divergence. In contrast, recent studies on the concept of modularity have argued the importance of a combination of coupling and decoupling of the constituent elements. Here, we examine the modularity of a mimicry wing pattern in a moth and explore an evolvable characteristic of the NGP. Results This study examined the wings of the noctuid moth Oraesia excavata, which closely resemble leaves with a leaf venation pattern. Based on a comparative morphological procedure, we found that this leaf pattern was formed by the NGP common elements. Using geometric morphometrics combined with network analysis, we found that each of the modules in the leaf pattern integrates the constituent components of the leaf venation pattern (i.e., the main and lateral veins). Moreover, the detected modules were established by coupling different common elements and decoupling even a single element into different modules. The modules of the O. excavata wing pattern were associated with leaf mimicry, not with the individuality of the NGP common elements. For comparison, we also investigated the modularity of a nonmimetic pattern in the noctuid moth Thyas juno. Quantitative analysis demonstrated that the modules of the T. juno wing pattern regularly corresponded to the individuality of the NGP common elements, unlike those in the O. excavata wing pattern. Conclusions This study provides the first evidence for modularity in a leaf mimicry pattern. The results suggest that the evolution of this pattern involves coupling and decoupling processes to originate these modules, free from the individuality of the NGP system. We propose that this evolution has been facilitated by a versatile characteristic of the NGP, allowing the association of freely modifiable subordinate common elements to make modules. PMID:23890367

Regulatory network analysis of Epstein-Barr virus identifies functional modules and hub genes involved in infectious mononucleosis.

PubMed

Poorebrahim, Mansour; Salarian, Ali; Najafi, Saeideh; Abazari, Mohammad Foad; Aleagha, Maryam Nouri; Dadras, Mohammad Nasr; Jazayeri, Seyed Mohammad; Ataei, Atousa; Poortahmasebi, Vahdat

2017-05-01

Epstein-Barr virus (EBV) is the most common cause of infectious mononucleosis (IM) and establishes lifetime infection associated with a variety of cancers and autoimmune diseases. The aim of this study was to develop an integrative gene regulatory network (GRN) approach and overlying gene expression data to identify the representative subnetworks for IM and EBV latent infection (LI). After identifying differentially expressed genes (DEGs) in both IM and LI gene expression profiles, functional annotations were applied using gene ontology (GO) and BiNGO tools, and construction of GRNs, topological analysis and identification of modules were carried out using several plugins of Cytoscape. In parallel, a human-EBV GRN was generated using the Hu-Vir database for further analyses. Our analysis revealed that the majority of DEGs in both IM and LI were involved in cell-cycle and DNA repair processes. However, these genes showed a significant negative correlation in the IM and LI states. Furthermore, cyclin-dependent kinase 2 (CDK2) - a hub gene with the highest centrality score - appeared to be the key player in cell cycle regulation in IM disease. The most significant functional modules in the IM and LI states were involved in the regulation of the cell cycle and apoptosis, respectively. Human-EBV network analysis revealed several direct targets of EBV proteins during IM disease. Our study provides an important first report on the response to IM/LI EBV infection in humans. An important aspect of our data was the upregulation of genes associated with cell cycle progression and proliferation.

Constellation Architecture Team-Lunar Scenario 12.0 Habitation Overview

NASA Technical Reports Server (NTRS)

Kennedy, Kriss J.; Toups, Larry D.; Rudisill, Marianne

2010-01-01

This paper will describe an overview of the Constellation Architecture Team Lunar Scenario 12.0 (LS-12) surface habitation approach and concept performed during the study definition. The Lunar Scenario 12 architecture study focused on two primary habitation approaches: a horizontally-oriented habitation module (LS-12.0) and a vertically-oriented habitation module (LS-12.1). This paper will provide an overview of the 12.0 lunar surface campaign, the associated outpost architecture, habitation functionality, concept description, system integration strategy, mass and power resource estimates. The Scenario 12 architecture resulted from combining three previous scenario attributes from Scenario 4 "Optimized Exploration", Scenario 5 "Fission Surface Power System" and Scenario 8 "Initial Extensive Mobility" into Scenario 12 along with an added emphasis on defining the excursion ConOps while the crew is away from the outpost location. This paper will describe an overview of the CxAT-Lunar Scenario 12.0 habitation concepts and their functionality. The Crew Operations area includes basic crew accommodations such as sleeping, eating, hygiene and stowage. The EVA Operations area includes additional EVA capability beyond the suitlock function such as suit maintenance, spares stowage, and suit stowage. The Logistics Operations area includes the enhanced accommodations for 180 days such as enhanced life support systems hardware, consumable stowage, spares stowage, interconnection to the other habitation elements, a common interface mechanism for future growth, and mating to a pressurized rover or Pressurized Logistics Module (PLM). The Mission & Science Operations area includes enhanced outpost autonomy such as an IVA glove box, life support, medical operations, and exercise equipment.

Design of visible and IR infrared dual-band common-path telescope system

NASA Astrophysics Data System (ADS)

Guo, YuLin; Yu, Xun; Tao, Yu; Jiang, Xu

2018-01-01

The use of visible and IR infrared dual-band combination can effectively improve the performance of photoelectric detection system,TV and IR system were designed with the common path by the common reflection optical system.A TV/IR infrared common-caliber and common-path system is designed,which can realize the Remote and all-day information.For the 640×512 cooled focal plane array,an infrared middle wave system was presented with a focal length of 600mm F number of 4 field of view(FOV) of 0.38°×0.43°, the system uses optical passive thermal design, has o compact structure and can meet 100% cold shield efficiency,meanwhile it meets the design requirements of lightweight and athermalization. For the 1920×1080 pixels CCD,a visible (TV) system ,which had 500mm focal length, 4F number,was completed.The final optical design along with their modulation transfer function is presented,showing excellent imaging performance in dual-band at the temperature range between -40° and 60°.

Common symbiosis genes CERBERUS and NSP1 provide additional insight into the establishment of arbuscular mycorrhizal and root nodule symbioses in Lotus japonicus.

PubMed

Nagae, Miwa; Takeda, Naoya; Kawaguchi, Masayoshi

2014-01-01

Arbuscular mycorrhizal symbiosis (AMS) and root nodule symbiosis (RNS) share several common symbiotic components, and many of the common symbiosis mutants block the entry of symbionts into the roots. We recently reported that CERBERUS (an E3 ubiquitin ligase) and NSP1 (a GRAS family transcription factor), required for RNS, also modulate AMS development in Lotus japonicus. The novel common symbiosis mutants, cerberus and nsp1, have low colonization of arbuscular mycorrhiza (AM) fungi, caused by a defect in internal hyphal elongation and by a decreased fungal entry into the roots, respectively. Here, we showed that CERBERUS was induced at the sites of symbiotic fungal or bacterial infection. NSP1 has been implicated in a strigolactone biosynthesis gene DWARF27 expression. Nevertheless, in nsp1, DWARF27 was induced by inoculation with AM fungi, implying the existence of a NSP1-independent regulatory mechanism of strigolactone biosynthesis during AMS establishment. These results support functional analysis of CERBERUS and NSP1, and also contribute to elucidation of common mechanisms in AMS and RNS.

[Not Available].

PubMed

Yanashima, Ryoji; Kitagawa, Noriyuki; Matsubara, Yoshiya; Weatheritt, Robert; Oka, Kotaro; Kikuchi, Shinichi; Tomita, Masaru; Ishizaki, Shun

2009-01-01

The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant differences were found between the original undirected graphs and the graphs in which inactive proteins were eliminated from the gene expression data. We analyzed signaling networks by focusing on those pathways that best reflected cellular function. Therefore, our analysis of pathways started from the ligands and progressed to transcription factors and cytoskeletal proteins. We employed the Python module to assess the target network. This involved comparing the original and restricted signaling cascades as a directed graph using microarray gene expression profiles of late onset Alzheimer's disease. The most commonly used method of shortest-path analysis neglects to consider the influences of alternative pathways that can affect the activation of transcription factors or cytoskeletal proteins. We therefore introduced included k-shortest paths and k-cycles in our network analysis using the Python modules, which allowed us to attain a reasonable computational time and identify k-shortest paths. This technique reflected results found in vivo and identified pathways not found when shortest path or degree analysis was applied. Our module enabled us to comprehensively analyse the characteristics of biomolecular networks and also enabled analysis of the effects of diseases considering the feedback loop and feedforward loop control structures as an alternative path.

Diabetes and Alzheimer's Disease: Can Tea Phytochemicals Play a Role in Prevention?

PubMed

Fernando, Warnakulasuriya M A D B; Somaratne, Geeshani; Goozee, Kathryn G; Williams, Shehan; Singh, Harjinder; Martins, Ralph N

2017-01-01

Dementia and diabetes mellitus are prevalent disorders in the elderly population. While recognized as two distinct diseases, diabetes has more recently recognized as a significant contributor to risk for developing dementia, and some studies make reference to type 3 diabetes, a condition resulting from insulin resistance in the brain. Alzheimer's disease, the most common form of dementia, and diabetes, interestingly, share underlying pathological processes, commonality in risk factors, and, importantly, pathways for intervention. Tea has been suggested to possess potent antioxidant properties. It is rich in phytochemicals including, flavonoids, tannins, caffeine, polyphenols, boheic acid, theophylline, theobromine, anthocyanins, gallic acid, and finally epigallocatechin-3-gallate, which is considered to be the most potent active ingredient. Flavonoid phytochemicals, known as catechins, within tea offer potential benefits for reducing the risk of diabetes and Alzheimer's disease by targeting common risk factors, including obesity, hyperlipidemia, hypertension, cardiovascular disease, and stroke. Studies also show that catechins may prevent the formation of amyloid-β plaques and enhance cognitive functions, and thus may be useful in treating patients who have Alzheimer's disease or dementia. Furthermore, other phytochemicals found within tea offer important antioxidant properties along with innate properties capable of modulating intracellular neuronal signal transduction pathways and mitochondrial function.

Large liquid rocket engine transient performance simulation system

NASA Technical Reports Server (NTRS)

Mason, J. R.; Southwick, R. D.

1989-01-01

Phase 1 of the Rocket Engine Transient Simulation (ROCETS) program consists of seven technical tasks: architecture; system requirements; component and submodel requirements; submodel implementation; component implementation; submodel testing and verification; and subsystem testing and verification. These tasks were completed. Phase 2 of ROCETS consists of two technical tasks: Technology Test Bed Engine (TTBE) model data generation; and system testing verification. During this period specific coding of the system processors was begun and the engineering representations of Phase 1 were expanded to produce a simple model of the TTBE. As the code was completed, some minor modifications to the system architecture centering on the global variable common, GLOBVAR, were necessary to increase processor efficiency. The engineering modules completed during Phase 2 are listed: INJTOO - main injector; MCHBOO - main chamber; NOZLOO - nozzle thrust calculations; PBRNOO - preburner; PIPE02 - compressible flow without inertia; PUMPOO - polytropic pump; ROTROO - rotor torque balance/speed derivative; and TURBOO - turbine. Detailed documentation of these modules is in the Appendix. In addition to the engineering modules, several submodules were also completed. These submodules include combustion properties, component performance characteristics (maps), and specific utilities. Specific coding was begun on the system configuration processor. All functions necessary for multiple module operation were completed but the SOLVER implementation is still under development. This system, the Verification Checkout Facility (VCF) allows interactive comparison of module results to store data as well as provides an intermediate checkout of the processor code. After validation using the VCF, the engineering modules and submodules were used to build a simple TTBE.

Plant cell surface receptor-mediated signaling - a common theme amid diversity.

PubMed

He, Yunxia; Zhou, Jinggeng; Shan, Libo; Meng, Xiangzong

2018-01-29

Sessile plants employ a diverse array of plasma membrane-bound receptors to perceive endogenous and exogenous signals for regulation of plant growth, development and immunity. These cell surface receptors include receptor-like kinases (RLKs) and receptor-like proteins (RLPs) that harbor different extracellular domains for perception of distinct ligands. Several RLK and RLP signaling pathways converge at the somatic embryogenesis receptor kinases (SERKs), which function as shared co-receptors. A repertoire of receptor-like cytoplasmic kinases (RLCKs) associate with the receptor complexes to relay intracellular signaling. Downstream of the receptor complexes, mitogen-activated protein kinase (MAPK) cascades are among the key signaling modules at which the signals converge, and these cascades regulate diverse cellular and physiological responses through phosphorylation of different downstream substrates. In this Review, we summarize the emerging common theme that underlies cell surface receptor-mediated signaling pathways in Arabidopsis thaliana : the dynamic association of RLKs and RLPs with specific co-receptors and RLCKs for signal transduction. We further discuss how signaling specificities are maintained through modules at which signals converge, with a focus on SERK-mediated receptor signaling. © 2018. Published by The Company of Biologists Ltd.

A Neural Signature Encoding Decisions under Perceptual Ambiguity

PubMed Central

Sun, Sai; Yu, Rongjun

2017-01-01

Abstract People often make perceptual decisions with ambiguous information, but it remains unclear whether the brain has a common neural substrate that encodes various forms of perceptual ambiguity. Here, we used three types of perceptually ambiguous stimuli as well as task instructions to examine the neural basis for both stimulus-driven and task-driven perceptual ambiguity. We identified a neural signature, the late positive potential (LPP), that encoded a general form of stimulus-driven perceptual ambiguity. In addition to stimulus-driven ambiguity, the LPP was also modulated by ambiguity in task instructions. To further specify the functional role of the LPP and elucidate the relationship between stimulus ambiguity, behavioral response, and the LPP, we employed regression models and found that the LPP was specifically associated with response latency and confidence rating, suggesting that the LPP encoded decisions under perceptual ambiguity. Finally, direct behavioral ratings of stimulus and task ambiguity confirmed our neurophysiological findings, which could not be attributed to differences in eye movements either. Together, our findings argue for a common neural signature that encodes decisions under perceptual ambiguity but is subject to the modulation of task ambiguity. Our results represent an essential first step toward a complete neural understanding of human perceptual decision making. PMID:29177189

[Hypertension and its related organ damage--pathophysiology and new diagnostic strategy].

PubMed

Shimosawa, Tatsuo

2013-03-01

Hypertension is the most common non-communicable disease. Although novel therapeutic agents have become available and blood pressure tends to be lowered, the morbidity and mortality rates of hypertension-induced renal failure or stroke in Japan have not decreased in recent decades. This might be because we cannot choose appropriate therapy based upon the pathophysiology of high blood pressure and the degree of organ damage. Salt-sensitive hypertension has a poorer prognosis than resistant hypertension regardless of blood pressure control and is more common in Asians than in Caucasians. Therefore, understanding the pathophysiology of salt sensitivity and diagnosing it is very important. Recent advances in research into salt-sensitive hypertension revealed that mineralocorticoid receptor activities independent of aldosterone induce both salt-sensitive hypertension and organ damage, which is closely related to oxidative stress. In an other study, sympathetic overactivity was related to salt sensitivity via epigenetic modulation. Current research into new surrogate markers is mostly focused on hunting for humoral factors, and novel directions to evaluate receptor functions such as mineralocorticoid receptor or epigenetic modulations would open a new door for the early diagnosis of organ damage and tailor-made therapy.

A Neural Signature Encoding Decisions under Perceptual Ambiguity.

PubMed

Sun, Sai; Yu, Rongjun; Wang, Shuo

2017-01-01

People often make perceptual decisions with ambiguous information, but it remains unclear whether the brain has a common neural substrate that encodes various forms of perceptual ambiguity. Here, we used three types of perceptually ambiguous stimuli as well as task instructions to examine the neural basis for both stimulus-driven and task-driven perceptual ambiguity. We identified a neural signature, the late positive potential (LPP), that encoded a general form of stimulus-driven perceptual ambiguity. In addition to stimulus-driven ambiguity, the LPP was also modulated by ambiguity in task instructions. To further specify the functional role of the LPP and elucidate the relationship between stimulus ambiguity, behavioral response, and the LPP, we employed regression models and found that the LPP was specifically associated with response latency and confidence rating, suggesting that the LPP encoded decisions under perceptual ambiguity. Finally, direct behavioral ratings of stimulus and task ambiguity confirmed our neurophysiological findings, which could not be attributed to differences in eye movements either. Together, our findings argue for a common neural signature that encodes decisions under perceptual ambiguity but is subject to the modulation of task ambiguity. Our results represent an essential first step toward a complete neural understanding of human perceptual decision making.

Cortico-Striatal-Thalamic Loop Circuits of the Salience Network: A Central Pathway in Psychiatric Disease and Treatment.

PubMed

Peters, Sarah K; Dunlop, Katharine; Downar, Jonathan

2016-01-01

The salience network (SN) plays a central role in cognitive control by integrating sensory input to guide attention, attend to motivationally salient stimuli and recruit appropriate functional brain-behavior networks to modulate behavior. Mounting evidence suggests that disturbances in SN function underlie abnormalities in cognitive control and may be a common etiology underlying many psychiatric disorders. Such functional and anatomical abnormalities have been recently apparent in studies and meta-analyses of psychiatric illness using functional magnetic resonance imaging (fMRI) and voxel-based morphometry (VBM). Of particular importance, abnormal structure and function in major cortical nodes of the SN, the dorsal anterior cingulate cortex (dACC) and anterior insula (AI), have been observed as a common neurobiological substrate across a broad spectrum of psychiatric disorders. In addition to cortical nodes of the SN, the network's associated subcortical structures, including the dorsal striatum, mediodorsal thalamus and dopaminergic brainstem nuclei, comprise a discrete regulatory loop circuit. The SN's cortico-striato-thalamo-cortical loop increasingly appears to be central to mechanisms of cognitive control, as well as to a broad spectrum of psychiatric illnesses and their available treatments. Functional imbalances within the SN loop appear to impair cognitive control, and specifically may impair self-regulation of cognition, behavior and emotion, thereby leading to symptoms of psychiatric illness. Furthermore, treating such psychiatric illnesses using invasive or non-invasive brain stimulation techniques appears to modulate SN cortical-subcortical loop integrity, and these effects may be central to the therapeutic mechanisms of brain stimulation treatments in many psychiatric illnesses. Here, we review clinical and experimental evidence for abnormalities in SN cortico-striatal-thalamic loop circuits in major depression, substance use disorders (SUD), anxiety disorders, schizophrenia and eating disorders (ED). We also review emergent therapeutic evidence that novel invasive and non-invasive brain stimulation treatments may exert therapeutic effects by normalizing abnormalities in the SN loop, thereby restoring the capacity for cognitive control. Finally, we consider a series of promising directions for future investigations on the role of SN cortico-striatal-thalamic loop circuits in the pathophysiology and treatment of psychiatric disorders.

Cortico-Striatal-Thalamic Loop Circuits of the Salience Network: A Central Pathway in Psychiatric Disease and Treatment

PubMed Central

Peters, Sarah K.; Dunlop, Katharine; Downar, Jonathan

2016-01-01

The salience network (SN) plays a central role in cognitive control by integrating sensory input to guide attention, attend to motivationally salient stimuli and recruit appropriate functional brain-behavior networks to modulate behavior. Mounting evidence suggests that disturbances in SN function underlie abnormalities in cognitive control and may be a common etiology underlying many psychiatric disorders. Such functional and anatomical abnormalities have been recently apparent in studies and meta-analyses of psychiatric illness using functional magnetic resonance imaging (fMRI) and voxel-based morphometry (VBM). Of particular importance, abnormal structure and function in major cortical nodes of the SN, the dorsal anterior cingulate cortex (dACC) and anterior insula (AI), have been observed as a common neurobiological substrate across a broad spectrum of psychiatric disorders. In addition to cortical nodes of the SN, the network’s associated subcortical structures, including the dorsal striatum, mediodorsal thalamus and dopaminergic brainstem nuclei, comprise a discrete regulatory loop circuit. The SN’s cortico-striato-thalamo-cortical loop increasingly appears to be central to mechanisms of cognitive control, as well as to a broad spectrum of psychiatric illnesses and their available treatments. Functional imbalances within the SN loop appear to impair cognitive control, and specifically may impair self-regulation of cognition, behavior and emotion, thereby leading to symptoms of psychiatric illness. Furthermore, treating such psychiatric illnesses using invasive or non-invasive brain stimulation techniques appears to modulate SN cortical-subcortical loop integrity, and these effects may be central to the therapeutic mechanisms of brain stimulation treatments in many psychiatric illnesses. Here, we review clinical and experimental evidence for abnormalities in SN cortico-striatal-thalamic loop circuits in major depression, substance use disorders (SUD), anxiety disorders, schizophrenia and eating disorders (ED). We also review emergent therapeutic evidence that novel invasive and non-invasive brain stimulation treatments may exert therapeutic effects by normalizing abnormalities in the SN loop, thereby restoring the capacity for cognitive control. Finally, we consider a series of promising directions for future investigations on the role of SN cortico-striatal-thalamic loop circuits in the pathophysiology and treatment of psychiatric disorders. PMID:28082874

Study on real-time images compounded using spatial light modulator

NASA Astrophysics Data System (ADS)

Xu, Jin; Chen, Zhebo; Ni, Xuxiang; Lu, Zukang

2007-01-01

Image compounded technology is often used on film and its facture. In common, image compounded use image processing arithmetic, get useful object, details, background or some other things from the images firstly, then compounding all these information into one image. When using this method, the film system needs a powerful processor, for the process function is very complex, we get the compounded image for a few time delay. In this paper, we introduce a new method of image real-time compounded, use this method, we can do image composite at the same time with movie shot. The whole system is made up of two camera-lens, spatial light modulator array and image sensor. In system, the spatial light modulator could be liquid crystal display (LCD), liquid crystal on silicon (LCoS), thin film transistor liquid crystal display (TFTLCD), Deformable Micro-mirror Device (DMD), and so on. Firstly, one camera-lens images the object on the spatial light modulator's panel, we call this camera-lens as first image lens. Secondly, we output an image to the panel of spatial light modulator. Then, the image of the object and image that output by spatial light modulator will be spatial compounded on the panel of spatial light modulator. Thirdly, the other camera-lens images the compounded image to the image sensor, and we call this camera-lens as second image lens. After these three steps, we will gain the compound images by image sensor. For the spatial light modulator could output the image continuously, then the image will be compounding continuously too, and the compounding procedure is completed in real-time. When using this method to compounding image, if we will put real object into invented background, we can output the invented background scene on the spatial light modulator, and the real object will be imaged by first image lens. Then, we get the compounded images by image sensor in real time. The same way, if we will put real background to an invented object, we can output the invented object on the spatial light modulator and the real background will be imaged by first image lens. Then, we can also get the compounded images by image sensor real time. Commonly, most spatial light modulator only can do modulate light intensity, so we can only do compounding BW images if use only one panel which without color filter. If we will get colorful compounded image, we need use the system like three spatial light modulator panel projection. In the paper, the system's optical system framework we will give out. In all experiment, the spatial light modulator used liquid crystal on silicon (LCoS). At the end of the paper, some original pictures and compounded pictures will be given on it. Although the system has a few shortcomings, we can conclude that, using this system to compounding images has no delay to do mathematic compounding process, it is a really real time images compounding system.

An integrative approach to inferring biologically meaningful gene modules.

PubMed

Cho, Ji-Hoon; Wang, Kai; Galas, David J

2011-07-26

The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Nuclear Technology. Course 28: Welding Inspection. Module 28-4, Weld Joint Verification.

ERIC Educational Resources Information Center

Espy, John

This fourth in a series of ten modules for a course titled Welding Inspection discusses the nomenclature, symbols, and the purposes of most common joint designs, preparations, and fit-ups. The module follows a typical format that includes the following sections: (1) introduction, (2) module prerequisites, (3) objectives, (4) notes to…

Hierarchical cortical transcriptome disorganization in autism.

PubMed

Lombardo, Michael V; Courchesne, Eric; Lewis, Nathan E; Pramparo, Tiziano

2017-01-01

Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology. Two ASD cortical transcriptome datasets were re-analyzed using consensus weighted gene co-expression network analysis (WGCNA) to identify common co-expression modules across datasets. Linear mixed-effect models and Bayesian replication statistics were used to identify replicable differentially expressed modules. Eigengene network analysis was then utilized to identify between-group differences in how co-expression modules interact and cluster into hierarchical meta-modular organization. Protein-protein interaction analyses were also used to determine whether dysregulated co-expression modules show enhanced interactions. We find replicable evidence for 10 gene co-expression modules that are differentially expressed in ASD cortex. Rather than being independent non-interacting sources of pathology, these dysregulated co-expression modules work in synergy and physically interact at the protein level. These systems-level transcriptional signals are characterized by downregulation of synaptic processes coordinated with upregulation of immune/inflammation, response to other organism, catabolism, viral processes, translation, protein targeting and localization, cell proliferation, and vasculature development. Hierarchical organization of meta-modules (clusters of highly correlated modules) is also highly affected in ASD. These findings highlight that dysregulation of the ASD cortical transcriptome is characterized by the dysregulation of multiple coordinated transcriptional programs producing synergistic systems-level effects that cannot be fully appreciated by studying the individual component biological processes in isolation.

Dissemination and support of ARGUS for accelerator applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User's Guide that documents the use of the code for all users. To release the code and the User's Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

Functional modules, mutational load and human genetic disease.

PubMed

Zaghloul, Norann A; Katsanis, Nicholas

2010-04-01

The ability to generate a massive amount of sequencing and genotyping data is transforming the study of human genetic disorders. Driven by such innovation, it is likely that whole exome and whole-genome resequencing will replace regionally focused approaches for gene discovery and clinical testing in the next few years. However, this opportunity brings a significant interpretative challenge to assigning function and phenotypic variance to common and rare alleles. Understanding the effect of individual mutations in the context of the remaining genomic variation represents a major challenge to our interpretation of disease. Here, we discuss the challenges of assigning mutation functionality and, drawing from the examples of ciliopathies as well as cohesinopathies and channelopathies, discuss possibilities for the functional modularization of the human genome. Functional modularization in addition to the development of physiologically relevant assays to test allele functionality will accelerate our understanding of disease architecture and enable the use of genome-wide sequence data for disease diagnosis and phenotypic prediction in individuals. Copyright 2010 Elsevier Ltd. All rights reserved.

Functional modules, mutational load and human genetic disease

PubMed Central

Zaghloul, Norann A.; Katsanis, Nicholas

2013-01-01

The ability to generate a massive amount of sequencing and genotyping data is transforming the study of human genetic disorders. Driven by such innovation, it is likely that whole exome and whole-genome resequencing will replace regionally focused approaches for gene discovery and clinical testing in the next few years. However, this opportunity brings a significant interpretative challenge to assigning function and phenotypic variance to common and rare alleles. Understanding the effect of individual mutations in the context of the remaining genomic variation represents a major challenge to our interpretation of disease. Here, we discuss the challenges of assigning mutation functionality and, drawing from the examples of ciliopathies as well as cohesinopathies and channelopathies, discuss possibilities for the functional modularization of the human genome. Functional modularization in addition to the development of physiologically-relevant assays to test allele functionality will accelerate our understanding of disease architecture and enable the use of genome-wide sequence data for disease diagnosis and phenotypic prediction in individuals. PMID:20226561

Impact: a low cost, reconfigurable, digital beamforming common module building block for next generation phased arrays

NASA Astrophysics Data System (ADS)

Paulsen, Lee; Hoffmann, Ted; Fulton, Caleb; Yeary, Mark; Saunders, Austin; Thompson, Dan; Chen, Bill; Guo, Alex; Murmann, Boris

2015-05-01

Phased array systems offer numerous advantages to the modern warfighter in multiple application spaces, including Radar, Electronic Warfare, Signals Intelligence, and Communications. However, a lack of commonality in the underlying technology base for DoD Phased Arrays has led to static systems with long development cycles, slow technology refreshes in response to emerging threats, and expensive, application-specific sub-components. The IMPACT module (Integrated Multi-use Phased Array Common Tile) is a multi-channel, reconfigurable, cost-effective beamformer that provides a common building block for multiple, disparate array applications.

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1, Introducing a Python Edition

NASA Astrophysics Data System (ADS)

Barron, Eric G.; Kaplan, G. H.; Bangert, J.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2011-01-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source-code library that provides common astrometric quantities and transformations. NOVAS calculations are accurate at the sub-milliarcsecond level. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and, currently, mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to harness the object-oriented nature of the Python language, and will implement the ability to handle large quantities of objects or observers using the array functionality in NumPy (a third-party scientific package for Python). NOVAS 3.1 also adds a module to transform GCRS vectors to the ITRS; the ITRS to GCRS transformation was already provided in NOVAS 3.0. The module that corrects an ITRS vector for polar motion has been modified to undo that correction upon demand. In the C edition, the ephemeris-access functions have been revised for use on 64-bit systems and for improved performance in general. NOVAS, including documentation, is available from the USNO website (http://www.usno.navy.mil/USNO/astronomical-applications/software-products/novas).

Dysbindin modulates brain function during visual processing in children.

PubMed

Mechelli, A; Viding, E; Kumar, A; Pettersson-Yeo, W; Fusar-Poli, P; Tognin, S; O'Donovan, M C; McGuire, P

2010-01-01

Schizophrenia is a neurodevelopmental disorder, and risk genes are thought to act through disruption of brain development. Several genetic studies have identified dystrobrevin binding protein 1 (DTNBP1, also known as dysbindin) as a potential susceptibility gene for schizophrenia, but its impact on brain function is poorly understood. It has been proposed that DTNBP1 may be associated with differences in visual processing. To test this, we examined the impact on visual processing in 61 healthy children aged 10-12 years of a genetic variant in DTNBP1 (rs2619538) that was common to all schizophrenia associated haplotypes in an earlier UK-Irish study. We tested the hypothesis that carriers of the risk allele would show altered occipital cortical function relative to noncarriers. Functional Magnetic Resonance Imaging (fMRI) was used to measure brain responses during a visual matching task. The data were analysed using statistical parametric mapping and statistical inferences were made at p<0.05 (corrected for multiple comparisons). Relative to noncarriers, carriers of the risk allele had greater activation in the lingual, fusiform gyrus and inferior occipital gyri. In these regions DTNBP1 genotype accounted for 19%, 20% and 14% of the inter-individual variance, respectively. Our results suggest that that genetic variation in DTNBP1 is associated with differences in the function of brain areas that mediate visual processing, and that these effects are evident in young children. These findings are consistent with the notion that the DTNBP1 gene influences brain development and can thereby modulate vulnerability to schizophrenia.

Interaction between effects of genes coding for dopamine and glutamate transmission on striatal and parahippocampal function.

PubMed

Pauli, Andreina; Prata, Diana P; Mechelli, Andrea; Picchioni, Marco; Fu, Cynthia H Y; Chaddock, Christopher A; Kane, Fergus; Kalidindi, Sridevi; McDonald, Colm; Kravariti, Eugenia; Toulopoulou, Timothea; Bramon, Elvira; Walshe, Muriel; Ehlert, Natascha; Georgiades, Anna; Murray, Robin; Collier, David A; McGuire, Philip

2013-09-01

The genes for the dopamine transporter (DAT) and the D-Amino acid oxidase activator (DAOA or G72) have been independently implicated in the risk for schizophrenia and in bipolar disorder and/or their related intermediate phenotypes. DAT and G72 respectively modulate central dopamine and glutamate transmission, the two systems most robustly implicated in these disorders. Contemporary studies have demonstrated that elevated dopamine function is associated with glutamatergic dysfunction in psychotic disorders. Using functional magnetic resonance imaging we examined whether there was an interaction between the effects of genes that influence dopamine and glutamate transmission (DAT and G72) on regional brain activation during verbal fluency, which is known to be abnormal in psychosis, in 80 healthy volunteers. Significant interactions between the effects of G72 and DAT polymorphisms on activation were evident in the striatum, parahippocampal gyrus, and supramarginal/angular gyri bilaterally, the right insula, in the right pre-/postcentral and the left posterior cingulate/retrosplenial gyri (P < 0.05, FDR-corrected across the whole brain). This provides evidence that interactions between the dopamine and the glutamate system, thought to be altered in psychosis, have an impact in executive processing which can be modulated by common genetic variation. Copyright © 2012 Wiley Periodicals, Inc., a Wiley company.

Role of Nicotinic and Muscarinic Receptors on Synaptic Plasticity and Neurological Diseases.

PubMed

Fuenzalida, Marco; Pérez, Miguel Ángel; Arias, Hugo R

2016-01-01

The cholinergic activity in the brain is fundamental for cognitive functions. The modulatory activity of the neurotransmitter acetylcholine (ACh) is mediated by activating a variety of nicotinic acetylcholine receptors (nAChR) and muscarinic acetylcholine receptors (mAChR). Accumulating evidence indicates that both nAChR and mAChRs can modulate the release of several other neurotransmitters, modify the threshold of long-term plasticity, finally improving learning and memory processes. Importantly, the expression, distribution, and/or function of these systems are altered in several neurological diseases. The aim of this review is to discuss our current knowledge on cholinergic receptors and their regulating synaptic functions and neuronal network activities as well as their use as targets for the development of new and clinically useful cholinergic ligands. These new therapies involve the development of novel and more selective cholinergic agonists and allosteric modulators as well as selective cholinesterase inhibitors, which may improve cognitive and behavioral symptoms, and also provide neuroprotection in several brain diseases. The review will focus on two nAChR receptor subtypes found in the mammalian brain and the most commonly targeted in drug discovery programs for neuropsychiatric disorder, the ligands of α4β2 nAChR and α7 nAChRs.

Proteomic profiles in hyperandrogenic syndromes.

PubMed

Misiti, S; Stigliano, A; Borro, M; Gentile, G; Michienzi, S; Cerquetti, L; Bucci, B; Argese, N; Brunetti, E; Simmaco, M; Toscano, V

2010-03-01

Polycystic ovary syndrome (PCOS) and congenital adrenal hyperplasia (CAH) represent the most common causes of hyperandrogenism. Although the etiopathogeneses of these syndromes are different, they share many clinical and biochemical signs, such as hirsutism, acne, and chronic anovulation. Experimental data have shown that peripheral T-lymphocytes function as molecular sensors, being able to record molecular signals either at staminal and mature cell levels, or hormones at systemic levels. Twenty PCOS women and 10 CAH with 21-hydroxylase deficiency, aged between 18-35 yr, were studied. T-cells purified from all patients and 20 healthy donors have been analyzed by 2-dimensional gel electrophoresis. Silver-stained proteomic map of each patient was compared with a control map obtained by pooling protein samples of the 20 healthy subjects. Spots of interest were identified by peptide mass fingerprint. Computer analysis evidenced several peptidic spots significantly modulated in all patients examined. Some proteins were modulated in both syndromes, others only in PCOS or in CAH. These proteins are involved in many physiological processes as the functional state of immune system, the regulation of the cytoskeleton structure, the oxidative stress, the coagulation process, and the insulin resistance. Identification of the physiological function of these proteins could help to understand ethiopathogenetic mechanisms of hyperandrogenic syndromes and its complications.

Cochlea-scaled spectral entropy predicts rate-invariant intelligibility of temporally distorted sentences.

PubMed

Stilp, Christian E; Kiefte, Michael; Alexander, Joshua M; Kluender, Keith R

2010-10-01

Some evidence, mostly drawn from experiments using only a single moderate rate of speech, suggests that low-frequency amplitude modulations may be particularly important for intelligibility. Here, two experiments investigated intelligibility of temporally distorted sentences across a wide range of simulated speaking rates, and two metrics were used to predict results. Sentence intelligibility was assessed when successive segments of fixed duration were temporally reversed (exp. 1), and when sentences were processed through four third-octave-band filters, the outputs of which were desynchronized (exp. 2). For both experiments, intelligibility decreased with increasing distortion. However, in exp. 2, intelligibility recovered modestly with longer desynchronization. Across conditions, performances measured as a function of proportion of utterance distorted converged to a common function. Estimates of intelligibility derived from modulation transfer functions predict a substantial proportion of the variance in listeners' responses in exp. 1, but fail to predict performance in exp. 2. By contrast, a metric of potential information, quantified as relative dissimilarity (change) between successive cochlear-scaled spectra, is introduced. This metric reliably predicts listeners' intelligibility across the full range of speaking rates in both experiments. Results support an information-theoretic approach to speech perception and the significance of spectral change rather than physical units of time.

Discovery and SAR of muscarinic receptor subtype 1 (M1) allosteric activators from a molecular libraries high throughput screen. Part 1: 2,5-dibenzyl-2H-pyrazolo[4,3-c]quinolin-3(5H)-ones as positive allosteric modulators.

PubMed

Han, Changho; Chatterjee, Arindam; Noetzel, Meredith J; Panarese, Joseph D; Smith, Emery; Chase, Peter; Hodder, Peter; Niswender, Colleen; Conn, P Jeffrey; Lindsley, Craig W; Stauffer, Shaun R

2015-01-15

Results from a 2012 high-throughput screen of the NIH Molecular Libraries Small Molecule Repository (MLSMR) against the human muscarinic receptor subtype 1 (M1) for positive allosteric modulators is reported. A content-rich screen utilizing an intracellular calcium mobilization triple-addition protocol allowed for assessment of all three modes of pharmacology at M1, including agonist, positive allosteric modulator, and antagonist activities in a single screening platform. We disclose a dibenzyl-2H-pyrazolo[4,3-c]quinolin-3(5H)-one hit (DBPQ, CID 915409) and examine N-benzyl pharmacophore/SAR relationships versus previously reported quinolin-3(5H)-ones and isatins, including ML137. SAR and consideration of recently reported crystal structures, homology modeling, and structure-function relationships using point mutations suggests a shared binding mode orientation at the putative common allosteric binding site directed by the pendant N-benzyl substructure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Shape Measurement by Means of Phase Retrieval using a Spatial Light Modulator

NASA Astrophysics Data System (ADS)

Agour, Mostafa; Huke, Philipp; Kopylow, Christoph V.; Falldorf, Claas

2010-04-01

We present a novel approach to investigate the shape of a diffusely reflecting technical object. It is based on a combination of a multiple-illumination contouring procedure and phase retrieval from a set of intensity measurements. Special consideration is given to the design of the experimental configuration for phase retrieval and the iterative algorithm to extract the 3D phase map. It is mainly based on a phase-only spatial light modulator (SLM) in the Fourier domain of a 4f-imaging system. The SLM is used to modulate the light incident in the Fourier plane with the transfer function of propagation. Thus, a set of consecutive intensity measurements of the wave field scattered by the investigated object in various propagation states can be realized in a common recording plane. In contrast to already existing methods, no mechanical adjustment is required during the recording process and thus the measuring time is considerably reduced. The method is applied to investigate the shape of micro-objects obtained from a metalforming process. Finally, the experimental results are compared to those provided by a standard interferometric contouring procedure.

Insights into TREM2 biology by network analysis of human brain gene expression data

PubMed Central

Forabosco, Paola; Ramasamy, Adaikalavan; Trabzuni, Daniah; Walker, Robert; Smith, Colin; Bras, Jose; Levine, Adam P.; Hardy, John; Pocock, Jennifer M.; Guerreiro, Rita; Weale, Michael E.; Ryten, Mina

2013-01-01

Rare variants in TREM2 cause susceptibility to late-onset Alzheimer's disease. Here we use microarray-based expression data generated from 101 neuropathologically normal individuals and covering 10 brain regions, including the hippocampus, to understand TREM2 biology in human brain. Using network analysis, we detect a highly preserved TREM2-containing module in human brain, show that it relates to microglia, and demonstrate that TREM2 is a hub gene in 5 brain regions, including the hippocampus, suggesting that it can drive module function. Using enrichment analysis we show significant overrepresentation of genes implicated in the adaptive and innate immune system. Inspection of genes with the highest connectivity to TREM2 suggests that it plays a key role in mediating changes in the microglial cytoskeleton necessary not only for phagocytosis, but also migration. Most importantly, we show that the TREM2-containing module is significantly enriched for genes genetically implicated in Alzheimer's disease, multiple sclerosis, and motor neuron disease, implying that these diseases share common pathways centered on microglia and that among the genes identified are possible new disease-relevant genes. PMID:23855984

Common and Distinct Neural Mechanisms of Attentional Switching and Response Conflict

PubMed Central

Kim, Chobok; Johnson, Nathan F.; Gold, Brian T.

2012-01-01

The human capacities for overcoming prepotent actions and flexibly switching between tasks represent cornerstones of cognitive control. Functional neuroimaging has implicated a diverse set of brain regions contributing to each of these cognitive control processes. However, the extent to which attentional switching and response conflict draw on shared or distinct neural mechanisms remains unclear. The current study examined the neural correlates of response conflict and attentional switching using event-related functional magnetic resonance imaging (fMRI) and a fully randomized 2×2 design. We manipulated an arrow-word version of the Stroop task to measure conflict and switching in the context of a single task decision, in response to a common set of stimuli. Under these common conditions, both behavioral and imaging data showed significant main effects of conflict and switching but no interaction. However, conjunction analyses identified frontal regions involved in both switching and response conflict, including the dorsal anterior cingulate cortex (dACC) and left inferior frontal junction. In addition, connectivity analyses demonstrated task-dependent functional connectivity patterns between dACC and inferior temporal cortex for attentional switching and between dACC and posterior parietal cortex for response conflict. These results suggest that the brain makes use of shared frontal regions, but can dynamically modulate the connectivity patterns of some of those regions, to deal with attentional switching and response conflict. PMID:22750124

Common and distinct neural mechanisms of attentional switching and response conflict.

PubMed

Kim, Chobok; Johnson, Nathan F; Gold, Brian T

2012-08-21

The human capacities for overcoming prepotent actions and flexibly switching between tasks represent cornerstones of cognitive control. Functional neuroimaging has implicated a diverse set of brain regions contributing to each of these cognitive control processes. However, the extent to which attentional switching and response conflict draw on shared or distinct neural mechanisms remains unclear. The current study examined the neural correlates of response conflict and attentional switching using event-related functional magnetic resonance imaging (fMRI) and a fully randomized 2×2 design. We manipulated an arrow-word version of the Stroop task to measure conflict and switching in the context of a single task decision, in response to a common set of stimuli. Under these common conditions, both behavioral and imaging data showed significant main effects of conflict and switching but no interaction. However, conjunction analyses identified frontal regions involved in both switching and response conflict, including the dorsal anterior cingulate cortex (dACC) and left inferior frontal junction. In addition, connectivity analyses demonstrated task-dependent functional connectivity patterns between dACC and inferior temporal cortex for attentional switching and between dACC and posterior parietal cortex for response conflict. These results suggest that the brain makes use of shared frontal regions, but can dynamically modulate the connectivity patterns of some of those regions, to deal with attentional switching and response conflict. Copyright © 2012 Elsevier B.V. All rights reserved.

A New Data Collection System for Ionospheric Modelling and Related Topics

DTIC Science & Technology

1993-04-15

Fluctuations of sgn, I strengt g d t1sr are cftcn os.;erved :,t utF frequencies in r ,:’i:- a t-e cayn r at r af’rer sunset. Marke d seasom c dependenc es in...Unfortunately there are few choices for real-time operating systems for PCs. The common alternate operating environments such as DeskView, MS Windows or...of the analog I/O and DMA support functions supplied by MetraByte. The processing module is where all the action is. After receiving a full data buffer

Dynamic range of frontoparietal functional modulation is associated with working memory capacity limitations in older adults.

PubMed

Hakun, Jonathan G; Johnson, Nathan F

2017-11-01

Older adults tend to over-activate regions throughout frontoparietal cortices and exhibit a reduced range of functional modulation during WM task performance compared to younger adults. While recent evidence suggests that reduced functional modulation is associated with poorer task performance, it remains unclear whether reduced range of modulation is indicative of general WM capacity-limitations. In the current study, we examined whether the range of functional modulation observed over multiple levels of WM task difficulty (N-Back) predicts in-scanner task performance and out-of-scanner psychometric estimates of WM capacity. Within our sample (60-77years of age), age was negatively associated with frontoparietal modulation range. Individuals with greater modulation range exhibited more accurate N-Back performance. In addition, despite a lack of significant relationships between N-Back and complex span task performance, range of frontoparietal modulation during the N-Back significantly predicted domain-general estimates of WM capacity. Consistent with previous cross-sectional findings, older individuals with less modulation range exhibited greater activation at the lowest level of task difficulty but less activation at the highest levels of task difficulty. Our results are largely consistent with existing theories of neurocognitive aging (e.g. CRUNCH) but focus attention on dynamic range of functional modulation asa novel marker of WM capacity-limitations in older adults. Copyright © 2017 Elsevier Inc. All rights reserved.

Morphological integration of anatomical, developmental, and functional postcranial modules in the crab-eating macaque (Macaca fascicularis).

PubMed

Conaway, Mark A; Schroeder, Lauren; von Cramon-Taubadel, Noreen

2018-03-22

Integration and modularity reflect the coordinated action of past evolutionary processes and, in turn, constrain or facilitate phenotypic evolvability. Here, we analyze magnitudes of integration in the macaque postcranium to test whether 20 a priori defined modules are (1) more tightly integrated than random sets of postcranial traits, and (2) are differentiated based on mode of definition, with developmental modules expected to be more integrated than functional or anatomical modules. The 3D morphometric data collected for eight limb and girdle bones for 60 macaques were collated into anatomical, developmental, and functional modules. A resampling technique was used to create random samples of integration values for each module for statistical comparison. Our results found that not all a priori defined modules were more strongly integrated than random samples of postcranial traits and that specific types of modules did not present consistent patterns of integration. Rather, girdle and joint modules were consistently less integrated than limb modules, and forelimb elements were less integrated than hindlimbs. The results suggest that morphometrically complex modules tend to be less integrated than simple limb bones, irrespective of the number of available traits. However, differences in integration of the fore- and hindlimb more likely reflects the multitude of locomotory, feeding, and social functions involved. It remains to be tested whether patterns of integration identified here are primate universals, and to what extent they vary depending on phylogenetic or functional factors. © 2018 Wiley Periodicals, Inc.

Temperature-dependent modulation of regional lymphatic contraction frequency and flow.

PubMed

Solari, Eleonora; Marcozzi, Cristiana; Negrini, Daniela; Moriondo, Andrea

2017-11-01

Lymph drainage and propulsion are sustained by an extrinsic mechanism, based on mechanical forces acting from the surrounding tissues against the wall of lymphatic vessels, and by an intrinsic mechanism attributable to active spontaneous contractions of the lymphatic vessel muscle. Despite being heterogeneous, the mechanisms underlying the generation of spontaneous contractions share a common biochemical nature and are thus modulated by temperature. In this study, we challenged excised tissues from rat diaphragm and hindpaw, endowed with spontaneously contracting lymphatic vessels, to temperatures from 24°C (hindpaw) or 33°C (diaphragmatic vessels) to 40°C while measuring lymphatic contraction frequency ( f c ) and amplitude. Both vessel populations displayed a sigmoidal relationship between f c and temperature, each centered around the average temperature of surrounding tissue (36.7 diaphragmatic and 32.1 hindpaw lymphatics). Although the slope factor of the sigmoidal fit to the f c change of hindpaw vessels was 2.3°C·cycles -1 ·min -1 , a value within the normal range displayed by simple biochemical reactions, the slope factor of the diaphragmatic lymphatics was 0.62°C·cycles -1 ·min -1 , suggesting the added involvement of temperature-sensing mechanisms. Lymph flow calculated as a function of temperature confirmed the relationship observed on f c data alone and showed that none of the two lymphatic vessel populations would be able to adapt to the optimal working temperature of the other tissue district. This poses a novel question whether lymphatic vessels might not adapt their function to accommodate the change if exposed to a surrounding temperature, which is different from their normal condition. NEW & NOTEWORTHY This study demonstrates to what extent lymphatic vessel intrinsic contractility and lymph flow are modulated by temperature and that this modulation is dependent on the body district that the vessels belong to, suggesting a possible functional misbehavior should lymphatic vessels be exposed to a chronically different temperature. Copyright © 2017 the American Physiological Society.

Sinusoidal modulation analysis for optical system MTF measurements.

PubMed

Boone, J M; Yu, T; Seibert, J A

1996-12-01

The modulation transfer function (MTF) is a commonly used metric for defining the spatial resolution characteristics of imaging systems. While the MTF is defined in terms of how an imaging system demodulates the amplitude of a sinusoidal input, this approach has not been in general use to measure MTFs in the medical imaging community because producing sinusoidal x-ray patterns is technically difficult. However, for optical systems such as charge coupled devices (CCD), which are rapidly becoming a part of many medical digital imaging systems, the direct measurement of modulation at discrete spatial frequencies using a sinusoidal test pattern is practical. A commercially available optical test pattern containing spatial frequencies ranging from 0.375 cycles/mm to 80 cycles/mm was sued to determine the MRF of a CCD-based optical system. These results were compared with the angulated slit method of Fujita [H. Fujita, D. Tsia, T. Itoh, K. Doi, J. Morishita, K. Ueda, and A. Ohtsuka, "A simple method for determining the modulation transfer function in digital radiography," IEEE Trans. Medical Imaging 11, 34-39 (1992)]. The use of a semiautomated profiled iterated reconstruction technique (PIRT) is introduced, where the shift factor between successive pixel rows (due to angulation) is optimized iteratively by least-squares error analysis rather than by hand measurement of the slit angle. PIRT was used to find the slit angle for the Fujita technique and to find the sine-pattern angle for the sine-pattern technique. Computer simulation of PIRT for the case of the slit image (a line spread function) demonstrated that it produced a more accurate angle determination than "hand" measurement, and there is a significant difference between the errors in the two techniques (Wilcoxon Signed Rank Test, p < 0.001). The sine-pattern method and the Fujita slit method produced comparable MTF curves for the CCD camera evaluated.

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.

PubMed

Cormier, Nathan; Kolisnik, Tyler; Bieda, Mark

2016-07-05

There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems have emphasized custom development of ChIP-seq pipelines. These systems are primarily based on custom programming of a single, complex pipeline or supply libraries of modules and do not produce the full range of outputs commonly produced for ChIP-seq datasets. It is desirable to have more comprehensive pipelines, in particular ones addressing common metadata tasks, such as pathway analysis, and pipelines producing standard complex graphical outputs. It is advantageous if these are highly modular systems, available as both turnkey pipelines and individual modules, that are easily comprehensible, modifiable and extensible to allow rapid alteration in response to new analysis developments in this growing area. Furthermore, it is advantageous if these pipelines allow data provenance tracking. We present a set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. This software presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others. These pipelines range from those performing a single task to those performing full analyses of ChIP-seq data. The pipelines are supplied as both Kepler workflows, which allow data provenance tracking, and, in the majority of cases, as standalone R scripts. These pipelines are designed for ease of modification and repurposing.

Evaluation method for the potential functionome harbored in the genome and metagenome.

PubMed

Takami, Hideto; Taniguchi, Takeaki; Moriya, Yuki; Kuwahara, Tomomi; Kanehisa, Minoru; Goto, Susumu

2012-12-12

One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various uncultivable microbes within unidentified phyla.

Evolution of functional specialization and division of labor.

PubMed

Rueffler, Claus; Hermisson, Joachim; Wagner, Günter P

2012-02-07

Division of labor among functionally specialized modules occurs at all levels of biological organization in both animals and plants. Well-known examples include the evolution of specialized enzymes after gene duplication, the evolution of specialized cell types, limb diversification in arthropods, and the evolution of specialized colony members in many taxa of marine invertebrates and social insects. Here, we identify conditions favoring the evolution of division of labor by means of a general mathematical model. Our starting point is the assumption that modules contribute to two different biological tasks and that the potential of modules to contribute to these tasks is traded off. Our results are phrased in terms of properties of performance functions that map the phenotype of modules to measures of performance. We show that division of labor is favored by three factors: positional effects that predispose modules for one of the tasks, accelerating performance functions, and synergistic interactions between modules. If modules can be lost or damaged, selection for robustness can counteract selection for functional specialization. To illustrate our theory we apply it to the evolution of specialized enzymes coded by duplicated genes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jing; Ma, Zihao; Carr, Steven A.

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC).more » Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. Molecular & Cellular Proteomics 16: 10.1074/mcp.M116.060301, 121–134, 2017.« less

Occupational Safety. Hand Tools. Pre-Apprenticeship Phase 1 Training.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This self-paced student training module on safety when using hand tools is one of a number of modules developed for Pre-apprenticeship Phase 1 Training. Purpose of the module is to teach students the correct safety techniques for operating common hand- and arm-powered tools, including selection, maintenance, technique, and uses. The module may…

Genetic Variation in Serotonin Transporter Modulates Tactile Hyperresponsiveness in ASD

PubMed Central

Schauder, Kimberly B.; Muller, Christopher L.; Veenstra-VanderWeele, Jeremy; Cascio, Carissa J.

2014-01-01

Several lines of evidence implicate dysfunction of the serotonin (5-HT) system in autism spectrum disorder (ASD). Specifically, the serotonin transporter (5-HTT, SERT) has been scrutinized as an ASD candidate risk gene. SERT plays key roles in the development of circuits that underlie sensory function, particularly in the somatosensory system. One previous study in ASD found association of a rare, hyperfunctional SERT variant with sensory aversion, but studies of common SERT variants have never examined sensory symptoms in ASD. Using standardized caregiver assessments of sensory function in children, we evaluated patterns of sensory responsiveness in 47 children with ASD and 38 typically developing (TD) children. Study participants were genotyped for the functional SERT promoter polymorphisms, 5-HTTLPR and rs25531, to test the hypothesis that the higher expressing genotypes would be associated with hyperresponsiveness to touch, a common sensory aversion in ASD. All measures of sensory hypo- and hyperresponsiveness were increased in children with ASD, with hyporesponsive sensory patterns negatively correlated to age and hyperresponsive sensory patterns positively correlated to repetitive behavior. Strikingly, high-expressing SERT genotypes were associated with increased tactile hyperresponsiveness in the ASD group. Our findings indicate genetic variation that increases SERT function may specifically impact somatosensory processing in ASD. PMID:25558276

An integrative approach to inferring biologically meaningful gene modules

PubMed Central

2011-01-01

Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level. PMID:21791051

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

PubMed Central

Wolfinger, Michael T.; Fallmann, Jörg; Eggenhofer, Florian; Amman, Fabian

2015-01-01

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. PMID:26236465

Ovulation induction in women with polycystic ovary syndrome: an update.

PubMed

Bhagavath, Balasubramanian; Carson, Sandra A

2012-03-01

Infertility is frequently caused by anovulation. The affected women present with irregular menstrual cycles and the most common diagnosis is polycystic ovary syndrome. Ovulation induction is commonly used to treat these women. Clomiphene citrate (a selective estrogen receptor modulator or SERM) remains the most used medication for treating this condition. Alternatives that have been used include other SERMs such as tamoxifen, aromatase inhibitors, insulin sensitizing agents, and ovarian drilling. Evidence for and against the effectiveness of these agents has fluctuated over the last decade. Controversies surrounding the use of ovulation induction such as development of functional cysts, high-order multiple births, and development of ovarian cancer have been further studied and some controversies have almost been laid to rest in the last decade. Copyright © 2012 Mosby, Inc. All rights reserved.

Guanfacine Modulates the Emotional Biasing of Amygdala-Prefrontal Connectivity for Cognitive Control

PubMed Central

Schulz, Kurt P.; Clerkin, Suzanne M.; Newcorn, Jeffrey H.; Halperin, Jeffrey M.; Fan, Jin

2014-01-01

Functional interactions between amygdala and prefrontal cortex provide a cortical entry point for emotional cues to bias cognitive control. Stimulation of α2 adrenoceptors enhances the prefrontal control functions and blocks the amygdala-dependent encoding of emotional cues. However, the impact of this stimulation on amygdala-prefrontal interactions and the emotional biasing of cognitive control have not been established. We tested the effect of the α2 adrenoceptor agonist guanfacine on psychophysiological interactions of amygdala with prefrontal cortex for the emotional biasing of response execution and inhibition. Fifteen healthy adults were scanned twice with event-related functional magnetic resonance imaging while performing an emotional go/no-go task following administration of oral guanfacine (1 mg) and placebo in a double-blind, counterbalanced design. Happy, sad, and neutral faces served as trial cues. Guanfacine moderated the effect of face emotion on the task-related functional connectivity of left and right amygdala with left inferior frontal gyrus compared to placebo, by selectively reversing the functional co-activation of the two regions for response execution cued by sad faces. This shift from positively to negatively correlated activation for guanfacine was associated with selective improvements in the relatively low accuracy of responses to sad faces seen for placebo. These results demonstrate the importance of functional interactions between amygdala and inferior frontal gyrus to both bottom-up biasing of cognitive control and top-down control of emotional processing, as well as for the α2 adrenoceptor-mediated modulation of these processes. These mechanisms offer a possibile method to address the emotional reactivity that is common to several psychiatric disorders. PMID:25059532

Contrasting Ecosystem-Effects of Morphologically Similar Copepods

PubMed Central

Matthews, Blake; Hausch, Stephen; Winter, Christian; Suttle, Curtis A.; Shurin, Jonathan B.

2011-01-01

Organisms alter the biotic and abiotic conditions of ecosystems. They can modulate the availability of resources to other species (ecosystem engineering) and shape selection pressures on other organisms (niche construction). Very little is known about how the engineering effects of organisms vary among and within species, and, as a result, the ecosystem consequences of species diversification and phenotypic evolution are poorly understood. Here, using a common gardening experiment, we test whether morphologically similar species and populations of Diaptomidae copepods (Leptodiaptomus ashlandi, Hesperodiaptomus franciscanus, Skistodiaptomus oregonensis) have similar or different effects on the structure and function of freshwater ecosystems. We found that copepod species had contrasting effects on algal biomass, ammonium concentrations, and sedimentation rates, and that copepod populations had contrasting effects on prokaryote abundance, sedimentation rates, and gross primary productivity. The average size of ecosystem-effect contrasts between species was similar to those between populations, and was comparable to those between fish species and populations measured in previous common gardening experiments. Our results suggest that subtle morphological variation among and within species can cause multifarious and divergent ecosystem-effects. We conclude that using morphological trait variation to assess the functional similarity of organisms may underestimate the importance of species and population diversity for ecosystem functioning. PMID:22140432

Mirroring "meaningful" actions: sensorimotor learning modulates imitation of goal-directed actions.

PubMed

Catmur, Caroline; Heyes, Cecilia

2017-06-19

Imitation is important in the development of social and technological skills throughout the lifespan. Experiments investigating the acquisition and modulation of imitation (and of its proposed neural substrate, the mirror neuron system) have produced evidence that the capacity for imitation depends on associative learning in which connections are formed between sensory and motor representations of actions. However, evidence that the development of imitation depends on associative learning has been found only for non-goal-directed actions. One reason for the lack of research on goal-directed actions is that imitation of such actions is commonly confounded with the tendency to respond in a spatially compatible manner. However, since the most prominent account of mirror neuron function, and hence of imitation, suggests that these cells encode goal-directed actions, it is important to establish whether sensorimotor learning can also modulate imitation of goal-directed actions. Experiment 1 demonstrated that imitation of goal-directed grasping can be measured while controlling for spatial compatibility, and Experiment 2 showed that this imitation effect can be modulated by sensorimotor training. Together these data support the hypothesis that the capacity for behavioural imitation, and the properties of the mirror neuron system, are constructed in the course of development through associative learning.

Characterization of pulse amplitude and pulse rate modulation for a human vestibular implant during acute electrical stimulation

NASA Astrophysics Data System (ADS)

Nguyen, T. A. K.; DiGiovanna, J.; Cavuscens, S.; Ranieri, M.; Guinand, N.; van de Berg, R.; Carpaneto, J.; Kingma, H.; Guyot, J.-P.; Micera, S.; Perez Fornos, A.

2016-08-01

Objective. The vestibular system provides essential information about balance and spatial orientation via the brain to other sensory and motor systems. Bilateral vestibular loss significantly reduces quality of life, but vestibular implants (VIs) have demonstrated potential to restore lost function. However, optimal electrical stimulation strategies have not yet been identified in patients. In this study, we compared the two most common strategies, pulse amplitude modulation (PAM) and pulse rate modulation (PRM), in patients. Approach. Four subjects with a modified cochlear implant including electrodes targeting the peripheral vestibular nerve branches were tested. Charge-equivalent PAM and PRM were applied after adaptation to baseline stimulation. Vestibulo-ocular reflex eye movement responses were recorded to evaluate stimulation efficacy during acute clinical testing sessions. Main results. PAM evoked larger amplitude eye movement responses than PRM. Eye movement response axes for lateral canal stimulation were marginally better aligned with PRM than with PAM. A neural network model was developed for the tested stimulation strategies to provide insights on possible neural mechanisms. This model suggested that PAM would consistently cause a larger ensemble firing rate of neurons and thus larger responses than PRM. Significance. Due to the larger magnitude of eye movement responses, our findings strongly suggest PAM as the preferred strategy for initial VI modulation.

Mechanotransduction: all signals point to cytoskeleton, matrix, and integrins

NASA Technical Reports Server (NTRS)

Alenghat, Francis J.; Ingber, Donald E.

2002-01-01

Mechanical stresses modulate cell function by either activating or tuning signal transduction pathways. Mechanotransduction, the process by which cells convert mechanical stimuli into a chemical response, occurs both in cells specialized for sensing mechanical cues and in parenchymal cells whose primary function is not mechanosensory. However, common among the various responses to mechanical stress is the importance of direct or indirect connections between the internal cytoskeleton, the extracellular matrix (ECM), and traditional signal transducing molecules. In many instances, these elements converge at focal adhesions, sites of structural attachment between the cytoskeleton and ECM that are anchored by cell surface integrin receptors. Alenghat and Ingber discuss the accumulating evidence for the central role of cytoskeleton, ECM, and integrin-anchored focal adhesions in several mechanotransduction pathways.

Innate immunity, insulin resistance and type 2 diabetes.

PubMed

Fernández-Real, José Manuel; Pickup, John C

2008-01-01

Recent evidence has disclosed previously unrecognized links among insulin resistance, obesity, circulating immune markers, immunogenetic susceptibility, macrophage function and chronic infection. Genetic variations leading to altered production or function of circulating innate immune proteins, cellular pattern-recognition receptors and inflammatory cytokines have been linked with insulin resistance, type 2 diabetes, obesity and atherosclerosis. Cellular innate immune associations with obesity and insulin resistance include increased white blood cell count and adipose tissue macrophage numbers. The innate immune response is modulated possibly by both predisposition (genetic or fetal programming), perhaps owing to evolutionary pressures caused by acute infections at the population level (pandemics), and chronic low exposure to environmental products or infectious agents. The common characteristics shared among innate immunity activation, obesity and insulin resistance are summarized.

Task-induced frequency modulation features for brain-computer interfacing.

PubMed

Jayaram, Vinay; Hohmann, Matthias; Just, Jennifer; Schölkopf, Bernhard; Grosse-Wentrup, Moritz

2017-10-01

Task-induced amplitude modulation of neural oscillations is routinely used in brain-computer interfaces (BCIs) for decoding subjects' intents, and underlies some of the most robust and common methods in the field, such as common spatial patterns and Riemannian geometry. While there has been some interest in phase-related features for classification, both techniques usually presuppose that the frequencies of neural oscillations remain stable across various tasks. We investigate here whether features based on task-induced modulation of the frequency of neural oscillations enable decoding of subjects' intents with an accuracy comparable to task-induced amplitude modulation. We compare cross-validated classification accuracies using the amplitude and frequency modulated features, as well as a joint feature space, across subjects in various paradigms and pre-processing conditions. We show results with a motor imagery task, a cognitive task, and also preliminary results in patients with amyotrophic lateral sclerosis (ALS), as well as using common spatial patterns and Laplacian filtering. The frequency features alone do not significantly out-perform traditional amplitude modulation features, and in some cases perform significantly worse. However, across both tasks and pre-processing in healthy subjects the joint space significantly out-performs either the frequency or amplitude features alone. This result only does not hold for ALS patients, for whom the dataset is of insufficient size to draw any statistically significant conclusions. Task-induced frequency modulation is robust and straight forward to compute, and increases performance when added to standard amplitude modulation features across paradigms. This allows more information to be extracted from the EEG signal cheaply and can be used throughout the field of BCIs.

HAL/SM system functional design specification. [systems analysis and design analysis of central processing units

NASA Technical Reports Server (NTRS)

Ross, C.; Williams, G. P. W., Jr.

1975-01-01

The functional design of a preprocessor, and subsystems is described. A structure chart and a data flow diagram are included for each subsystem. Also a group of intermodule interface definitions (one definition per module) is included immediately following the structure chart and data flow for a particular subsystem. Each of these intermodule interface definitions consists of the identification of the module, the function the module is to perform, the identification and definition of parameter interfaces to the module, and any design notes associated with the module. Also described are compilers and computer libraries.

Optical Peaking Enhancement in High-Speed Ring Modulators

PubMed Central

Müller, J.; Merget, F.; Azadeh, S. Sharif; Hauck, J.; García, S. Romero; Shen, B.; Witzens, J.

2014-01-01

Ring resonator modulators (RRM) combine extreme compactness, low power consumption and wavelength division multiplexing functionality, making them a frontrunner for addressing the scalability requirements of short distance optical links. To extend data rates beyond the classically assumed bandwidth capability, we derive and experimentally verify closed form equations of the electro-optic response and asymmetric side band generation resulting from inherent transient time dynamics and leverage these to significantly improve device performance. An equivalent circuit description with a commonly used peaking amplifier model allows straightforward assessment of the effect on existing communication system architectures. A small signal analytical expression of peaking in the electro-optic response of RRMs is derived and used to extend the electro-optic bandwidth of the device above 40 GHz as well as to open eye diagrams penalized by intersymbol interference at 32, 40 and 44 Gbps. Predicted peaking and asymmetric side band generation are in excellent agreement with experiments. PMID:25209255

Vectors a Fortran 90 module for 3-dimensional vector and dyadic arithmetic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brock, B.C.

1998-02-01

A major advance contained in the new Fortran 90 language standard is the ability to define new data types and the operators associated with them. Writing computer code to implement computations with real and complex three-dimensional vectors and dyadics is greatly simplified if the equations can be implemented directly, without the need to code the vector arithmetic explicitly. The Fortran 90 module described here defines new data types for real and complex 3-dimensional vectors and dyadics, along with the common operations needed to work with these objects. Routines to allow convenient initialization and output of the new types are alsomore » included. In keeping with the philosophy of data abstraction, the details of the implementation of the data types are maintained private, and the functions and operators are made generic to simplify the combining of real, complex, single- and double-precision vectors and dyadics.« less

A quantitative theory of gamma synchronization in macaque V1.

PubMed

Lowet, Eric; Roberts, Mark J; Peter, Alina; Gips, Bart; De Weerd, Peter

2017-08-31

Gamma-band synchronization coordinates brief periods of excitability in oscillating neuronal populations to optimize information transmission during sensation and cognition. Commonly, a stable, shared frequency over time is considered a condition for functional neural synchronization. Here, we demonstrate the opposite: instantaneous frequency modulations are critical to regulate phase relations and synchronization. In monkey visual area V1, nearby local populations driven by different visual stimulation showed different gamma frequencies. When similar enough, these frequencies continually attracted and repulsed each other, which enabled preferred phase relations to be maintained in periods of minimized frequency difference. Crucially, the precise dynamics of frequencies and phases across a wide range of stimulus conditions was predicted from a physics theory that describes how weakly coupled oscillators influence each other's phase relations. Hence, the fundamental mathematical principle of synchronization through instantaneous frequency modulations applies to gamma in V1 and is likely generalizable to other brain regions and rhythms.

Arthropod toxins and their antinociceptive properties: From venoms to painkillers.

PubMed

Monge-Fuentes, Victoria; Arenas, Claudia; Galante, Priscilla; Gonçalves, Jacqueline Coimbra; Mortari, Márcia Renata; Schwartz, Elisabeth Ferroni

2018-03-29

The complex process of pain control commonly involves the use of systemic analgesics; however, in many cases, a more potent and effective polypharmacological approach is needed to promote clinically significant improvement. Additionally, considering side effects caused by current painkillers, drug discovery is once more turning to nature as a source of more efficient therapeutic alternatives. In this context, arthropod venoms contain a vast array of bioactive substances that have evolved to selectively bind to specific pharmacological targets involved in the pain signaling pathway, playing an important role as pain activators or modulators, the latter serving as promising analgesic agents. The current review explores how the pain pathway works and surveys neuroactive compounds obtained from arthropods' toxins, which function as pain modulators through their interaction with specific ion channels and membrane receptors, emerging as promising candidates for drug design and development. Copyright © 2018 Elsevier Inc. All rights reserved.

Screening for modulators of cisplatin sensitivity: unbiased screens reveal common themes.

PubMed

Nijwening, Jeroen H; Kuiken, Hendrik J; Beijersbergen, Roderick L

2011-02-01

Cisplatin is a widely used chemotherapeutic agent to treat a variety of solid tumors. The cytotoxic mode of action of cisplatin is mediated by inducing conformational changes in DNA including intra- and inter-strand crosslink adducts. Recognition of these adducts results in the activation of the DNA damage response resulting in cell cycle arrest, repair, and potentially, apoptosis. Despite the clinical efficacy of cisplatin, many tumors are either intrinsically resistant or acquire resistance during treatment. The identification of cisplatin drug response modulators can help us understand these resistance mechanisms, provide biomarkers for treatment strategies, or provide drug targets for combination therapy. Here we discuss functional genetic screens, including one performed by us, set up to identify genes whose inhibition results in increased sensitivity to cisplatin. In summary, the validated genes identified in these screens mainly operate in DNA damage response including nucleotide excision repair, translesion synthesis, and homologous recombination.

Bandwidth efficient bidirectional 5 Gb/s overlapped-SCM WDM PON with electronic equalization and forward-error correction.

PubMed

Buset, Jonathan M; El-Sahn, Ziad A; Plant, David V

2012-06-18

We demonstrate an improved overlapped-subcarrier multiplexed (O-SCM) WDM PON architecture transmitting over a single feeder using cost sensitive intensity modulation/direct detection transceivers, data re-modulation and simple electronics. Incorporating electronic equalization and Reed-Solomon forward-error correction codes helps to overcome the bandwidth limitation of a remotely seeded reflective semiconductor optical amplifier (RSOA)-based ONU transmitter. The O-SCM architecture yields greater spectral efficiency and higher bit rates than many other SCM techniques while maintaining resilience to upstream impairments. We demonstrate full-duplex 5 Gb/s transmission over 20 km and analyze BER performance as a function of transmitted and received power. The architecture provides flexibility to network operators by relaxing common design constraints and enabling full-duplex operation at BER ∼ 10(-10) over a wide range of OLT launch powers from 3.5 to 8 dBm.

Galectins in the Pathogenesis of Rheumatoid Arthritis

PubMed Central

Li, Song; Yu, Yangsheng; Koehn, Christopher D; Zhang, Zhixin; Su, Kaihong

2013-01-01

Rheumatoid arthritis (RA) is a complex and common systemic autoimmune disease characterized by synovial inflammation and hyperplasia. Multiple proteins, cells, and pathways have been identified to contribute to the pathogenesis of RA. Galectins are a group of lectins that bind to β-galactoside carbohydrates on the cell surface and in the extracellular matrix. They are expressed in a wide variety of tissues and organs with the highest expression in the immune system. Galectins are potent immune regulators and modulate a range of pathological processes, such as inflammation, autoimmunity, and cancer. Accumulated evidence shows that several family members of galectins play positive or negative roles in the disease development of RA, through their effects on T and B lymphocytes, myeloid lineage cells, and fibroblast-like synoviocytes. In this review, we will summarize the function of different galectins in immune modulation and their distinct roles in RA pathogenesis. PMID:24416634

A quantitative theory of gamma synchronization in macaque V1

PubMed Central

Roberts, Mark J; Peter, Alina; Gips, Bart; De Weerd, Peter

2017-01-01

Gamma-band synchronization coordinates brief periods of excitability in oscillating neuronal populations to optimize information transmission during sensation and cognition. Commonly, a stable, shared frequency over time is considered a condition for functional neural synchronization. Here, we demonstrate the opposite: instantaneous frequency modulations are critical to regulate phase relations and synchronization. In monkey visual area V1, nearby local populations driven by different visual stimulation showed different gamma frequencies. When similar enough, these frequencies continually attracted and repulsed each other, which enabled preferred phase relations to be maintained in periods of minimized frequency difference. Crucially, the precise dynamics of frequencies and phases across a wide range of stimulus conditions was predicted from a physics theory that describes how weakly coupled oscillators influence each other’s phase relations. Hence, the fundamental mathematical principle of synchronization through instantaneous frequency modulations applies to gamma in V1 and is likely generalizable to other brain regions and rhythms. PMID:28857743

Introduction to the computational structural mechanics testbed

NASA Technical Reports Server (NTRS)

Lotts, C. G.; Greene, W. H.; Mccleary, S. L.; Knight, N. F., Jr.; Paulson, S. S.; Gillian, R. E.

1987-01-01

The Computational Structural Mechanics (CSM) testbed software system based on the SPAR finite element code and the NICE system is described. This software is denoted NICE/SPAR. NICE was developed at Lockheed Palo Alto Research Laboratory and contains data management utilities, a command language interpreter, and a command language definition for integrating engineering computational modules. SPAR is a system of programs used for finite element structural analysis developed for NASA by Lockheed and Engineering Information Systems, Inc. It includes many complementary structural analysis, thermal analysis, utility functions which communicate through a common database. The work on NICE/SPAR was motivated by requirements for a highly modular and flexible structural analysis system to use as a tool in carrying out research in computational methods and exploring computer hardware. Analysis examples are presented which demonstrate the benefits gained from a combination of the NICE command language with a SPAR computational modules.

Common Fractions. [Student Worksheets for Vocational Agricultural Courses].

ERIC Educational Resources Information Center

Jewell, Larry R.

This learning module provides students with practice in applying mathematical operations to vocational agriculture. The module consists of unit objectives, definitions, information, problems to solve, worksheets suitable for various levels of vocational agriculture instruction, and answer keys for the problems and worksheets. This module, which…

Catecholamines and cognition after traumatic brain injury

PubMed Central

Jenkins, Peter O.; Mehta, Mitul A.

2016-01-01

Abstract Cognitive problems are one of the main causes of ongoing disability after traumatic brain injury. The heterogeneity of the injuries sustained and the variability of the resulting cognitive deficits makes treating these problems difficult. Identifying the underlying pathology allows a targeted treatment approach aimed at cognitive enhancement. For example, damage to neuromodulatory neurotransmitter systems is common after traumatic brain injury and is an important cause of cognitive impairment. Here, we discuss the evidence implicating disruption of the catecholamines (dopamine and noradrenaline) and review the efficacy of catecholaminergic drugs in treating post-traumatic brain injury cognitive impairments. The response to these therapies is often variable, a likely consequence of the heterogeneous patterns of injury as well as a non-linear relationship between catecholamine levels and cognitive functions. This individual variability means that measuring the structure and function of a person’s catecholaminergic systems is likely to allow more refined therapy. Advanced structural and molecular imaging techniques offer the potential to identify disruption to the catecholaminergic systems and to provide a direct measure of catecholamine levels. In addition, measures of structural and functional connectivity can be used to identify common patterns of injury and to measure the functioning of brain ‘networks’ that are important for normal cognitive functioning. As the catecholamine systems modulate these cognitive networks, these measures could potentially be used to stratify treatment selection and monitor response to treatment in a more sophisticated manner. PMID:27256296

Critical protein GAPDH and its regulatory mechanisms in cancer cells

PubMed Central

Zhang, Jin-Ying; Zhang, Fan; Hong, Chao-Qun; Giuliano, Armando E.; Cui, Xiao-Jiang; Zhou, Guang-Ji; Zhang, Guo-Jun; Cui, Yu-Kun

2015-01-01

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), initially identified as a glycolytic enzyme and considered as a housekeeping gene, is widely used as an internal control in experiments on proteins, mRNA, and DNA. However, emerging evidence indicates that GAPDH is implicated in diverse functions independent of its role in energy metabolism; the expression status of GAPDH is also deregulated in various cancer cells. One of the most common effects of GAPDH is its inconsistent role in the determination of cancer cell fate. Furthermore, studies have described GAPDH as a regulator of cell death; other studies have suggested that GAPDH participates in tumor progression and serves as a new therapeutic target. However, related regulatory mechanisms of its numerous cellular functions and deregulated expression levels remain unclear. GAPDH is tightly regulated at transcriptional and posttranscriptional levels, which are involved in the regulation of diverse GAPDH functions. Several cancer-related factors, such as insulin, hypoxia inducible factor-1 (HIF-1), p53, nitric oxide (NO), and acetylated histone, not only modulate GAPDH gene expression but also affect protein functions via common pathways. Moreover, posttranslational modifications (PTMs) occurring in GAPDH in cancer cells result in new activities unrelated to the original glycolytic function of GAPDH. In this review, recent findings related to GAPDH transcriptional regulation and PTMs are summarized. Mechanisms and pathways involved in GAPDH regulation and its different roles in cancer cells are also described. PMID:25859407

Expert system development for commonality analysis in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1987-01-01

This report is a combination of foundational mathematics and software design. A mathematical model of the Commonality Analysis problem was developed and some important properties discovered. The complexity of the problem is described herein and techniques, both deterministic and heuristic, for reducing that complexity are presented. Weaknesses are pointed out in the existing software (System Commonality Analysis Tool) and several improvements are recommended. It is recommended that: (1) an expert system for guiding the design of new databases be developed; (2) a distributed knowledge base be created and maintained for the purpose of encoding the commonality relationships between design items in commonality databases; (3) a software module be produced which automatically generates commonality alternative sets from commonality databases using the knowledge associated with those databases; and (4) a more complete commonality analysis module be written which is capable of generating any type of feasible solution.

Small Heat Shock Proteins Are Novel Common Determinants of Alcohol and Nicotine Sensitivity in Caenorhabditis elegans

PubMed Central

Johnson, James R.; Rajamanoharan, Dayani; McCue, Hannah V.; Rankin, Kim

2016-01-01

Addiction to drugs is strongly determined by multiple genetic factors. Alcohol and nicotine produce distinct pharmacological effects within the nervous system through discrete molecular targets; yet, data from family and twin analyses support the existence of common genetic factors for addiction in general. The mechanisms underlying addiction, however, are poorly described and common genetic factors for alcohol and nicotine remain unidentified. We investigated the role that the heat shock transcription factor, HSF-1, and its downstream effectors played as common genetic modulators of sensitivity to addictive substances. Using Caenorhabditis elegans, an exemplary model organism with substance dose-dependent responses similar to mammals, we demonstrate that HSF-1 altered sensitivity to both alcohol and nicotine. Using a combination of a targeted RNAi screen of downstream factors and transgenic approaches we identified that these effects were contingent upon the constitutive neuronal expression of HSP-16.48, a small heat shock protein (HSP) homolog of human α-crystallin. Furthermore we demonstrated that the function of HSP-16.48 in drug sensitivity surprisingly was independent of chaperone activity during the heat shock stress response. Instead we identified a distinct domain within the N-terminal region of the HSP-16.48 protein that specified its function in comparison to related small HSPs. Our findings establish and characterize a novel genetic determinant underlying sensitivity to diverse addictive substances. PMID:26773049

Response functions for sine- and square-wave modulations of disparity.

NASA Technical Reports Server (NTRS)

Richards, W.

1972-01-01

Depth sensations cannot be elicited by modulations of disparity that are more rapid than about 6 Hz, regardless of the modulation amplitude. Vergence tracking also fails at similar modulation rates, suggesting that this portion of the oculomotor system is limited by the behavior of disparity detectors. For sinusoidal modulations of disparity between 1/2 to 2 deg of disparity, most depth-response functions exhibit a low-frequency decrease that is not observed with square-wave modulations of disparity.

Quantum model for electro-optical amplitude modulation.

PubMed

Capmany, José; Fernández-Pousa, Carlos R

2010-11-22

We present a quantum model for electro-optic amplitude modulation, which is built upon quantum models of the main photonic components that constitute the modulator, that is, the guided-wave beamsplitter and the electro-optic phase modulator and accounts for all the different available modulator structures. General models are developed both for single and dual drive configurations and specific results are obtained for the most common configurations currently employed. Finally, the operation with two-photon input for the control of phase-modulated photons and the important topic of multicarrier modulation are also addressed.

Cosine Directional Tuning of Theta Cell Burst Frequencies: Evidence for Spatial Coding by Oscillatory Interference

PubMed Central

Welday, Adam C.; Shlifer, I. Gary; Bloom, Matthew L.; Zhang, Kechen

2011-01-01

The rodent septohippocampal system contains “theta cells,” which burst rhythmically at 4–12 Hz, but the functional significance of this rhythm remains poorly understood (Buzsáki, 2006). Theta rhythm commonly modulates the spike trains of spatially tuned neurons such as place (O'Keefe and Dostrovsky, 1971), head direction (Tsanov et al., 2011a), grid (Hafting et al., 2005), and border cells (Savelli et al., 2008; Solstad et al., 2008). An “oscillatory interference” theory has hypothesized that some of these spatially tuned neurons may derive their positional firing from phase interference among theta oscillations with frequencies that are modulated by the speed and direction of translational movements (Burgess et al., 2005, 2007). This theory is supported by studies reporting modulation of theta frequency by movement speed (Rivas et al., 1996; Geisler et al., 2007; Jeewajee et al., 2008a), but modulation of theta frequency by movement direction has never been observed. Here we recorded theta cells from hippocampus, medial septum, and anterior thalamus of freely behaving rats. Theta cell burst frequencies varied as the cosine of the rat's movement direction, and this directional tuning was influenced by landmark cues, in agreement with predictions of the oscillatory interference theory. Computer simulations and mathematical analysis demonstrated how a postsynaptic neuron can detect location-dependent synchrony among inputs from such theta cells, and thereby mimic the spatial tuning properties of place, grid, or border cells. These results suggest that theta cells may serve a high-level computational function by encoding a basis set of oscillatory signals that interfere with one another to synthesize spatial memory representations. PMID:22072668

Respiratory modulation of cardiovascular rhythms before and after short-duration human spaceflight.

PubMed

Verheyden, B; Beckers, F; Couckuyt, K; Liu, J; Aubert, A E

2007-12-01

Astronauts commonly return from space with altered short-term cardiovascular dynamics and blunted baroreflex sensitivity. Although many studies have addressed this issue, post-flight effects on the dynamic circulatory control remain incompletely understood. It is not clear how long the cardiovascular system needs to recover from spaceflight as most post-flight investigations only extended between a few days and 2 weeks. In this study, we examined the effect of short-duration spaceflight (1-2 weeks) on respiratory-mediated cardiovascular rhythms in five cosmonauts. Two paced-breathing protocols at 6 and 12 breaths min(-1) were performed in the standing and supine positions before spaceflight, and after 1 and 25 days upon return. Dynamic baroreflex function was evaluated by transfer function analysis between systolic pressure and the RR intervals. Post-flight orthostatic blood pressure control was preserved in all cosmonauts. In the standing position after spaceflight there was an increase in heart rate (HR) of approx. 20 beats min(-1) or more. Averaged for all five cosmonauts, respiratory sinus dysrhythmia and transfer gain reduced to 40% the day after landing, and had returned to pre-flight levels after 25 days. Low-frequency gain decreased from 6.6 (3.4) [mean (SD)] pre-flight to 3.9 (1.6) post-flight and returned to 5.7 (1.3) ms mmHg(-1) after 25 days upon return to Earth. Unlike alterations in the modulation of HR, blood pressure dynamics were not significantly different between pre- and post-flight sessions. Our results indicate that short-duration spaceflight reduces respiratory modulation of HR and decreases cardiac baroreflex gain without affecting post-flight arterial blood pressure dynamics. Altered respiratory modulation of human autonomic rhythms does not persist until 25 days upon return to Earth.

Pain perception and hypnosis: findings from recent functional neuroimaging studies.

PubMed

Del Casale, Antonio; Ferracuti, Stefano; Rapinesi, Chiara; Serata, Daniele; Caltagirone, Saverio Simone; Savoja, Valeria; Piacentino, Daria; Callovini, Gemma; Manfredi, Giovanni; Sani, Gabriele; Kotzalidis, Georgios D; Girardi, Paolo

2015-01-01

Hypnosis modulates pain perception and tolerance by affecting cortical and subcortical activity in brain regions involved in these processes. By reviewing functional neuroimaging studies focusing on pain perception under hypnosis, the authors aimed to identify brain activation-deactivation patterns occurring in hypnosis-modulated pain conditions. Different changes in brain functionality occurred throughout all components of the pain network and other brain areas. The anterior cingulate cortex appears to be central in modulating pain circuitry activity under hypnosis. Most studies also showed that the neural functions of the prefrontal, insular, and somatosensory cortices are consistently modified during hypnosis-modulated pain conditions. Functional neuroimaging studies support the clinical use of hypnosis in the management of pain conditions.

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.

PubMed

Luecken, M D; Page, M J T; Crosby, A J; Mason, S; Reinert, G; Deane, C M

2018-03-15

Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favor communities of well-studied proteins. We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker's ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities and identifies functional modules that may correspond to more novel biology. The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker/. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online.

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants1

PubMed Central

Tohge, Takayuki; Klie, Sebastian; Fernie, Alisdair R.

2016-01-01

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant’s genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html. PMID:26754669

BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks

PubMed Central

Shen, Hong-Bin

2011-01-01

Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their components. Many methods were proposed to capture cohesive modules so that there is a higher density of edges within modules than those across them. Recent studies reveal that cohesively interacting modules of proteins is not a universal organizing principle in PINs, which has opened up new avenues for revisiting functional modules in PINs. In this paper, functional clusters in PINs are found to be able to form unorthodox structures defined as bi-sparse module. In contrast to the traditional cohesive module, the nodes in the bi-sparse module are sparsely connected internally and densely connected with other bi-sparse or cohesive modules. We present a novel protocol called the BinTree Seeking (BTS) for mining both bi-sparse and cohesive modules in PINs based on Edge Density of Module (EDM) and matrix theory. BTS detects modules by depicting links and nodes rather than nodes alone and its derivation procedure is totally performed on adjacency matrix of networks. The number of modules in a PIN can be automatically determined in the proposed BTS approach. BTS is tested on three real PINs and the results demonstrate that functional modules in PINs are not dominantly cohesive but can be sparse. BTS software and the supporting information are available at: www.csbio.sjtu.edu.cn/bioinf/BTS/. PMID:22140454

Safety for Compressed Gas and Air Equipment. Module SH-26. Safety and Health.

ERIC Educational Resources Information Center

Center for Occupational Research and Development, Inc., Waco, TX.

This student module on safety for compressed gas and air equipment is one of 50 modules concerned with job safety and health. This module presents technical data about commonly used gases and stresses the procedures necessary for safe handling of compressed gases. Following the introduction, 14 objectives (each keyed to a page in the text) the…

Function Specifications for the A-7E Function Driver Module.

DTIC Science & Technology

1981-11-27

Computer interface specifications (HEN181). The services and values provided by the Shared Services module are accurately described in the Shared Services Module...None$) FD.7.l.3.1 FD.7.1.7.1 5517a FD.App3 -5 Appendix 3 Event List (Alphabetical) Events Signalled by other Shared Services submodules @F( ABSCI+ip az...the Shared Services and Device Interface modules. Al; Answer this question for each table that appears in the function driver specification being

Non-degradative Ubiquitination of Protein Kinases

PubMed Central

Ball, K. Aurelia; Johnson, Jeffrey R.; Lewinski, Mary K.; Guatelli, John; Verschueren, Erik; Krogan, Nevan J.; Jacobson, Matthew P.

2016-01-01

Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well. PMID:27253329

Extracting a shape function for a signal with intra-wave frequency modulation.

PubMed

Hou, Thomas Y; Shi, Zuoqiang

2016-04-13

In this paper, we develop an effective and robust adaptive time-frequency analysis method for signals with intra-wave frequency modulation. To handle this kind of signals effectively, we generalize our data-driven time-frequency analysis by using a shape function to describe the intra-wave frequency modulation. The idea of using a shape function in time-frequency analysis was first proposed by Wu (Wu 2013 Appl. Comput. Harmon. Anal. 35, 181-199. (doi:10.1016/j.acha.2012.08.008)). A shape function could be any smooth 2π-periodic function. Based on this model, we propose to solve an optimization problem to extract the shape function. By exploring the fact that the shape function is a periodic function with respect to its phase function, we can identify certain low-rank structure of the signal. This low-rank structure enables us to extract the shape function from the signal. Once the shape function is obtained, the instantaneous frequency with intra-wave modulation can be recovered from the shape function. We demonstrate the robustness and efficiency of our method by applying it to several synthetic and real signals. One important observation is that this approach is very stable to noise perturbation. By using the shape function approach, we can capture the intra-wave frequency modulation very well even for noise-polluted signals. In comparison, existing methods such as empirical mode decomposition/ensemble empirical mode decomposition seem to have difficulty in capturing the intra-wave modulation when the signal is polluted by noise. © 2016 The Author(s).

Putting desire on a budget: dopamine and energy expenditure, reconciling reward and resources

PubMed Central

Beeler, Jeff A.; Frazier, Cristianne R. M.; Zhuang, Xiaoxi

2012-01-01

Accumulating evidence indicates integration of dopamine function with metabolic signals, highlighting a potential role for dopamine in energy balance, frequently construed as modulating reward in response to homeostatic state. Though its precise role remains controversial, the reward perspective of dopamine has dominated investigation of motivational disorders, including obesity. In the hypothesis outlined here, we suggest instead that the primary role of dopamine in behavior is to modulate activity to adapt behavioral energy expenditure to the prevailing environmental energy conditions, with the role of dopamine in reward and motivated behaviors derived from its primary role in energy balance. Dopamine has long been known to modulate activity, exemplified by psychostimulants that act via dopamine. More recently, there has been nascent investigation into the role of dopamine in modulating voluntary activity, with some investigators suggesting that dopamine may serve as a final common pathway that couples energy sensing to regulated voluntary energy expenditure. We suggest that interposed between input from both the internal and external world, dopamine modulates behavioral energy expenditure along two axes: a conserve-expend axis that regulates generalized activity and an explore-exploit axes that regulates the degree to which reward value biases the distribution of activity. In this view, increased dopamine does not promote consumption of tasty food. Instead increased dopamine promotes energy expenditure and exploration while decreased dopamine favors energy conservation and exploitation. This hypothesis provides a mechanistic interpretation to an apparent paradox: the well-established role of dopamine in food seeking and the findings that low dopaminergic functions are associated with obesity. Our hypothesis provides an alternative perspective on the role of dopamine in obesity and reinterprets the “reward deficiency hypothesis” as a perceived energy deficit. We propose that dopamine, by facilitating energy expenditure, should be protective against obesity. We suggest the apparent failure of this protective mechanism in Western societies with high prevalence of obesity arises as a consequence of sedentary lifestyles that thwart energy expenditure. PMID:22833718

Climbing fibers predict movement kinematics and performance errors.

PubMed

Streng, Martha L; Popa, Laurentiu S; Ebner, Timothy J

2017-09-01

Requisite for understanding cerebellar function is a complete characterization of the signals provided by complex spike (CS) discharge of Purkinje cells, the output neurons of the cerebellar cortex. Numerous studies have provided insights into CS function, with the most predominant view being that they are evoked by error events. However, several reports suggest that CSs encode other aspects of movements and do not always respond to errors or unexpected perturbations. Here, we evaluated CS firing during a pseudo-random manual tracking task in the monkey ( Macaca mulatta ). This task provides extensive coverage of the work space and relative independence of movement parameters, delivering a robust data set to assess the signals that activate climbing fibers. Using reverse correlation, we determined feedforward and feedback CSs firing probability maps with position, velocity, and acceleration, as well as position error, a measure of tracking performance. The direction and magnitude of the CS modulation were quantified using linear regression analysis. The major findings are that CSs significantly encode all three kinematic parameters and position error, with acceleration modulation particularly common. The modulation is not related to "events," either for position error or kinematics. Instead, CSs are spatially tuned and provide a linear representation of each parameter evaluated. The CS modulation is largely predictive. Similar analyses show that the simple spike firing is modulated by the same parameters as the CSs. Therefore, CSs carry a broader array of signals than previously described and argue for climbing fiber input having a prominent role in online motor control. NEW & NOTEWORTHY This article demonstrates that complex spike (CS) discharge of cerebellar Purkinje cells encodes multiple parameters of movement, including motor errors and kinematics. The CS firing is not driven by error or kinematic events; instead it provides a linear representation of each parameter. In contrast with the view that CSs carry feedback signals, the CSs are predominantly predictive of upcoming position errors and kinematics. Therefore, climbing fibers carry multiple and predictive signals for online motor control. Copyright © 2017 the American Physiological Society.

Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology

PubMed Central

2010-01-01

Background In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on multiple organisms and non-recording interaction data in the existing PPI database, it is still emergent to design novel computational techniques that can be able to correctly and scalably analyze interaction data sets. Indeed there are a number of large scale biological data sets providing indirect evidence for protein-protein interaction relationships. Results The main aim of this paper is to present a prior knowledge based mining strategy to identify functional modules from PPI networks with the aid of Gene Ontology. Higher similarity value in Gene Ontology means that two gene products are more functionally related to each other, so it is better to group such gene products into one functional module. We study (i) to encode the functional pairs into the existing PPI networks; and (ii) to use these functional pairs as pairwise constraints to supervise the existing functional module identification algorithms. Topology-based modularity metric and complex annotation in MIPs will be used to evaluate the identified functional modules by these two approaches. Conclusions The experimental results on Yeast PPI networks and GO have shown that the prior knowledge based learning methods perform better than the existing algorithms. PMID:21172053

Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles.

PubMed

Chang, Xiao; Liu, Shuai; Yu, Yong-Tao; Li, Yi-Xue; Li, Yuan-Yuan

2010-08-12

The Saccharopolyspora erythraea genome sequence was released in 2007. In order to look at the gene regulations at whole transcriptome level, an expression microarray was specifically designed on the S. erythraea strain NRRL 2338 genome sequence. Based on these data, we set out to investigate the potential transcriptional regulatory networks and their organization. In view of the hierarchical structure of bacterial transcriptional regulation, we constructed a hierarchical coexpression network at whole transcriptome level. A total of 27 modules were identified from 1255 differentially expressed transcript units (TUs) across time course, which were further classified in to four groups. Functional enrichment analysis indicated the biological significance of our hierarchical network. It was indicated that primary metabolism is activated in the first rapid growth phase (phase A), and secondary metabolism is induced when the growth is slowed down (phase B). Among the 27 modules, two are highly correlated to erythromycin production. One contains all genes in the erythromycin-biosynthetic (ery) gene cluster and the other seems to be associated with erythromycin production by sharing common intermediate metabolites. Non-concomitant correlation between production and expression regulation was observed. Especially, by calculating the partial correlation coefficients and building the network based on Gaussian graphical model, intrinsic associations between modules were found, and the association between those two erythromycin production-correlated modules was included as expected. This work created a hierarchical model clustering transcriptome data into coordinated modules, and modules into groups across the time course, giving insight into the concerted transcriptional regulations especially the regulation corresponding to erythromycin production of S. erythraea. This strategy may be extendable to studies on other prokaryotic microorganisms.

Brain functional connectivity changes in children that differ in impulsivity temperamental trait

PubMed Central

Inuggi, Alberto; Sanz-Arigita, Ernesto; González-Salinas, Carmen; Valero-García, Ana V.; García-Santos, Jose M.; Fuentes, Luis J.

2014-01-01

Impulsivity is a core personality trait forming part of normal behavior and contributing to adaptive functioning. However, in typically developing children, altered patterns of impulsivity constitute a risk factor for the development of behavioral problems. Since both pathological and non-pathological states are commonly characterized by continuous transitions, we used a correlative approach to investigate the potential link between personality and brain dynamics. We related brain functional connectivity of typically developing children, measured with magnetic resonance imaging at rest, with their impulsivity scores obtained from a questionnaire completed by their parents. We first looked for areas within the default mode network (DMN) whose functional connectivity might be modulated by trait impulsivity. Then, we calculated the functional connectivity among these regions and the rest of the brain in order to assess if impulsivity trait altered their relationships. We found two DMN clusters located at the posterior cingulate cortex and the right angular gyrus which were negatively correlated with impulsivity scores. The whole-brain correlation analysis revealed the classic network of correlating and anti-correlating areas with respect to the DMN. The impulsivity trait modulated such pattern showing that the canonical anti-phasic relation between DMN and action-related network was reduced in high impulsive children. These results represent the first evidence that the impulsivity, measured as personality trait assessed through parents' report, exerts a modulatory influence over the functional connectivity of resting state brain networks in typically developing children. The present study goes further to connect developmental approaches, mainly based on data collected through the use of questionnaires, and behavioral neuroscience, interested in how differences in brain structure and functions reflect in differences in behavior. PMID:24834038

Brain functional connectivity changes in children that differ in impulsivity temperamental trait.

PubMed

Inuggi, Alberto; Sanz-Arigita, Ernesto; González-Salinas, Carmen; Valero-García, Ana V; García-Santos, Jose M; Fuentes, Luis J

2014-01-01

Impulsivity is a core personality trait forming part of normal behavior and contributing to adaptive functioning. However, in typically developing children, altered patterns of impulsivity constitute a risk factor for the development of behavioral problems. Since both pathological and non-pathological states are commonly characterized by continuous transitions, we used a correlative approach to investigate the potential link between personality and brain dynamics. We related brain functional connectivity of typically developing children, measured with magnetic resonance imaging at rest, with their impulsivity scores obtained from a questionnaire completed by their parents. We first looked for areas within the default mode network (DMN) whose functional connectivity might be modulated by trait impulsivity. Then, we calculated the functional connectivity among these regions and the rest of the brain in order to assess if impulsivity trait altered their relationships. We found two DMN clusters located at the posterior cingulate cortex and the right angular gyrus which were negatively correlated with impulsivity scores. The whole-brain correlation analysis revealed the classic network of correlating and anti-correlating areas with respect to the DMN. The impulsivity trait modulated such pattern showing that the canonical anti-phasic relation between DMN and action-related network was reduced in high impulsive children. These results represent the first evidence that the impulsivity, measured as personality trait assessed through parents' report, exerts a modulatory influence over the functional connectivity of resting state brain networks in typically developing children. The present study goes further to connect developmental approaches, mainly based on data collected through the use of questionnaires, and behavioral neuroscience, interested in how differences in brain structure and functions reflect in differences in behavior.

A Glutathione Peroxidase, Intracellular Peptidases and the TOR Complexes Regulate Peptide Transporter PEPT-1 in C. elegans

PubMed Central

Benner, Jacqueline; Daniel, Hannelore; Spanier, Britta

2011-01-01

The intestinal peptide transporter PEPT-1 in Caenorhabditis elegans is a rheogenic H+-dependent carrier responsible for the absorption of di- and tripeptides. Transporter-deficient pept-1(lg601) worms are characterized by impairments in growth, development and reproduction and develop a severe obesity like phenotype. The transport function of PEPT-1 as well as the influx of free fatty acids was shown to be dependent on the membrane potential and on the intracellular pH homeostasis, both of which are regulated by the sodium-proton exchanger NHX-2. Since many membrane proteins commonly function as complexes, there could be proteins that possibly modulate PEPT-1 expression and function. A systematic RNAi screening of 162 genes that are exclusively expressed in the intestine combined with a functional transport assay revealed four genes with homologues existing in mammals as predicted PEPT-1 modulators. While silencing of a glutathione peroxidase surprisingly caused an increase in PEPT-1 transport function, silencing of the ER to Golgi cargo transport protein and of two cytosolic peptidases reduced PEPT-1 transport activity and this even corresponded with lower PEPT-1 protein levels. These modifications of PEPT-1 function by gene silencing of homologous genes were also found to be conserved in the human epithelial cell line Caco-2/TC7 cells. Peptidase inhibition, amino acid supplementation and RNAi silencing of targets of rapamycin (TOR) components in C. elegans supports evidence that intracellular peptide hydrolysis and amino acid concentration are a part of a sensing system that controls PEPT-1 expression and function and that involves the TOR complexes TORC1 and TORC2. PMID:21980510

SU-E-T-97: Dependence Of Optically Stimulated Luminescent Dosimeter (OSLD) Out Of Field Response On Volumetric Modulated Arc Therapy (VMAT) Field Modulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ware, S; Clouser, E

2014-06-01

Purpose: To determine the out of field response of Microstar ii OSLDs as a function of field modulation and distance in VMAT plan delivery. This work has potential application in fetal dose monitoring or measurements on cardiac pacemakers Methods: VMAT plans were created in Eclipse and optimized to varying degrees of modulation. Three plans were chosen to represent low, medium and high degrees of modulation (modulation factors as defined by MU/cGy). Plans were delivered to slabs of solid water with dimensions 60cm length, 30cm width, and 10cm height. For each modulation factor, 2 OSLDs were placed at 1cm depth withmore » out of field distances of 1, 2, 3, 5, 8 and 10cm and the plan delivered isocentrically to a depth of 5cm. This technique was repeated for a Farmer Chamber by incrementing the table by the appropriate distance. The charge readings for the Farmer Chamber were converted to dose and the ratios taken as functions of modulation factors and distances out of field Results: Examination of the results as a function of out of field distance shows a trend of increasing OSLD/Farmer Chamber ratios for all modulation factors. The slopes appear to be roughly equivalent for all modulation factors investigated. Results as a function of modulation showed a downward trend for all out of field distances, with the greatest differences seen at 5cm and 8cm Conclusion: This study demonstrates that the response of OSLD dosimeters change as a function of out of field distance and modulation. The differences seen are within the stated accuracy of the system for the out of field distances and modulations investigated. Additional investigation is warranted to see if the OSLD response changes appreciably with longer out of field distances or wider ranges of modulation.« less

Analysis of Phaseolus vulgaris Response to Its Association with Trichoderma harzianum (ALL-42) in the Presence or Absence of the Phytopathogenic Fungi Rhizoctonia solani and Fusarium solani

PubMed Central

Pereira, Jackeline L.; Queiroz, Rayner M. L.; Charneau, Sébastien O.; Felix, Carlos R.; Ricart, Carlos A. O.; da Silva, Francilene Lopes; Steindorff, Andrei Stecca; Ulhoa, Cirano J.; Noronha, Eliane F.

2014-01-01

The present study was carried out to evaluate the ability of Trichoderma harzianum (ALL 42-isolated from Brazilian Cerrado soil) to promote common bean growth and to modulate its metabolism and defense response in the presence or absence of the phytopathogenic fungi Rhizoctonia solani and Fusarium solani using a proteomic approach. T. harzianum was able to promote common bean plants growth as shown by the increase in root/foliar areas and by size in comparison to plants grown in its absence. The interaction was shown to modulate the expression of defense-related genes (Glu1, pod3 and lox1) in roots of P. vulgaris. Proteomic maps constructed using roots and leaves of plants challenged or unchallenged by T. harzianum and phytopathogenic fungi showed differences. Reference gels presented differences in spot distribution (absence/presence) and relative volumes of common spots (up or down-regulation). Differential spots were identified by peptide fingerprinting MALDI-TOF mass spectrometry. A total of 48 identified spots (19 for leaves and 29 for roots) were grouped into protein functional classes. For leaves, 33%, 22% and 11% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively. For roots, 17.2%, 24.1% and 10.3% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively. PMID:24878929

Analysis of Phaseolus vulgaris response to its association with Trichoderma harzianum (ALL-42) in the presence or absence of the phytopathogenic fungi Rhizoctonia solani and Fusarium solani.

PubMed

Pereira, Jackeline L; Queiroz, Rayner M L; Charneau, Sébastien O; Felix, Carlos R; Ricart, Carlos A O; da Silva, Francilene Lopes; Steindorff, Andrei Stecca; Ulhoa, Cirano J; Noronha, Eliane F

2014-01-01

The present study was carried out to evaluate the ability of Trichoderma harzianum (ALL 42-isolated from Brazilian Cerrado soil) to promote common bean growth and to modulate its metabolism and defense response in the presence or absence of the phytopathogenic fungi Rhizoctonia solani and Fusarium solani using a proteomic approach. T. harzianum was able to promote common bean plants growth as shown by the increase in root/foliar areas and by size in comparison to plants grown in its absence. The interaction was shown to modulate the expression of defense-related genes (Glu1, pod3 and lox1) in roots of P. vulgaris. Proteomic maps constructed using roots and leaves of plants challenged or unchallenged by T. harzianum and phytopathogenic fungi showed differences. Reference gels presented differences in spot distribution (absence/presence) and relative volumes of common spots (up or down-regulation). Differential spots were identified by peptide fingerprinting MALDI-TOF mass spectrometry. A total of 48 identified spots (19 for leaves and 29 for roots) were grouped into protein functional classes. For leaves, 33%, 22% and 11% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively. For roots, 17.2%, 24.1% and 10.3% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively.

The design of automatic software testing module for civil aviation information system

NASA Astrophysics Data System (ADS)

Qi, Qi; Sun, Yang

2018-05-01

In this paper, the practical innovation design is carried out according to the urgent needs of the automatic testing module of civil aviation information system. Firstly, the background and significance of the automatic testing module of civil aviation information system is expounded, and the current research status of automatic testing module and the advantages and disadvantages of related software are analyzed. Then, from the three aspects of macro demand, module functional requirement and module nonfunctional demand, we further study the needs of automatic testing module of civil aviation information system. Finally, from the four aspects of module structure, module core function, database and security, we have made an innovative plan for the automatic testing module of civil aviation information system.

Two candidate genes for two quantitative trait loci epistatically attenuate hypertension in a novel pathway.

PubMed

Chauvet, Cristina; Ménard, Annie; Deng, Alan Y

2015-09-01

Multiple quantitative trait loci (QTLs) for blood pressure (BP) have been detected in rat models of human polygenic hypertension. They influence BP physiologically via epistatic modules. Little is known about the causal genes and virtually nothing is known on modularized mechanisms governing their regulatory connections. Two genes responsible for two individual BP QTLs on rat Chromosome 18 have been identified that belong to the same epistatic module. Treacher Collins-Franceschetti syndrome 1 (Tcof1) gene is the only function candidate for C18QTL3. Haloacid dehalogenase like hydrolase domain containing 2 (Hdhd2), although a gene of previously unknown function, is C18QTL4, and encodes a newly identified phosphatase. The current work has provided the premier evidence that Hdhd2/C18QTL4 and Tcof1/C18QTL3 may be involved in polygenic hypertension. Hdhd2/C18QTL4 can regulate the function of Tcof1/C18QTL3 via de-phosphorylation, and, for the first time, furbishes a molecular mechanism in support of a genetically epistatic hierarchy between two BP QTLs, and thus authenticates the epistasis-common pathway paradigm. The pathway initiated by Hdhd2/C18QTL4 upstream of Tcof1/C18QTL3 reveals novel mechanistic insights into BP modulations. Their discovery might yield innovative therapeutic targets and diagnostic tools predicated on a novel BP cause and mechanism that is determined by a regulatory hierarchy. Optimizing the de-phosphorylation capability and its downstream target could be antihypertensive. The conceptual paradigm of an order and regulatory hierarchy may help unravel genetic and molecular relationships among certain human BP QTLs.

Synchronization of pulses from mode-locked lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, G.T.

A study of the synchronization of mode-locked lasers is presented. In particular, we investigate the timing of the laser output pulses with respect to the radio frequency (RF) signal driving the mode-locking elements in the laser cavity. Two types of mode-locked lasers are considered: a cw loss-modulated mode-locked argon ion laser; and a q-switched active-passive mode-locked Nd:YAG laser. We develop theoretical models for the treatment of laser pulse synchronization in both types of lasers. Experimental results are presented on a combined laser system that synchronizes pulses from both an argon ion and a Nd:YAG laser by using a common RFmore » signal to drive independent mode-lockers in both laser cavities. Shot to shot jitter as low as 18 ps (RMS) was measured between the output pulses from the two lasers. The theory of pulse synchronization for the cw loss-modulated mode-locked argon ion laser is based on the relationship between the timing of the mode-locked laser pulse (with respect to the peak of the RF signal) and the length of the laser cavity. Experiments on the argon laser include the measurement of the phase shift of the mode-locked pulse as a function of cavity length and intracavity intensity. The theory of synchronization of the active-passive mode-locked Nd:YAG laser is an extension of the pulse selection model of the active-passive laser. Experiments on the active-passive Nd:YAG laser include: measurement of the early noise fluctuations; measurement of the duration of the linear build-up stage (time between laser threshold and saturation of the absorber); measurement of jitter as a function of the mode-locker modulation depth; and measurement of the output pulse phase shift as a function of cavity length.« less

Conical : An extended module for computing a numerically satisfactory pair of solutions of the differential equation for conical functions

NASA Astrophysics Data System (ADS)

Dunster, T. M.; Gil, A.; Segura, J.; Temme, N. M.

2017-08-01

Conical functions appear in a large number of applications in physics and engineering. In this paper we describe an extension of our module Conical (Gil et al., 2012) for the computation of conical functions. Specifically, the module includes now a routine for computing the function R-1/2+ iτ m (x) , a real-valued numerically satisfactory companion of the function P-1/2+ iτ m (x) for x > 1. In this way, a natural basis for solving Dirichlet problems bounded by conical domains is provided. The module also improves the performance of our previous algorithm for the conical function P-1/2+ iτ m (x) and it includes now the computation of the first order derivative of the function. This is also considered for the function R-1/2+ iτ m (x) in the extended algorithm.

Mechanistic analysis of the function of agonists and allosteric modulators: reconciling two-state and operational models

PubMed Central

Roche, David; Gil, Debora; Giraldo, Jesús

2013-01-01

Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism. Linked Articles Another recent review on allosteric modulation can be found at: Kenakin, T (2013). New concepts in pharmacological efficacy at 7TM receptors: IUPHAR Review 2. British Journal of Pharmacology 168: 554–575. doi: 10.1111/j.1476-5381.2012.02223.x And in this issue of BJP there is an article on a new allosteric modulator: Newman AS, Batis N, Grafton G, Caputo F, Brady CA, Lambert J, Peters JA, Gordon J, Brain KL, Powell AD and Barnes NM (2013). 5-Chloroindole: a potent allosteric modulator of the 5-HT3 receptor. British Journal of Pharmacology 169: 1228–1238. doi: 10.1111/bph.12213 PMID:23647200

A Deletion Variant of the α2b-Adrenoceptor Modulates the Stress-Induced Shift from "Cognitive" to "Habit" Memory.

PubMed

Wirz, Lisa; Wacker, Jan; Felten, Andrea; Reuter, Martin; Schwabe, Lars

2017-02-22

Stress induces a shift from hippocampus-based "cognitive" toward dorsal striatum-based "habitual" learning and memory. This shift is thought to have important implications for stress-related psychopathologies, including post-traumatic stress disorder (PTSD). However, there is large individual variability in the stress-induced bias toward habit memory, and the factors underlying this variability are completely unknown. Here we hypothesized that a functional deletion variant of the gene encoding the α2b-adrenoceptor ( ADRA2B ), which has been linked to emotional memory processes and increased PTSD risk, modulates the stress-induced shift from cognitive toward habit memory. In two independent experimental studies, healthy humans were genotyped for the ADRA2B deletion variant. After a stress or control manipulation, participants completed a dual-solution learning task while electroencephalographic (Study I) or fMRI measurements (Study II) were taken. Carriers compared with noncarriers of the ADRA2B deletion variant exhibited a significantly reduced bias toward habit memory after stress. fMRI results indicated that, whereas noncarriers of the ADRA2B deletion variant showed increased functional connectivity between amygdala and putamen after stress, this increase in connectivity was absent in carriers of the deletion variant, who instead showed overall enhanced connectivity between amygdala and entorhinal cortex. Our results indicate that a common genetic variation of the noradrenergic system modulates the impact of stress on the balance between cognitive and habitual memory systems, most likely via altered amygdala orchestration of these systems. SIGNIFICANCE STATEMENT Stressful events have a powerful effect on human learning and memory. Specifically, accumulating evidence suggests that stress favors more rigid dorsal striatum-dependent habit memory, at the expense of flexible hippocampus-dependent cognitive memory. Although this shift may have important implications for understanding mental disorders, such as post-traumatic stress disorder, little is known about the source of individual differences in the sensitivity for the stress-induced bias toward habit memory. We report here that a common genetic variation of the noradrenergic system, a known risk factor for post-traumatic stress disorder, modulates the stress-induced shift from cognitive to habit memory, most likely through altered crosstalk between the hippocampus and dorsal striatum with the amygdala, a key structure in emotional memory. Copyright © 2017 the authors 0270-6474/17/372149-12$15.00/0.

Identifying osteosarcoma metastasis associated genes by weighted gene co-expression network analysis (WGCNA).

PubMed

Tian, Honglai; Guan, Donghui; Li, Jianmin

2018-06-01

Osteosarcoma (OS), the most common malignant bone tumor, accounts for the heavy healthy threat in the period of children and adolescents. OS occurrence usually correlates with early metastasis and high death rate. This study aimed to better understand the mechanism of OS metastasis.Based on Gene Expression Omnibus (GEO) database, we downloaded 4 expression profile data sets associated with OS metastasis, and selected differential expressed genes. Weighted gene co-expression network analysis (WGCNA) approach allowed us to investigate the most OS metastasis-correlated module. Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to give annotation of selected OS metastasis-associated genes.We select 897 differential expressed genes from OS metastasis and OS non-metastasis groups. Based on these selected genes, WGCNA further explored 142 genes included in the most OS metastasis-correlated module. Gene Ontology functional and KEGG pathway enrichment analyses showed that significantly OS metastasis-associated genes were involved in pathway correlated with insulin-like growth factor binding.Our research figured out several potential molecules participating in metastasis process and factors acting as biomarker. With this study, we could better explore the mechanism of OS metastasis and further discover more therapy targets.

Intrinsic functional network architecture of human semantic processing: Modules and hubs.

PubMed

Xu, Yangwen; Lin, Qixiang; Han, Zaizhu; He, Yong; Bi, Yanchao

2016-05-15

Semantic processing entails the activation of widely distributed brain areas across the temporal, parietal, and frontal lobes. To understand the functional structure of this semantic system, we examined its intrinsic functional connectivity pattern using a database of 146 participants. Focusing on areas consistently activated during semantic processing generated from a meta-analysis of 120 neuroimaging studies (Binder et al., 2009), we found that these regions were organized into three stable modules corresponding to the default mode network (Module DMN), the left perisylvian network (Module PSN), and the left frontoparietal network (Module FPN). These three dissociable modules were integrated by multiple connector hubs-the left angular gyrus (AG) and the left superior/middle frontal gyrus linking all three modules, the left anterior temporal lobe linking Modules DMN and PSN, the left posterior portion of dorsal intraparietal sulcus (IPS) linking Modules DMN and FPN, and the left posterior middle temporal gyrus (MTG) linking Modules PSN and FPN. Provincial hubs, which converge local information within each system, were also identified: the bilateral posterior cingulate cortices/precuneus, the bilateral border area of the posterior AG and the superior lateral occipital gyrus for Module DMN; the left supramarginal gyrus, the middle part of the left MTG and the left orbital inferior frontal gyrus (IFG) for Module FPN; and the left triangular IFG and the left IPS for Module FPN. A neuro-functional model for semantic processing was derived based on these findings, incorporating the interactions of memory, language, and control. Copyright © 2016 Elsevier Inc. All rights reserved.

Pre-Treatment. Training Module 2.102.2.77.

ERIC Educational Resources Information Center

Kirkwood Community Coll., Cedar Rapids, IA.

This document is an instructional module package designed in the objective format for use by an instructor familiar with pre-treatment unit operation. Included are objectives, instructor guide, student handouts and transparency masters. The module considers design, operation, maintenance, and safety of common methods of grit removal, screening,…

A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.

PubMed

Taroni, Jaclyn N; Greene, Casey S; Martyanov, Viktor; Wood, Tammara A; Christmann, Romy B; Farber, Harrison W; Lafyatis, Robert A; Denton, Christopher P; Hinchcliff, Monique E; Pioli, Patricia A; Mahoney, J Matthew; Whitfield, Michael L

2017-03-23

Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues. We used this signature to query tissue-specific functional genomic networks. We performed novel network analyses to contrast the skin and lung microenvironments and to assess the functional role of the inflammatory and fibrotic genes in each organ. Lastly, we tested the expression of macrophage activation state-associated gene sets for enrichment in skin and lung using a Wilcoxon rank sum test. We identified a common pathogenic gene expression signature-an immune-fibrotic axis-indicative of pro-fibrotic macrophages (MØs) in multiple tissues (skin, lung, esophagus, and peripheral blood mononuclear cells) affected by SSc. While the co-expression of these genes is common to all tissues, the functional consequences of this upregulation differ by organ. We used this disease-associated signature to query tissue-specific functional genomic networks to identify common and tissue-specific pathologies of SSc and related conditions. In contrast to skin, in the lung-specific functional network we identify a distinct lung-resident MØ signature associated with lipid stimulation and alternative activation. In keeping with our network results, we find distinct MØ alternative activation transcriptional programs in SSc-associated PF lung and in the skin of patients with an "inflammatory" SSc gene expression signature. Our results suggest that the innate immune system is central to SSc disease processes but that subtle distinctions exist between tissues. Our approach provides a framework for examining molecular signatures of disease in fibrosis and autoimmune diseases and for leveraging publicly available data to understand common and tissue-specific disease processes in complex human diseases.

Hardware architecture design of image restoration based on time-frequency domain computation

NASA Astrophysics Data System (ADS)

Wen, Bo; Zhang, Jing; Jiao, Zipeng

2013-10-01

The image restoration algorithms based on time-frequency domain computation is high maturity and applied widely in engineering. To solve the high-speed implementation of these algorithms, the TFDC hardware architecture is proposed. Firstly, the main module is designed, by analyzing the common processing and numerical calculation. Then, to improve the commonality, the iteration control module is planed for iterative algorithms. In addition, to reduce the computational cost and memory requirements, the necessary optimizations are suggested for the time-consuming module, which include two-dimensional FFT/IFFT and the plural calculation. Eventually, the TFDC hardware architecture is adopted for hardware design of real-time image restoration system. The result proves that, the TFDC hardware architecture and its optimizations can be applied to image restoration algorithms based on TFDC, with good algorithm commonality, hardware realizability and high efficiency.

Interpreting fMRI data: maps, modules and dimensions

PubMed Central

Op de Beeck, Hans P.; Haushofer, Johannes; Kanwisher, Nancy G.

2009-01-01

Neuroimaging research over the past decade has revealed a detailed picture of the functional organization of the human brain. Here we focus on two fundamental questions that are raised by the detailed mapping of sensory and cognitive functions and illustrate these questions with findings from the object-vision pathway. First, are functionally specific regions that are located close together best understood as distinct cortical modules or as parts of a larger-scale cortical map? Second, what functional properties define each cortical map or module? We propose a model in which overlapping continuous maps of simple features give rise to discrete modules that are selective for complex stimuli. PMID:18200027

Evaluation method for the potential functionome harbored in the genome and metagenome

PubMed Central

2012-01-01

Background One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Results Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. Conclusions The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various uncultivable microbes within unidentified phyla. PMID:23234305

Temporal modulation transfer functions in cochlear implantees using a method that limits overall loudness cues

PubMed Central

Fraser, Matthew; McKay, Colette M.

2012-01-01

Temporal modulation transfer functions (TMTFs) were measured for six users of cochlear implants, using different carrier rates and levels. Unlike most previous studies investigating modulation detection, the experimental design limited potential effects of overall loudness cues. Psychometric functions (percent correct discrimination of modulated from unmodulated stimuli versus modulation depth) were obtained. For each modulation depth, each modulated stimulus was loudness balanced to the unmodulated reference stimulus, and level jitter was applied in the discrimination task. The loudness-balance data showed that the modulated stimuli were louder than the unmodulated reference stimuli with the same average current, thus confirming the need to limit loudness cues when measuring modulation detection. TMTFs measured in this way had a low-pass characteristic, with a cut-off frequency (at comfortably loud levels) similar to that for normal-hearing listeners. A reduction in level caused degradation in modulation detection efficiency and a lower-cut-off frequency (i.e. poorer temporal resolution). An increase in carrier rate also led to a degradation in modulation detection efficiency, but only at lower levels or higher modulation frequencies. When detection thresholds were expressed as a proportion of dynamic range, there was no effect of carrier rate for the lowest modulation frequency (50 Hz) at either level. PMID:22146425

Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hongmin; Astrof, Nathan S.; Liu, Jin-Huan

2009-09-15

Volatile anesthetics (VAs), such as isoflurane, induce a general anesthetic state by binding to specific targets (i.e., ion channels) in the central nervous system (CNS). Simultaneously, VAs modulate immune functions, possibly via direct interaction with alternative targets on leukocytes. One such target, the integrin lymphocyte function-associated antigen-1 (LFA-1), has been shown previously to be inhibited by isoflurane. A better understanding of the mechanism by which isoflurane alters protein function requires the detailed information about the drug-protein interaction at an atomic level. Here, we describe the crystal structure of the LFA-1 ligand-binding domain (I domain) in complex with isoflurane at 1.6more » {angstrom}. We discovered that isoflurane binds to an allosteric cavity previously implicated as critical for the transition of LFA-1 from the low- to the high-affinity state. The isoflurane binding site in the I domain involves an array of amphiphilic interactions, thereby resembling a 'common anesthetic binding motif' previously predicted for authentic VA binding sites. These results suggest that the allosteric modulation of protein function by isoflurane, as demonstrated for the integrin LFA-1, might represent a unified mechanism shared by the interactions of volatile anesthetics with targets in the CNS. Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems.« less

IGDS/TRAP Interface Program (ITIP). Detailed Design Specification (DDS). [network flow diagrams for coal gasification studies

NASA Technical Reports Server (NTRS)

Jefferys, S.; Johnson, W.; Lewis, R.; Rich, R.

1981-01-01

The software modules which comprise the IGDS/TRAP Interface Program are described. A hierarchical input processing output (HIPO) chart for each user command is given. The description consists of: (1) function of the user command; (2) calling sequence; (3) moduls which call this use command; (4) modules called by this user command; (5) IGDS commands used by this user command; and (6) local usage of global registers. Each HIPO contains the principal functions performed within the module. Also included with each function are a list of the inputs which may be required to perform the function and a list of the outputs which may be created as a result of performing the function.

An NPARC Turbulence Module with Wall Functions

NASA Technical Reports Server (NTRS)

Zhu, J.; Shih, T.-H.

1997-01-01

The turbulence module recently developed for the NPARC code has been extended to include wall functions. The Van Driest transformation is used so that the wall functions can be applied to both incompressible and compressible flows. The module is equipped with three two-equation K-epsilon turbulence models: Chien, Shih-Lumley and CMOTR models. Details of the wall functions as well as their numerical implementation are reported. It is shown that the inappropriate artificial viscosity in the near-wall region has a big influence on the solution of the wall function approach. A simple way to eliminate this influence is proposed, which gives satisfactory results during the code validation. The module can be easily linked to the NPARC code for practical applications.

Task-induced frequency modulation features for brain-computer interfacing

NASA Astrophysics Data System (ADS)

Jayaram, Vinay; Hohmann, Matthias; Just, Jennifer; Schölkopf, Bernhard; Grosse-Wentrup, Moritz

2017-10-01

Objective. Task-induced amplitude modulation of neural oscillations is routinely used in brain-computer interfaces (BCIs) for decoding subjects’ intents, and underlies some of the most robust and common methods in the field, such as common spatial patterns and Riemannian geometry. While there has been some interest in phase-related features for classification, both techniques usually presuppose that the frequencies of neural oscillations remain stable across various tasks. We investigate here whether features based on task-induced modulation of the frequency of neural oscillations enable decoding of subjects’ intents with an accuracy comparable to task-induced amplitude modulation. Approach. We compare cross-validated classification accuracies using the amplitude and frequency modulated features, as well as a joint feature space, across subjects in various paradigms and pre-processing conditions. We show results with a motor imagery task, a cognitive task, and also preliminary results in patients with amyotrophic lateral sclerosis (ALS), as well as using common spatial patterns and Laplacian filtering. Main results. The frequency features alone do not significantly out-perform traditional amplitude modulation features, and in some cases perform significantly worse. However, across both tasks and pre-processing in healthy subjects the joint space significantly out-performs either the frequency or amplitude features alone. This result only does not hold for ALS patients, for whom the dataset is of insufficient size to draw any statistically significant conclusions. Significance. Task-induced frequency modulation is robust and straight forward to compute, and increases performance when added to standard amplitude modulation features across paradigms. This allows more information to be extracted from the EEG signal cheaply and can be used throughout the field of BCIs.

Dissemination and support of ARGUS for accelerator applications. Technical progress report, April 24, 1991--January 20, 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User`s Guide that documents the use of the code for all users. To release the code and the User`s Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

PubMed Central

2014-01-01

Background RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. Results We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification” includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module “mRNA identification” includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module “Target screening” provides expression profiling analyses and graphic visualization. The module “Self-testing” offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program’s functionality. Conclusions eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory. PMID:24593312

Cardiac e-learning: Development of a web-based implantable cardioverter defibrillator educational system.

PubMed

Hickey, Kathleen T; Johnson, Mary P; Biviano, Angelo; Aboelela, Sally; Thomas, Tami; Bakken, Suzanne; Garan, Hasan; Zimmerman, John L; Whang, William

2011-04-01

The objective of this study was to design a Web-based implantable cardioverter defibrillator (ICD) module that would allow greater access to learning which could occur at an individual's convenience outside the fast-paced clinical environment. A Web-based ICD software educational program was developed to provide general knowledge of the function of the ICD and the interpretation of the stored electrocardiograms. This learning tool could be accessed at any time via the Columbia University Internet server, using a unique, password protected login. A series of basic and advanced ICD terms were presented using actual ICD screenshots and videos that simulated scenarios the practitioner would most commonly encounter in the fast-paced clinical setting. To determine the usefulness of the site and improve the module, practitioners were asked to complete a brief (less than 5 min) online survey at the end of the module. Twenty-six practitioners have logged into our Web site: 20 nurses/nurse practitioners, four cardiac fellows, and two other practitioners. The majority of respondents rated the program as easy to use and useful. The success of this module has led to it becoming part of the training for student nurse practitioners before a clinical electrophysiology rotation, and the module is accessed by our cardiac entry level fellows before a rotation in the intensive care unit or electrophysiology service. Remote electronic arrhythmia learning is a successful example of the melding of technology and education to enhance clinical learning.

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

PubMed

Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

2014-03-05

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

Experience Drives Synchronization: The phase and Amplitude Dynamics of Neural Oscillations to Musical Chords Are Differentially Modulated by Musical Expertise.

PubMed

Pallesen, Karen Johanne; Bailey, Christopher J; Brattico, Elvira; Gjedde, Albert; Palva, J Matias; Palva, Satu

2015-01-01

Musical expertise is associated with structural and functional changes in the brain that underlie facilitated auditory perception. We investigated whether the phase locking (PL) and amplitude modulations (AM) of neuronal oscillations in response to musical chords are correlated with musical expertise and whether they reflect the prototypicality of chords in Western tonal music. To this aim, we recorded magnetoencephalography (MEG) while musicians and non-musicians were presented with common prototypical major and minor chords, and with uncommon, non-prototypical dissonant and mistuned chords, while watching a silenced movie. We then analyzed the PL and AM of ongoing oscillations in the theta (4-8 Hz) alpha (8-14 Hz), beta- (14-30 Hz) and gamma- (30-80 Hz) bands to these chords. We found that musical expertise was associated with strengthened PL of ongoing oscillations to chords over a wide frequency range during the first 300 ms from stimulus onset, as opposed to increased alpha-band AM to chords over temporal MEG channels. In musicians, the gamma-band PL was strongest to non-prototypical compared to other chords, while in non-musicians PL was strongest to minor chords. In both musicians and non-musicians the long-latency (> 200 ms) gamma-band PL was also sensitive to chord identity, and particularly to the amplitude modulations (beats) of the dissonant chord. These findings suggest that musical expertise modulates oscillation PL to musical chords and that the strength of these modulations is dependent on chord prototypicality.

An Update on CRF Mechanisms Underlying Alcohol Use Disorders and Dependence

PubMed Central

Quadros, Isabel Marian Hartmann; Macedo, Giovana Camila; Domingues, Liz Paola; Favoretto, Cristiane Aparecida

2016-01-01

Alcohol is the most commonly used and abused substance worldwide. The emergence of alcohol use disorders, and alcohol dependence in particular, is accompanied by functional changes in brain reward and stress systems, which contribute to escalated alcohol drinking and seeking. Corticotropin-releasing factor (CRF) systems have been critically implied in the transition toward problematic alcohol drinking and alcohol dependence. This review will discuss how dysregulation of CRF function contributes to the vulnerability for escalated alcohol drinking and other consequences of alcohol consumption, based on preclinical evidence. CRF signaling, mostly via CRF1 receptors, seems to be particularly important in conditions of excessive alcohol taking and seeking, including during early and protracted withdrawal, relapse, as well as during withdrawal-induced anxiety and escalated aggression promoted by alcohol. Modulation of CRF1 function seems to exert a less prominent role over low to moderate alcohol intake, or to species-typical behaviors. While CRF mechanisms in the hypothalamic–pituitary–adrenal axis have some contribution to the neurobiology of alcohol abuse and dependence, a pivotal role for extra-hypothalamic CRF pathways, particularly in the extended amygdala, is well characterized. More recent studies further suggest a direct modulation of brain reward function by CRF signaling in the ventral tegmental area, nucleus accumbens, and the prefrontal cortex, among other structures. This review will further discuss a putative role for other components of the CRF system that contribute for the overall balance of CRF function in reward and stress pathways, including CRF2 receptors, CRF-binding protein, and urocortins, a family of CRF-related peptides. PMID:27818644

Psychiatric risk factor ANK3/Ankyrin-G nanodomains regulate the structure and function of glutamatergic synapses

PubMed Central

Smith, Katharine R.; Kopeikina, Katherine J.; Fawcett-Patel, Jessica M.; Leaderbrand, Katherine; Gao, Ruoqi; Schürmann, Britta; Myczek, Kristoffer; Radulovic, Jelena; Swanson, Geoffrey T.; Penzes, Peter

2014-01-01

Summary Recent evidence implicates glutamatergic synapses as key pathogenic sites in psychiatric disorders. Common and rare variants in the ANK3 gene, encoding ankyrin-G, have been associated with bipolar disorder, schizophrenia, and autism. Here we demonstrate that ankyrin-G is integral to AMPAR-mediated synaptic transmission and maintenance of spine morphology. Using super-resolution microscopy we find that ankyrin-G forms distinct nanodomain structures within the spine head and neck. At these sites, it modulates mushroom spine structure and function, likely as a perisynaptic scaffold and barrier within the spine neck. Neuronal activity promotes ankyrin-G accumulation in distinct spine subdomains, where it differentially regulates NMDA receptor-dependent plasticity. These data implicate subsynaptic nanodomains containing a major psychiatric risk molecule, ankyrin-G, as having location-specific functions, and opens directions for basic and translational investigation of psychiatric risk molecules. PMID:25374361

Co-regulation of female sexual behavior and pregnancy induction: an exploratory synthesis.

PubMed

Erskine, Mary S; Lehmann, Michael L; Cameron, Nicole M; Polston, Eva K

2004-08-31

This paper will review both new and old data that address the question of whether brain mechanisms involved in reproductive function act in a coordinated way to control female sexual behavior and the induction of pregnancy/pseudopregnancy (P/PSP) by vaginocervical stimulation. Although it is clear that female sexual behavior, including pacing behavior, is important for induction of P/PSP, there has been no concerted effort to examine whether or how common mechanisms may control both functions. Because initiation of P/PSP requires that the female receive vaginocervical stimulation, central mechanisms controlling P/PSP may be modulated by or interactive with those that control female sexual behavior. This paper presents a synthesis of the literature and recent data from our lab for the purpose of examining whether there are interactions between behavioral and neuroendocrine mechanisms which reciprocally influence both reproductive functions.

Cocoa, Blood Pressure, and Vascular Function

PubMed Central

Ludovici, Valeria; Barthelmes, Jens; Nägele, Matthias P.; Enseleit, Frank; Ferri, Claudio; Flammer, Andreas J.; Ruschitzka, Frank; Sudano, Isabella

2017-01-01

Cardiovascular disease (CVD) represents the most common cause of death worldwide. The consumption of natural polyphenol-rich foods, and cocoa in particular, has been related to a reduced risk of CVD, including coronary heart disease and stroke. Intervention studies strongly suggest that cocoa exerts a beneficial impact on cardiovascular health, through the reduction of blood pressure (BP), improvement of vascular function, modulation of lipid and glucose metabolism, and reduction of platelet aggregation. These potentially beneficial effects have been shown in healthy subjects as well as in patients with risk factors (arterial hypertension, diabetes, and smoking) or established CVD (coronary heart disease or heart failure). Several potential mechanisms are supposed to be responsible for the positive effect of cocoa; among them activation of nitric oxide (NO) synthase, increased bioavailability of NO as well as antioxidant, and anti-inflammatory properties. It is the aim of this review to summarize the findings of cocoa and chocolate on BP and vascular function. PMID:28824916

Functional abdominal pain syndrome.

PubMed

Clouse, Ray E; Mayer, Emeran A; Aziz, Qasim; Drossman, Douglas A; Dumitrascu, Dan L; Mönnikes, Hubert; Naliboff, Bruce D

2006-04-01

Functional abdominal pain syndrome (FAPS) differs from the other functional bowel disorders; it is less common, symptoms largely are unrelated to food intake and defecation, and it has higher comorbidity with psychiatric disorders. The etiology and pathophysiology are incompletely understood. Because FAPS likely represents a heterogeneous group of disorders, peripheral neuropathic pain mechanisms, alterations in endogenous pain modulation systems, or both may be involved in any one patient. The diagnosis of FAPS is made on the basis of positive symptom criteria and a longstanding history of symptoms; in the absence of alarm symptoms, an extensive diagnostic evaluation is not required. Management is based on a therapeutic physician-patient relationship and empirical treatment algorithms using various classes of centrally acting drugs, including antidepressants and anticonvulsants. The choice, dose, and combination of drugs are influenced by psychiatric comorbidities. Psychological treatment options include psychotherapy, relaxation techniques, and hypnosis. Refractory FAPS patients may benefit from a multidisciplinary pain clinic approach.

Method of monolithic module assembly

DOEpatents

Gee, James M.; Garrett, Stephen E.; Morgan, William P.; Worobey, Walter

1999-01-01

Methods for "monolithic module assembly" which translate many of the advantages of monolithic module construction of thin-film PV modules to wafered c-Si PV modules. Methods employ using back-contact solar cells positioned atop electrically conductive circuit elements affixed to a planar support so that a circuit capable of generating electric power is created. The modules are encapsulated using encapsulant materials such as EVA which are commonly used in photovoltaic module manufacture. The methods of the invention allow multiple cells to be electrically connected in a single encapsulation step rather than by sequential soldering which characterizes the currently used commercial practices.

Common theme for drugs effective in overactive bladder treatment: Inhibition of afferent signaling from the bladder

PubMed Central

Hood, Brandy; Andersson, Karl-Erik

2013-01-01

The overactive bladder syndrome and detrusor overactivity are conditions that can have major effects on quality of life and social functioning. Antimuscarinic drugs are still first-line treatment. These drugs often have good initial response rates, but adverse effects and decreasing efficacy cause long-term compliance problems, and alternatives are needed. The recognition of the functional contribution of the urothelium/suburothelium, the autonomous detrusor muscle activity during bladder filling and the diversity of nerve transmitters involved has sparked interest in both peripheral and central modulation of overactive bladder syndrome/detrusor overactivity pathophysiology. Three drugs recently approved for treatment of overactive bladder syndrome/detrusor overactivity (mirabegron, tadalafil and onabotulinum toxin A), representing different pharmacological mechanisms; that is, β-adrenoceptor agonism, phosphodiesterase type 5 inhibition, and inhibition of nerve release of efferent and afferent transmitters, all seem to have one effect in common: inhibition of the afferent nervous activity generated by the bladder during filling. In the present review, the different mechanisms forming the pharmacological basis for the use of these drugs are discussed. PMID:23072271

Common hyperspectral image database design

NASA Astrophysics Data System (ADS)

Tian, Lixun; Liao, Ningfang; Chai, Ali

2009-11-01

This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes.

PubMed

Mueller, A J; Tew, S R; Vasieva, O; Clegg, P D; Canty-Laird, E G

2016-09-27

Phenotypic plasticity of adult somatic cells has provided emerging avenues for the development of regenerative therapeutics. In musculoskeletal biology the mechanistic regulatory networks of genes governing the phenotypic plasticity of cartilage and tendon cells has not been considered systematically. Additionally, a lack of strategies to effectively reproduce in vitro functional models of cartilage and tendon is retarding progress in this field. De- and redifferentiation represent phenotypic transitions that may contribute to loss of function in ageing musculoskeletal tissues. Applying a systems biology network analysis approach to global gene expression profiles derived from common in vitro culture systems (monolayer and three-dimensional cultures) this study demonstrates common regulatory mechanisms governing de- and redifferentiation transitions in cartilage and tendon cells. Furthermore, evidence of convergence of gene expression profiles during monolayer expansion of cartilage and tendon cells, and the expression of key developmental markers, challenges the physiological relevance of this culture system. The study also suggests that oxidative stress and PI3K signalling pathways are key modulators of in vitro phenotypes for cells of musculoskeletal origin.

Performance evaluation of MLP and RBF feed forward neural network for the recognition of off-line handwritten characters

NASA Astrophysics Data System (ADS)

Rishi, Rahul; Choudhary, Amit; Singh, Ravinder; Dhaka, Vijaypal Singh; Ahlawat, Savita; Rao, Mukta

2010-02-01

In this paper we propose a system for classification problem of handwritten text. The system is composed of preprocessing module, supervised learning module and recognition module on a very broad level. The preprocessing module digitizes the documents and extracts features (tangent values) for each character. The radial basis function network is used in the learning and recognition modules. The objective is to analyze and improve the performance of Multi Layer Perceptron (MLP) using RBF transfer functions over Logarithmic Sigmoid Function. The results of 35 experiments indicate that the Feed Forward MLP performs accurately and exhaustively with RBF. With the change in weight update mechanism and feature-drawn preprocessing module, the proposed system is competent with good recognition show.

Semantic integration to identify overlapping functional modules in protein interaction networks

PubMed Central

Cho, Young-Rae; Hwang, Woochang; Ramanathan, Murali; Zhang, Aidong

2007-01-01

Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification. PMID:17650343

Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases

PubMed Central

Bauer-Mehren, Anna; Bundschus, Markus; Rautschka, Michael; Mayer, Miguel A.; Sanz, Ferran; Furlong, Laura I.

2011-01-01

Background Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult. Principal Findings We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell. Conclusions For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases. Availability The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download. PMID:21695124

Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases.

PubMed

Bauer-Mehren, Anna; Bundschus, Markus; Rautschka, Michael; Mayer, Miguel A; Sanz, Ferran; Furlong, Laura I

2011-01-01

Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult. We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell. For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases. The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download.

Health, migration and border management: analysis and capacity-building at Europe's borders.

PubMed

Hollings, Jennifer; Samuilova, Mariya; Petrova-Benedict, Roumyana

2012-04-01

Three key elements were analysed in Hungary, Poland and Slovakia as a basis for strengthening the capacity of staff and structures related to health, migration and border management: public health concerns linked to migration, health needs and rights of migrants and the occupational health of staff. This IOM project was implemented through an in-depth situation analysis as well as the development of training modules and public health guidelines. Findings indicate a paucity of existing data, gaps in the health care for migrants and few existing tools for border officials and health professionals. Sets of training modules were developed for each of these groups, including common modules on migration and the right to health and intercultural communication, as well as targeted health modules. The guidelines promote good practices in the context of border management and detention. The EU is working towards a common immigration policy and integrated border management; however, a harmonized approach to migration and health is still lacking. Further research and piloting of the developed materials is needed to fully establish an adaptable, common toolkit.

Triple-mode single-transistor graphene amplifier and its applications.

PubMed

Yang, Xuebei; Liu, Guanxiong; Balandin, Alexander A; Mohanram, Kartik

2010-10-26

We propose and experimentally demonstrate a triple-mode single-transistor graphene amplifier utilizing a three-terminal back-gated single-layer graphene transistor. The ambipolar nature of electronic transport in graphene transistors leads to increased amplifier functionality as compared to amplifiers built with unipolar semiconductor devices. The ambipolar graphene transistors can be configured as n-type, p-type, or hybrid-type by changing the gate bias. As a result, the single-transistor graphene amplifier can operate in the common-source, common-drain, or frequency multiplication mode, respectively. This in-field controllability of the single-transistor graphene amplifier can be used to realize the modulation necessary for phase shift keying and frequency shift keying, which are widely used in wireless applications. It also offers new opportunities for designing analog circuits with simpler structure and higher integration densities for communications applications.

Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations

PubMed Central

Morra, Giulia; Potestio, Raffaello; Micheletti, Cristian; Colombo, Giorgio

2012-01-01

Understanding how local protein modifications, such as binding small-molecule ligands, can trigger and regulate large-scale motions of large protein domains is a major open issue in molecular biology. We address various aspects of this problem by analyzing and comparing atomistic simulations of Hsp90 family representatives for which crystal structures of the full length protein are available: mammalian Grp94, yeast Hsp90 and E.coli HtpG. These chaperones are studied in complex with the natural ligands ATP, ADP and in the Apo state. Common key aspects of their functional dynamics are elucidated with a novel multi-scale comparison of their internal dynamics. Starting from the atomic resolution investigation of internal fluctuations and geometric strain patterns, a novel analysis of domain dynamics is developed. The results reveal that the ligand-dependent structural modulations mostly consist of relative rigid-like movements of a limited number of quasi-rigid domains, shared by the three proteins. Two common primary hinges for such movements are identified. The first hinge, whose functional role has been demonstrated by several experimental approaches, is located at the boundary between the N-terminal and Middle-domains. The second hinge is located at the end of a three-helix bundle in the Middle-domain and unfolds/unpacks going from the ATP- to the ADP-state. This latter site could represent a promising novel druggable allosteric site common to all chaperones. PMID:22457611

Hardware Demonstration: Radiated Emissions as a Function of Common Mode Current

NASA Technical Reports Server (NTRS)

Mc Closkey, John; Roberts, Jen

2016-01-01

This presentation describes the electromagnetic compatibility (EMC) tests performed on the Integrated Science Instrument Module (ISIM), the science payload of the James Webb Space Telescope (JWST), at NASAs Goddard Space Flight Center (GSFC) in August 2015. By its very nature of being an integrated payload, it could be treated as neither a unit level test nor an integrated spacecraft observatory test. Non-standard test criteria are described along with non-standard test methods that had to be developed in order to evaluate them. Results are presented to demonstrate that all test criteria were met in less than the time allocated.

Introduction to the thematic minireview series on redox-active protein modifications and signaling.

PubMed

Banerjee, Ruma

2013-09-13

The dynamics of redox metabolism necessitate cellular strategies for sensing redox changes and for responding to them. A common mechanism for receiving and transmitting redox changes is via reversible modifications of protein cysteine residues. A plethora of cysteine modifications have been described, including sulfenylation, glutathionylation, and disulfide formation. These post-translational modifications have the potential to alter protein structure and/or function and to modulate cellular processes ranging from division to death and from circadian rhythms to secretion. The focus of this thematic minireview series is cysteine modifications in response to reactive oxygen and nitrogen species.

Silicon photonic transceiver circuit for high-speed polarization-based discrete variable quantum key distribution

DOE PAGES

Cai, Hong; Long, Christopher M.; DeRose, Christopher T.; ...

2017-01-01

We demonstrate a silicon photonic transceiver circuit for high-speed discrete variable quantum key distribution that employs a common structure for transmit and receive functions. The device is intended for use in polarization-based quantum cryptographic protocols, such as BB84. Our characterization indicates that the circuit can generate the four BB84 states (TE/TM/45°/135° linear polarizations) with >30 dB polarization extinction ratios and gigabit per second modulation speed, and is capable of decoding any polarization bases differing by 90° with high extinction ratios.

Silicon photonic transceiver circuit for high-speed polarization-based discrete variable quantum key distribution.

PubMed

Cai, Hong; Long, Christopher M; DeRose, Christopher T; Boynton, Nicholas; Urayama, Junji; Camacho, Ryan; Pomerene, Andrew; Starbuck, Andrew L; Trotter, Douglas C; Davids, Paul S; Lentine, Anthony L

2017-05-29

We demonstrate a silicon photonic transceiver circuit for high-speed discrete variable quantum key distribution that employs a common structure for transmit and receive functions. The device is intended for use in polarization-based quantum cryptographic protocols, such as BB84. Our characterization indicates that the circuit can generate the four BB84 states (TE/TM/45°/135° linear polarizations) with >30 dB polarization extinction ratios and gigabit per second modulation speed, and is capable of decoding any polarization bases differing by 90° with high extinction ratios.

Silicon photonic transceiver circuit for high-speed polarization-based discrete variable quantum key distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Hong; Long, Christopher M.; DeRose, Christopher T.

We demonstrate a silicon photonic transceiver circuit for high-speed discrete variable quantum key distribution that employs a common structure for transmit and receive functions. The device is intended for use in polarization-based quantum cryptographic protocols, such as BB84. Our characterization indicates that the circuit can generate the four BB84 states (TE/TM/45°/135° linear polarizations) with >30 dB polarization extinction ratios and gigabit per second modulation speed, and is capable of decoding any polarization bases differing by 90° with high extinction ratios.

The chloroplast division mutant caa33 of Arabidopsis thaliana reveals a crucial impact of chloroplast homeostasis on stress acclimation and retrograde plastid-to-nucleus signaling

PubMed Central

Šimková, Klára; Kim, Chanhong; Gacek, Katarzyna; Baruah, Aiswarya; Laloi, Christophe; Apel, Klaus

2011-01-01

SUMMARY Retrograde plastid-to-nucleus signaling tightly controls and coordinates nuclear and plastid gene expression that is required for plastid biogenesis and chloroplast activities. As chloroplasts act as sensors of environmental changes, plastid-derived signaling also modulates stress responses of plants by transferring stress-related signals and altering nuclear gene expression. Various mutant screens have been undertaken to identify constituents of plastid signaling pathways. Almost all mutations identified in these screens have in common that they target plastid-specific but not extra-plastidic functions. They have been suggested to define either genuine constituents of retrograde signaling pathways or components required for the synthesis of plastid signals. Here we report the characterization of the caa33 (constitutive activator of AAA-ATPase) mutant, which reveals another way of how mutations that affect plastid functions may modulate retrograde plastid signaling. caa33 disturbs a plastid-specific function by impeding plastid division thereby perturbing plastid homeostasis. This results in pre-conditioning plants by activating the expression of stress genes, enhancing pathogen resistance and attenuating the plant’s capacity to respond to plastid signals. Our study reveals an intimate link between chloroplast activity and the plant’s susceptibility to stress and emphasizes the need to consider the possible impact of pre-conditioning on retrograde plastid-to-nucleus signaling. PMID:22014227

Effect of rifaximin on gut microbiota composition in advanced liver disease and its complications

PubMed Central

Ponziani, Francesca Romana; Gerardi, Viviana; Pecere, Silvia; D’Aversa, Francesca; Lopetuso, Loris; Zocco, Maria Assunta; Pompili, Maurizio; Gasbarrini, Antonio

2015-01-01

Liver cirrhosis is a paradigm of intestinal dysbiosis. The qualitative and quantitative derangement of intestinal microbial community reported in cirrhotic patients seems to be strictly related with the impairment of liver function. A kind of gut microbial “fingerprint”, characterized by the reduced ratio of “good” to “potentially pathogenic” bacteria has recently been outlined, and is associated with the increase in Model for End-Stage Liver Disease and Child Pugh scores. Moreover, in patients presenting with cirrhosis complications such as spontaneous bacterial peritonitis (SBP), hepatic encephalopathy (HE), and, portal hypertension intestinal microbiota modifications or the isolation of bacteria deriving from the gut are commonly reported. Rifaximin is a non-absorbable antibiotic used in the management of several gastrointestinal diseases. Beyond bactericidal/bacteriostatic, immune-modulating and anti-inflammatory activity, a little is known about its interaction with gut microbial environment. Rifaximin has been demonstrated to exert beneficial effects on cognitive function in patients with HE, and also to prevent the development of SBP, to reduce endotoxemia and to improve hemodynamics in cirrhotics. These results are linked to a shift in gut microbes functionality, triggering the production of favorable metabolites. The low incidence of drug-related adverse events due to the small amount of circulating drug makes rifaximin a relatively safe antibiotic for the modulation of gut microbiota in advanced liver disease. PMID:26604640

Comprehending text versus reading words in young readers with varying reading ability: Distinct patterns of functional connectivity from common processing hubs

PubMed Central

Aboud, Katherine S.; Bailey, Stephen K.; Petrill, Stephen A.; Cutting, Laurie E.

2016-01-01

Skilled reading depends on recognizing words efficiently in isolation (word-level processing; WL) and extracting meaning from text (discourse-level processing; DL); deficiencies in either result in poor reading. FMRI has revealed consistent overlapping networks in word and passage reading, as well as unique regions for DL processing, however less is known about how WL and DL processes interact. Here we examined functional connectivity from seed regions derived from where BOLD signal overlapped during word and passage reading in 38 adolescents ranging in reading ability, hypothesizing that even though certain regions support word- and higher-level language, connectivity patterns from overlapping regions would be task modulated. Results indeed revealed that the left-lateralized semantic and working memory (WM) seed regions showed task-dependent functional connectivity patterns: during DL processes, semantic and WM nodes all correlated with the left angular gyrus, a region implicated in semantic memory/coherence building. In contrast, during WL, these nodes coordinated with a traditional WL area (left occipitotemporal region). Additionally, these WL and DL findings were modulated by decoding and comprehension abilities, respectively, with poorer abilities correlating with decreased connectivity. Findings indicate that key regions may uniquely contribute to multiple levels of reading; we speculate that these connectivity patterns may be especially salient for reading outcomes and intervention response. PMID:27147257

A common oxytocin receptor gene (OXTR) polymorphism modulates intranasal oxytocin effects on the neural response to social cooperation in humans.

PubMed

Feng, C; Lori, A; Waldman, I D; Binder, E B; Haroon, E; Rilling, J K

2015-09-01

Intranasal oxytocin (OT) can modulate social-emotional functioning and related brain activity in humans. Consequently, OT has been discussed as a potential treatment for psychiatric disorders involving social behavioral deficits. However, OT effects are often heterogeneous across individuals. Here we explore individual differences in OT effects on the neural response to social cooperation as a function of the rs53576 polymorphism of the oxytocin receptor gene (OXTR). Previously, we conducted a double-blind, placebo-controlled study in which healthy men and women were randomized to treatment with intranasal OT or placebo. Afterwards, they were imaged with functional magnetic resonance imaging while playing an iterated Prisoner's Dilemma Game with same-sex partners. Within the left ventral caudate nucleus, intranasal OT treatment increased activation to reciprocated cooperation in men, but tended to decrease activation in women. Here, we show that these sex differences in OT effects are specific to individuals with the rs53576 GG genotype, and are not found for other genotypes (rs53576 AA/AG). Thus, OT may increase the reward or salience of positive social interactions for male GG homozygotes, while decreasing those processes for female GG homozygotes. These results suggest that rs53576 genotype is an important variable to consider in future investigations of the clinical efficacy of intranasal OT treatment. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

CONTROL OF SLEEP AND WAKEFULNESS

PubMed Central

Brown, Ritchie E.; Basheer, Radhika; McKenna, James T.; Strecker, Robert E.; McCarley, Robert W.

2013-01-01

This review summarizes the brain mechanisms controlling sleep and wakefulness. Wakefulness promoting systems cause low-voltage, fast activity in the electroencephalogram (EEG). Multiple interacting neurotransmitter systems in the brain stem, hypothalamus, and basal forebrain converge onto common effector systems in the thalamus and cortex. Sleep results from the inhibition of wake-promoting systems by homeostatic sleep factors such as adenosine and nitric oxide and GABAergic neurons in the preoptic area of the hypothalamus, resulting in large-amplitude, slow EEG oscillations. Local, activity-dependent factors modulate the amplitude and frequency of cortical slow oscillations. Non-rapid-eye-movement (NREM) sleep results in conservation of brain energy and facilitates memory consolidation through the modulation of synaptic weights. Rapid-eye-movement (REM) sleep results from the interaction of brain stem cholinergic, aminergic, and GABAergic neurons which control the activity of glutamatergic reticular formation neurons leading to REM sleep phenomena such as muscle atonia, REMs, dreaming, and cortical activation. Strong activation of limbic regions during REM sleep suggests a role in regulation of emotion. Genetic studies suggest that brain mechanisms controlling waking and NREM sleep are strongly conserved throughout evolution, underscoring their enormous importance for brain function. Sleep disruption interferes with the normal restorative functions of NREM and REM sleep, resulting in disruptions of breathing and cardiovascular function, changes in emotional reactivity, and cognitive impairments in attention, memory, and decision making. PMID:22811426

Kidins220/ARMS as a functional mediator of multiple receptor signalling pathways.

PubMed

Neubrand, Veronika E; Cesca, Fabrizia; Benfenati, Fabio; Schiavo, Giampietro

2012-04-15

An increasing body of evidence suggests that several membrane receptors--in addition to activating distinct signalling cascades--also engage in substantial crosstalk with each other, thereby adjusting their signalling outcome as a function of specific input information. However, little is known about the molecular mechanisms that control their coordination and integration of downstream signalling. A protein that is likely to have a role in this process is kinase-D-interacting substrate of 220 kDa [Kidins220, also known as ankyrin repeat-rich membrane spanning (ARMS), hereafter referred to as Kidins220/ARMS]. Kidins220/ARMS is a conserved membrane protein that is preferentially expressed in the nervous system and interacts with the microtubule and actin cytoskeleton. It interacts with neurotrophin, ephrin, vascular endothelial growth factor (VEGF) and glutamate receptors, and is a common downstream target of several trophic stimuli. Kidins220/ARMS is required for neuronal differentiation and survival, and its expression levels modulate synaptic plasticity. Kidins220/ARMS knockout mice show developmental defects mainly in the nervous and cardiovascular systems, suggesting a crucial role for this protein in modulating the cross talk between different signalling pathways. In this Commentary, we summarise existing knowledge regarding the physiological functions of Kidins220/ARMS, and highlight some interesting directions for future studies on the role of this protein in health and disease.

Laminated photovoltaic modules using back-contact solar cells

DOEpatents

Gee, James M.; Garrett, Stephen E.; Morgan, William P.; Worobey, Walter

1999-09-14

Photovoltaic modules which comprise back-contact solar cells, such as back-contact crystalline silicon solar cells, positioned atop electrically conductive circuit elements affixed to a planar support so that a circuit capable of generating electric power is created. The modules are encapsulated using encapsulant materials such as EVA which are commonly used in photovoltaic module manufacture. The module designs allow multiple cells to be electrically connected in a single encapsulation step rather than by sequential soldering which characterizes the currently used commercial practices.

SLAC modulator system improvements and reliability results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donaldson, A.R.

1998-06-01

In 1995, an improvement project was completed on the 244 klystron modulators in the linear accelerator. The modulator system has been previously described. This article offers project details and their resulting effect on modulator and component reliability. Prior to the project, the authors had collected four operating cycles (1991 through 1995) of MTTF data. In this discussion, the '91 data will be excluded since the modulators operated at 60 Hz. The five periods following the '91 run were reviewed due to the common repetition rate at 120 Hz.

Seeking a unified framework for cerebellar function and dysfunction: from circuit operations to cognition

PubMed Central

D'Angelo, Egidio; Casali, Stefano

2013-01-01

Following the fundamental recognition of its involvement in sensory-motor coordination and learning, the cerebellum is now also believed to take part in the processing of cognition and emotion. This hypothesis is recurrent in numerous papers reporting anatomical and functional observations, and it requires an explanation. We argue that a similar circuit structure in all cerebellar areas may carry out various operations using a common computational scheme. On the basis of a broad review of anatomical data, it is conceivable that the different roles of the cerebellum lie in the specific connectivity of the cerebellar modules, with motor, cognitive, and emotional functions (at least partially) segregated into different cerebro-cerebellar loops. We here develop a conceptual and operational framework based on multiple interconnected levels (a meta-levels hypothesis): from cellular/molecular to network mechanisms leading to generation of computational primitives, thence to high-level cognitive/emotional processing, and finally to the sphere of mental function and dysfunction. The main concept explored is that of intimate interplay between timing and learning (reminiscent of the “timing and learning machine” capabilities long attributed to the cerebellum), which reverberates from cellular to circuit mechanisms. Subsequently, integration within large-scale brain loops could generate the disparate cognitive/emotional and mental functions in which the cerebellum has been implicated. We propose, therefore, that the cerebellum operates as a general-purpose co-processor, whose effects depend on the specific brain centers to which individual modules are connected. Abnormal functioning in these loops could eventually contribute to the pathogenesis of major brain pathologies including not just ataxia but also dyslexia, autism, schizophrenia, and depression. PMID:23335884

Feline immunodeficiency virus OrfA alters gene expression of splicing factors and proteasome-ubiquitination proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundstrom, Magnus; Chatterji, Udayan; Schaffer, Lana

2008-02-20

Expression of the feline immunodeficiency virus (FIV) accessory protein OrfA (or Orf2) is critical for efficient viral replication in lymphocytes, both in vitro and in vivo. OrfA has been reported to exhibit functions in common with the human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) accessory proteins Vpr and Tat, although the function of OrfA has not been fully explained. Here, we use microarray analysis to characterize how OrfA modulates the gene expression profile of T-lymphocytes. The primary IL-2-dependent T-cell line 104-C1 was transduced to express OrfA. Functional expression of OrfA was demonstrated by trans complementation of the OrfA-defectivemore » clone, FIV-34TF10. OrfA-expressing cells had a slightly reduced cell proliferation rate but did not exhibit any significant alteration in cell cycle distribution. Reverse-transcribed RNA from cells expressing green fluorescent protein (GFP) or GFP + OrfA were hybridized to Affymetrix HU133 Plus 2.0 microarray chips representing more than 47,000 genome-wide transcripts. By using two statistical approaches, 461 (Rank Products) and 277 (ANOVA) genes were identified as modulated by OrfA expression. The functional relevance of the differentially expressed genes was explored by Ingenuity Pathway Analysis. The analyses revealed alterations in genes critical for RNA post-transcriptional modifications and protein ubiquitination as the two most significant functional outcomes of OrfA expression. In these two groups, several subunits of the spliceosome, cellular splicing factors and family members of the proteasome-ubiquitination system were identified. These findings provide novel information on the versatile function of OrfA during FIV infection and indicate a fine-tuning mechanism of the cellular environment by OrfA to facilitate efficient FIV replication.« less

Modulating Intrinsic Connectivity: Adjacent Subregions within Supplementary Motor Cortex, Dorsolateral Prefrontal Cortex, and Parietal Cortex Connect to Separate Functional Networks during Task and Also Connect during Rest

PubMed Central

Roth, Jennifer K.; Johnson, Marcia K.; Tokoglu, Fuyuze; Murphy, Isabella; Constable, R. Todd

2014-01-01

Supplementary motor area (SMA), the inferior frontal junction (IFJ), superior frontal junction (SFJ) and parietal cortex are active in many cognitive tasks. In a previous study, we found that subregions of each of these major areas were differentially active in component processes of executive function during working memory tasks. In the present study, each of these subregions was used as a seed in a whole brain functional connectivity analysis of working memory and resting state data. These regions show functional connectivity to different networks, thus supporting the parcellation of these major regions into functional subregions. Many regions showing significant connectivity during the working memory residual data (with task events regressed from the data) were also significantly connected during rest suggesting that these network connections to subregions within major regions of cortex are intrinsic. For some of these connections, task demands modulate activity in these intrinsic networks. Approximately half of the connections significant during task were significant during rest, indicating that some of the connections are intrinsic while others are recruited only in the service of the task. Furthermore, the network connections to traditional ‘task positive’ and ‘task negative’ (a.k.a ‘default mode’) regions shift from positive connectivity to negative connectivity depending on task demands. These findings demonstrate that such task-identified subregions are part of distinct networks, and that these networks have different patterns of connectivity for task as they do during rest, engaging connections both to task positive and task negative regions. These results have implications for understanding the parcellation of commonly active regions into more specific functional networks. PMID:24637793

Identification of susceptible genes for complex chronic diseases based on disease risk functional SNPs and interaction networks.

PubMed

Li, Wan; Zhu, Lina; Huang, Hao; He, Yuehan; Lv, Junjie; Li, Weimin; Chen, Lina; He, Weiming

2017-10-01

Complex chronic diseases are caused by the effects of genetic and environmental factors. Single nucleotide polymorphisms (SNPs), one common type of genetic variations, played vital roles in diseases. We hypothesized that disease risk functional SNPs in coding regions and protein interaction network modules were more likely to contribute to the identification of disease susceptible genes for complex chronic diseases. This could help to further reveal the pathogenesis of complex chronic diseases. Disease risk SNPs were first recognized from public SNP data for coronary heart disease (CHD), hypertension (HT) and type 2 diabetes (T2D). SNPs in coding regions that were classified into nonsense and missense by integrating several SNP functional annotation databases were treated as functional SNPs. Then, regions significantly associated with each disease were screened using random permutations for disease risk functional SNPs. Corresponding to these regions, 155, 169 and 173 potential disease susceptible genes were identified for CHD, HT and T2D, respectively. A disease-related gene product interaction network in environmental context was constructed for interacting gene products of both disease genes and potential disease susceptible genes for these diseases. After functional enrichment analysis for disease associated modules, 5 CHD susceptible genes, 7 HT susceptible genes and 3 T2D susceptible genes were finally identified, some of which had pleiotropic effects. Most of these genes were verified to be related to these diseases in literature. This was similar for disease genes identified from another method proposed by Lee et al. from a different aspect. This research could provide novel perspectives for diagnosis and treatment of complex chronic diseases and susceptible genes identification for other diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Guanfacine modulates the emotional biasing of amygdala-prefrontal connectivity for cognitive control.

PubMed

Schulz, Kurt P; Clerkin, Suzanne M; Newcorn, Jeffrey H; Halperin, Jeffrey M; Fan, Jin

2014-09-01

Functional interactions between amygdala and prefrontal cortex provide a cortical entry point for emotional cues to bias cognitive control. Stimulation of α2 adrenoceptors enhances the prefrontal control functions and blocks the amygdala-dependent encoding of emotional cues. However, the impact of this stimulation on amygdala-prefrontal interactions and the emotional biasing of cognitive control have not been established. We tested the effect of the α2 adrenoceptor agonist guanfacine on psychophysiological interactions of amygdala with prefrontal cortex for the emotional biasing of response execution and inhibition. Fifteen healthy adults were scanned twice with event-related functional magnetic resonance imaging while performing an emotional go/no-go task following administration of oral guanfacine (1mg) and placebo in a double-blind, counterbalanced design. Happy, sad, and neutral faces served as trial cues. Guanfacine moderated the effect of face emotion on the task-related functional connectivity of left and right amygdala with left inferior frontal gyrus compared to placebo, by selectively reversing the functional co-activation of the two regions for response execution cued by sad faces. This shift from positively to negatively correlated activation for guanfacine was associated with selective improvements in the relatively low accuracy of responses to sad faces seen for placebo. These results demonstrate the importance of functional interactions between amygdala and inferior frontal gyrus to both bottom-up biasing of cognitive control and top-down control of emotional processing, as well as for the α2 adrenoceptor-mediated modulation of these processes. These mechanisms offer a possibile method to address the emotional reactivity that is common to several psychiatric disorders. Copyright © 2014 Elsevier B.V. and ECNP. All rights reserved.

Parametric fMRI of paced motor responses uncovers novel whole-brain imaging biomarkers in spinocerebellar ataxia type 3.

PubMed

Duarte, João Valente; Faustino, Ricardo; Lobo, Mercês; Cunha, Gil; Nunes, César; Ferreira, Carlos; Januário, Cristina; Castelo-Branco, Miguel

2016-10-01

Machado-Joseph Disease, inherited type 3 spinocerebellar ataxia (SCA3), is the most common form worldwide. Neuroimaging and neuropathology have consistently demonstrated cerebellar alterations. Here we aimed to discover whole-brain functional biomarkers, based on parametric performance-level-dependent signals. We assessed 13 patients with early SCA3 and 14 healthy participants. We used a combined parametric behavioral/functional neuroimaging design to investigate disease fingerprints, as a function of performance levels, coupled with structural MRI and voxel-based morphometry. Functional magnetic resonance imaging (fMRI) was designed to parametrically analyze behavior and neural responses to audio-paced bilateral thumb movements at temporal frequencies of 1, 3, and 5 Hz. Our performance-level-based design probing neuronal correlates of motor coordination enabled the discovery that neural activation and behavior show critical loss of parametric modulation specifically in SCA3, associated with frequency-dependent cortico/subcortical activation/deactivation patterns. Cerebellar/cortical rate-dependent dissociation patterns could clearly differentiate between groups irrespective of grey matter loss. Our findings suggest functional reorganization of the motor network and indicate a possible role of fMRI as a tool to monitor disease progression in SCA3. Accordingly, fMRI patterns proved to be potential biomarkers in early SCA3, as tested by receiver operating characteristic analysis of both behavior and neural activation at different frequencies. Discrimination analysis based on BOLD signal in response to the applied parametric finger-tapping task significantly often reached >80% sensitivity and specificity in single regions-of-interest.Functional fingerprints based on cerebellar and cortical BOLD performance dependent signal modulation can thus be combined as diagnostic and/or therapeutic targets in hereditary ataxia. Hum Brain Mapp 37:3656-3668, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Sex and disease-related alterations of anterior insula functional connectivity in chronic abdominal pain.

PubMed

Hong, Jui-Yang; Kilpatrick, Lisa A; Labus, Jennifer S; Gupta, Arpana; Katibian, David; Ashe-McNalley, Cody; Stains, Jean; Heendeniya, Nuwanthi; Smith, Suzanne R; Tillisch, Kirsten; Naliboff, Bruce; Mayer, Emeran A

2014-10-22

Resting-state functional magnetic resonance imaging has been used to investigate intrinsic brain connectivity in healthy subjects and patients with chronic pain. Sex-related differences in the frequency power distribution within the human insula (INS), a brain region involved in the integration of interoceptive, affective, and cognitive influences, have been reported. Here we aimed to test sex and disease-related alterations in the intrinsic functional connectivity of the dorsal anterior INS. The anterior INS is engaged during goal-directed tasks and modulates the default mode and executive control networks. By comparing functional connectivity of the dorsal anterior INS in age-matched female and male healthy subjects and patients with irritable bowel syndrome (IBS), a common chronic abdominal pain condition, we show evidence for sex and disease-related alterations in the functional connectivity of this region: (1) male patients compared with female patients had increased positive connectivity of the dorsal anterior INS bilaterally with the medial prefrontal cortex (PFC) and dorsal posterior INS; (2) female patients compared with male patients had greater negative connectivity of the left dorsal anterior INS with the left precuneus; (3) disease-related differences in the connectivity between the bilateral dorsal anterior INS and the dorsal medial PFC were observed in female subjects; and (4) clinical characteristics were significantly correlated to the insular connectivity with the dorsal medial PFC in male IBS subjects and with the precuneus in female IBS subjects. These findings are consistent with the INS playing an important role in modulating the intrinsic functional connectivity of major networks in the resting brain and show that this role is influenced by sex and diagnosis. Copyright © 2014 the authors 0270-6474/14/3414252-08$15.00/0.

Nucleoli and stress granules: connecting distant relatives.

PubMed

Mahboubi, Hicham; Stochaj, Ursula

2014-10-01

Nucleoli and cytoplasmic stress granules (SGs) are subcellular compartments that modulate the response to endogenous and environmental signals to control cell survival. In our opinion, nucleoli and SGs are functionally linked; they are distant relatives that combine forces when cellular homeostasis is threatened. Several lines of evidence support this idea; nucleoli and SGs share molecular building blocks, are regulated by common signaling pathways and communicate when vital cellular functions become compromised. Together, nucleoli and SGs orchestrate physiological responses that are directly relevant to stress and human health. As both compartments have established roles in neurodegenerative diseases, cancer and virus infections, we propose that these conditions will benefit from therapeutic interventions that target simultaneously nucleoli and SGs. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Picornaviral Polymerase Structure, Function, and Fidelity Modulation

PubMed Central

Peersen, Olve B.

2017-01-01

Like all positive strand RNA viruses, the picornaviruses replicate their genomes using a virally encoded RNA-dependent RNA polymerase enzyme known as 3Dpol. Over the past decade we have made tremendous advances in our understanding of 3Dpol structure and function, including the discovery of a novel mechanism for closing the active site that allows these viruses to easily fine tune replication fidelity and quasispecies distributions. This review summarizes current knowledge of picornaviral polymerase structure and how the enzyme interacts with RNA and other viral proteins to form stable and processive elongation complexes. The picornaviral RdRPs are among the smallest viral polymerases, but their fundamental molecular mechanism for catalysis appears to be generally applicable as a common feature of all positive strand RNA virus polymerases. PMID:28163093

Stem cell aging: mechanisms, regulators and therapeutic opportunities

PubMed Central

Oh, Juhyun; Lee, Yang David; Wagers, Amy J

2014-01-01

Aging tissues experience a progressive decline in homeostatic and regenerative capacities, which has been attributed to degenerative changes in tissue-specific stem cells, stem cell niches and systemic cues that regulate stem cell activity. Understanding the molecular pathways involved in this age-dependent deterioration of stem cell function will be critical for developing new therapies for diseases of aging that target the specific causes of age-related functional decline. Here we explore key molecular pathways that are commonly perturbed as tissues and stem cells age and degenerate. We further consider experimental evidence both supporting and refuting the notion that modulation of these pathways per se can reverse aging phenotypes. Finally, we ask whether stem cell aging establishes an epigenetic ‘memory’ that is indelibly written or one that can be reset. PMID:25100532

Development of a UAS-based survey module for ecological research

NASA Astrophysics Data System (ADS)

Meng, R.; McMahon, A. M.; Serbin, S.

2016-12-01

The development of small unmanned aircraft system (UAS, < 25 kg) techniques is enabling measurements of terrestrial ecosystems at unprecedented temporal and spatial scales. Given the potential for improved mission safety, high revisit frequency, and reduced operation cost, UAS platforms are of particular interest in the development for scientific research. Our group is developing a UAS-based survey module for ecological research (e.g. scaling and mapping plant functional traits). However, in addition to technical challenges, the complicated regulations required to operate a UAS for research (e.g. Certificates of Waiver or Authorization, COA, for each location) and complying with Federal Aviation Administration (FAA) restrictions, which still actively evolving, can have significant impacts on research and schedules. Here we briefly discuss our lessons-learned related to FAA registration and COA procedures, requirements, and regulations in the US, accompanied by our hand-on experiences (our group currently have two COA granted and three more under review by FAA). We then introduce our design for a modular data collection software framework. This framework is open source (available on GitHub) and cross-platform compatible (written in Python), providing flexibility in development and deployment hardware configurations. In addition our framework uses a central module to coordinate the data acquisition, synchronization with the UAS control system and data storage through a common interface and interchangeable, hardware specific software modules. Utilizing this structure and a common data transfer format, the system can be easily reconfigured to meet the needs of a specific platform or operation, eliminating the need to redevelop acquisition systems for specific instrument/platform configurations. On-site data measurement tests of UAS-based survey module were conducted and data quality from multi-sensors (e.g. a high-resolution digital camera, spectroradiometer, and a thermal infrared camera) was reported. Finally, the results of this prototype study show that the UAS techniques can be used to develop a low-cost alternative for ecological research, but much effort is still needed to carefully deal with flight regulations and integrate off-the-shelf instrumentation, by the practitioner.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

PubMed Central

Wilhelm, Linda; Besemer, Katharina; Fragner, Lena; Peter, Hannes; Weckwerth, Wolfram; Battin, Tom J

2015-01-01

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams. PMID:25978543

Scaling of Topologically Similar Functional Modules Defines Mouse Primary Auditory and Somatosensory Microcircuitry

PubMed Central

Sadovsky, Alexander J.

2013-01-01

Mapping the flow of activity through neocortical microcircuits provides key insights into the underlying circuit architecture. Using a comparative analysis we determined the extent to which the dynamics of microcircuits in mouse primary somatosensory barrel field (S1BF) and auditory (A1) neocortex generalize. We imaged the simultaneous dynamics of up to 1126 neurons spanning multiple columns and layers using high-speed multiphoton imaging. The temporal progression and reliability of reactivation of circuit events in both regions suggested common underlying cortical design features. We used circuit activity flow to generate functional connectivity maps, or graphs, to test the microcircuit hypothesis within a functional framework. S1BF and A1 present a useful test of the postulate as both regions map sensory input anatomically, but each area appears organized according to different design principles. We projected the functional topologies into anatomical space and found benchmarks of organization that had been previously described using physiology and anatomical methods, consistent with a close mapping between anatomy and functional dynamics. By comparing graphs representing activity flow we found that each region is similarly organized as highlighted by hallmarks of small world, scale free, and hierarchical modular topologies. Models of prototypical functional circuits from each area of cortex were sufficient to recapitulate experimentally observed circuit activity. Convergence to common behavior by these models was accomplished using preferential attachment to scale from an auditory up to a somatosensory circuit. These functional data imply that the microcircuit hypothesis be framed as scalable principles of neocortical circuit design. PMID:23986241

GABAergic modulation of human social interaction in a prisoner's dilemma model by acute administration of alprazolam.

PubMed

Lane, Scott D; Gowin, Joshua L

2009-10-01

Recent work in neuroeconomics has used game theory paradigms to examine neural systems that subserve human social interaction and decision making. Attempts to modify social interaction through pharmacological manipulation have been less common. Here we show dose-dependent modification of human social behavior in a prisoner's dilemma model after acute administration of the γ-aminobutyric acid (GABA)-A modulating benzodiazepine alprazolam. Nine healthy adults received doses of placebo, 0.5, 1.0, and 2.0 mg alprazolam in a counterbalanced within-subject design, while completing multiple test blocks per day on an iterated prisoner's dilemma game. During test blocks in which peak subjective effects of alprazolam were reported, cooperative choices were significantly decreased as a function of dose. Consistent with previous reports showing that high acute doses of GABA-modulating drugs are associated with violence and other antisocial behavior, our data suggest that at sufficiently high doses, alprazolam can decrease cooperation. These behavioral changes may be facilitated by changes in inhibitory control facilitated by GABA. Game theory paradigms may prove useful in behavioral pharmacology studies seeking to measure social interaction, and may help inform the emerging field of neuroeconomics.

GABAergic modulation of human social interaction in a prisoner’s dilemma model via acute administration of alprazolam

PubMed Central

Lane, Scott D.; Gowin, Joshua L.

2010-01-01

Recent work in neuroeconomics has utilized game theory paradigms to examine neural systems that subserve human social interaction and decision making. Attempts to modify social interaction through pharmacological manipulation have been less common. Here we show dose-dependent modification of human social behavior in a prisoner’s dilemma (PD) model following acute administration of the GABA-A modulating benzodiazepine alprazolam. Nine healthy adults received doses of placebo, 0.5, 1.0, and 2.0 mg alprazolam in a counterbalanced within-subject design, while completing multiple test blocks per day on an iterated PD game. During test blocks in which peak subjective effects of alprazolam were reported, cooperative choices were significantly decreased as a function of dose. Consistent with previous reports showing that high acute doses of GABA-modulating drugs are associated with violence and other antisocial behavior, our data suggest that at sufficiently high doses, alprazolam can decrease cooperation. These behavioral changes may be facilitated by changes in inhibitory control facilitated by GABA. Game theory paradigms may prove useful in behavioral pharmacology studies seeking to measure social interaction, and may help inform the emerging field of neuroeconomics. PMID:19667972

Improved linearity using harmonic error rejection in a full-field range imaging system

NASA Astrophysics Data System (ADS)

Payne, Andrew D.; Dorrington, Adrian A.; Cree, Michael J.; Carnegie, Dale A.

2008-02-01

Full field range imaging cameras are used to simultaneously measure the distance for every pixel in a given scene using an intensity modulated illumination source and a gain modulated receiver array. The light is reflected from an object in the scene, and the modulation envelope experiences a phase shift proportional to the target distance. Ideally the waveforms are sinusoidal, allowing the phase, and hence object range, to be determined from four measurements using an arctangent function. In practice these waveforms are often not perfectly sinusoidal, and in some cases square waveforms are instead used to simplify the electronic drive requirements. The waveforms therefore commonly contain odd harmonics which contribute a nonlinear error to the phase determination, and therefore an error in the range measurement. We have developed a unique sampling method to cancel the effect of these harmonics, with the results showing an order of magnitude improvement in the measurement linearity without the need for calibration or lookup tables, while the acquisition time remains unchanged. The technique can be applied to existing range imaging systems without having to change or modify the complex illumination or sensor systems, instead only requiring a change to the signal generation and timing electronics.

The Spleen: A Hub Connecting Nervous and Immune Systems in Cardiovascular and Metabolic Diseases

PubMed Central

Lori, Andrea; Perrotta, Marialuisa; Lembo, Giuseppe; Carnevale, Daniela

2017-01-01

Metabolic disorders have been identified as major health problems affecting a large portion of the world population. In addition, obesity and insulin resistance are principal risk factors for the development of cardiovascular diseases. Altered immune responses are common features of both hypertension and obesity and, moreover, the involvement of the nervous system in the modulation of immune system is gaining even more attention in both pathophysiological contexts. For these reasons, during the last decades, researches focused their efforts on the comprehension of the molecular mechanisms connecting immune system to cardiovascular and metabolic diseases. On the other hand, it has been reported that in these pathological conditions, central neural pathways modulate the activity of the peripheral nervous system, which is strongly involved in onset and progression of the disease. It is interesting to notice that neural reflex can also participate in the modulation of immune functions. In this scenario, the spleen becomes the crucial hub allowing the interaction of different systems differently involved in metabolic and cardiovascular diseases. Here, we summarize the major findings that dissect the role of the immune system in disorders related to metabolic and cardiovascular dysfunctions, and how this could also be influenced by neural reflexes. PMID:28590409

Nanoparticle interface to biology: applications in probing and modulating biological processes.

PubMed

Kah, James Chen Yong; Yeo, Eugenia Li Ling; Koh, Wee Ling; Poinard, Barbara Elodie Ariane; Neo, Dawn Jing Hui

2013-01-01

Nanomaterials can be considered as "pseudo" subcellular entities that are similar to endogenous biomolecules because of their size and ability to interact with other biomolecules. The interaction between nanoparticles and biomolecules gives rise to the nano-bio interface between a nanoparticle and its biological environment. This is often defined in terms of the biomolecules that are present on the surface of the nanoparticles. The nano-bio interface alters the surface characteristics and is what the biological system sees and interacts with. The nanoparticle can thus be viewed as a "scaffold" to which molecules are attached. Intelligent design of this nano-bio interface is therefore crucial to the functionality of nanoscale systems in biology. In this review, we discuss the most common nano-bio interfaces formed from molecules including DNA, polymers, proteins, and antibodies, and discuss their applications in probing and modulating biological processes. We focus our discussion on the nano-bio interface formed on gold nanoparticles as our nanoparticle "scaffold" of interest in part because of our research interest as well as their unique physicochemical properties. While not exhaustive, this review provides a good overview of the latest advances in the use of gold nanomaterial interface to probe and modulate biological processes.

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

PubMed

Wang, Yi; Thilmony, Roger; Zhao, Yunjun; Chen, Guoping; Gu, Yong Q

2014-01-01

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Increased Global Interaction Across Functional Brain Modules During Cognitive Emotion Regulation.

PubMed

Brandl, Felix; Mulej Bratec, Satja; Xie, Xiyao; Wohlschläger, Afra M; Riedl, Valentin; Meng, Chun; Sorg, Christian

2017-07-13

Cognitive emotion regulation (CER) enables humans to flexibly modulate their emotions. While local theories of CER neurobiology suggest interactions between specialized local brain circuits underlying CER, e.g., in subparts of amygdala and medial prefrontal cortices (mPFC), global theories hypothesize global interaction increases among larger functional brain modules comprising local circuits. We tested the global CER hypothesis using graph-based whole-brain network analysis of functional MRI data during aversive emotional processing with and without CER. During CER, global between-module interaction across stable functional network modules increased. Global interaction increase was particularly driven by subregions of amygdala and cuneus-nodes of highest nodal participation-that overlapped with CER-specific local activations, and by mPFC and posterior cingulate as relevant connector hubs. Results provide evidence for the global nature of human CER, complementing functional specialization of embedded local brain circuits during successful CER. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Adenosine receptors and muscarinic receptors cooperate in acetylcholine release modulation in the neuromuscular synapse.

PubMed

Santafe, M M; Priego, M; Obis, T; Garcia, N; Tomàs, M; Lanuza, M A; Tomàs, J

2015-07-01

Adenosine receptors (ARs) are present in the motor terminals at the mouse neuromuscular junction. ARs and the presynaptic muscarinic acetylcholine receptors (mAChRs) share the functional control of the neuromuscular junction. We analysed their mutual interaction in transmitter release modulation. In electrophysiological experiments with unaltered synaptic transmission (muscles paralysed by blocking the voltage-dependent sodium channel of the muscle cells with μ-conotoxin GIIIB), we found that: (i) a collaborative action between different AR subtypes reduced synaptic depression at a moderate activity level (40 Hz); (ii) at high activity levels (100 Hz), endogenous adenosine production in the synaptic cleft was sufficient to reduce depression through A1 -type receptors (A1 Rs) and A2 A-type receptors (A2 A Rs); (iii) when the non-metabolizable 2-chloroadenosine (CADO) agonist was used, both the quantal content and depression were reduced; (iv) the protective effect of CADO on depression was mediated by A1 Rs, whereas A2 A Rs seemed to modulate A1 Rs; (v) ARs and mAChRs absolutely depended upon each other for the modulation of evoked and spontaneous acetylcholine release in basal conditions and in experimental conditions with CADO stimulation; (vi) the purinergic and muscarinic mechanisms cooperated in the control of depression by sharing a common pathway although the purinergic control was more powerful than the muscarinic control; and (vii) the imbalance of the ARs created by using subtype-selective and non-selective inhibitory and stimulatory agents uncoupled protein kinase C from evoked transmitter release. In summary, ARs (A1 Rs, A2 A Rs) and mAChRs (M1 , M2 ) cooperated in the control of activity-dependent synaptic depression and may share a common protein kinase C pathway. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Light beam frequency comb generator

DOEpatents

Priatko, G.J.; Kaskey, J.A.

1992-11-24

A light beam frequency comb generator uses an acousto-optic modulator to generate a plurality of light beams with frequencies which are uniformly separated and possess common noise and drift characteristics. A well collimated monochromatic input light beam is passed through this modulator to produce a set of both frequency shifted and unshifted optical beams. An optical system directs one or more frequency shifted beams along a path which is parallel to the path of the input light beam such that the frequency shifted beams are made incident on the modulator proximate to but separated from the point of incidence of the input light beam. After the beam is thus returned to and passed through the modulator repeatedly, a plurality of mutually parallel beams are generated which are frequency-shifted different numbers of times and possess common noise and drift characteristics. 2 figs.

Light beam frequency comb generator

DOEpatents

Priatko, Gordon J.; Kaskey, Jeffrey A.

1992-01-01

A light beam frequency comb generator uses an acousto-optic modulator to generate a plurality of light beams with frequencies which are uniformly separated and possess common noise and drift characteristics. A well collimated monochromatic input light beam is passed through this modulator to produce a set of both frequency shifted and unshifted optical beams. An optical system directs one or more frequency shifted beams along a path which is parallel to the path of the input light beam such that the frequency shifted beams are made incident on the modulator proximate to but separated from the point of incidence of the input light beam. After the beam is thus returned to and passed through the modulator repeatedly, a plurality of mutually parallel beams are generated which are frequency-shifted different numbers of times and possess common noise and drift characteristics.

Fertilizing ROSES through the STEM: Interdisciplinary Modules as Pre-service Research Experiences for Secondary STEM Educators (IMPRESS-Ed)

NASA Astrophysics Data System (ADS)

Kavic, Michael; Wiita, P. J.; Benoit, M.; Magee, N.

2013-01-01

IMPRESS-Ed is a program designed to provide authentic summer research experiences in the space, earth, and atmospheric sciences for pre-service K-12 educators at Long Island University (LIU) and The College of New Jersey (TCNJ). In 2011 and 2012, the program involved five students and took place over eight weeks with recruitment occurring during the preceding academic year. The program was divided into two modules: A common core module and an individual mentored research experience. The common module consisted of three units focusing on data-driven pedagogical approaches in astrophysics, tectonophysics, and atmospheric science, respectively. The common module also featured training sessions in observational astronomy, and use of a 3D geowall and state of the art planetarium. Participants in the program are also offered the opportunity to utilize the available TCNJ facilities with their future students. The individual mentored research module matched student interests with potential projects. All five students demonstrated strong gains in earth and space science literacy compared to a baseline measurement. Each student also reported gaining confidence to incorporate data and research-driven instruction in the space and earth sciences into the K-12 STEM classroom setting. All five research projects were also quite successful: several of the students plan to continue research during the academic year and two students are presenting research findings as first authors here at AAS. Other research results are likely to be presented at this year's American Geophysical Union meeting.

Multi-pulse multi-delay (MPMD) multiple access modulation for UWB

DOEpatents

Dowla, Farid U.; Nekoogar, Faranak

2007-03-20

A new modulation scheme in UWB communications is introduced. This modulation technique utilizes multiple orthogonal transmitted-reference pulses for UWB channelization. The proposed UWB receiver samples the second order statistical function at both zero and non-zero lags and matches the samples to stored second order statistical functions, thus sampling and matching the shape of second order statistical functions rather than just the shape of the received pulses.

Regulatory T-cells in autoimmune diseases: challenges, controversies and--yet--unanswered questions.

PubMed

Grant, Charlotte R; Liberal, Rodrigo; Mieli-Vergani, Giorgina; Vergani, Diego; Longhi, Maria Serena

2015-02-01

Regulatory T cells (Tregs) are central to the maintenance of self-tolerance and tissue homeostasis. Markers commonly used to define human Tregs in the research setting include high expression of CD25, FOXP3 positivity and low expression/negativity for CD127. Many other markers have been proposed, but none unequivocally identifies bona fide Tregs. Tregs are equipped with an array of mechanisms of suppression, including the modulation of antigen presenting cell maturation and function, the killing of target cells, the disruption of metabolic pathways and the production of anti-inflammatory cytokines. Treg impairment has been reported in a number of human autoimmune conditions and includes Treg numerical and functional defects and conversion into effector cells in response to inflammation. In addition to intrinsic Treg impairment, resistance of effector T cells to Treg control has been described. Discrepancies in the literature are common, reflecting differences in the choice of study participants and the technical challenges associated with investigating this cell population. Studies differ in terms of the methodology used to define and isolate putative regulatory cells and to assess their suppressive function. In this review we outline studies describing Treg frequency and suppressive function in systemic and organ specific autoimmune diseases, with a specific focus on the challenges faced when investigating Tregs in these conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA.

PubMed

Song, Zhonghua; Zhao, Wenhua; Cao, Danfeng; Zhang, Jinqing; Chen, Shouhua

2018-01-01

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC.

Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA

PubMed Central

Song, Zhonghua; Zhao, Wenhua; Cao, Danfeng; Zhang, Jinqing; Chen, Shouhua

2018-01-01

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC. PMID:29489999

Umbral Calculus and Holonomic Modules in Positive Characteristic

NASA Astrophysics Data System (ADS)

Kochubei, Anatoly N.

2006-03-01

In the framework of analysis over local fields of positive characteristic, we develop algebraic tools for introducing and investigating various polynomial systems. In this survey paper we describe a function field version of umbral calculus developed on the basis of a relation of binomial type satisfied by the Carlitz polynomials. We consider modules over the Weyl-Carlitz ring, a function field counterpart of the Weyl algebra. It is shown that some basic objects of function field arithmetic, like the Carlitz module, Thakur's hypergeometric polynomials, and analogs of binomial coefficients arising in the positive characteristic version of umbral calculus, generate holonomic modules.

Oxytocin And Vasopressin Modulation Of The Neural Correlates Of Motivation And Emotion: Results From Functional MRI Studies In Awake Rats

PubMed Central

Febo, Marcelo; Ferris, Craig F.

2014-01-01

Oxytocin and vasopressin modulate a range of species typical behavioral functions that include social recognition, maternal-infant attachment, and modulation of memory, offensive aggression, defensive fear reactions, and reward seeking. We have employed novel functional magnetic resonance mapping techniques in awake rats to explore the roles of these neuropeptides in the maternal and non-maternal brain. Results from the functional neuroimaging studies that are summarized here have directly and indirectly confirmed and supported previous findings. Oxytocin is released within the lactating rat brain during suckling stimulation and activates specific subcortical networks in the maternal brain. Both vasopressin and oxytocin modulate brain regions involved unconditioned fear, processing of social stimuli and the expression of agonistic behaviors. Across studies there are relatively consistent brain networks associated with internal motivational drives and emotional states that are modulated by oxytocin and vasopressin. PMID:24486356

Genetics in Parkinson disease: Mendelian versus non-Mendelian inheritance.

PubMed

Hernandez, Dena G; Reed, Xylena; Singleton, Andrew B

2016-10-01

Parkinson's disease is a common, progressive neurodegenerative disorder, affecting 3% of those older than 75 years of age. Clinically, Parkinson's disease (PD) is associated with resting tremor, postural instability, rigidity, bradykinesia, and a good response to levodopa therapy. Over the last 15 years, numerous studies have confirmed that genetic factors contribute to the complex pathogenesis of PD. Highly penetrant mutations producing rare, monogenic forms of the disease have been discovered in singular genes such as SNCA, Parkin, DJ-1, PINK 1, LRRK2, and VPS35. Unique variants with incomplete penetrance in LRRK2 and GBA have been shown to be strong risk factors for PD in certain populations. Additionally, over 20 common variants with small effect sizes are now recognized to modulate the risk for PD. Investigating Mendelian forms of PD has provided precious insight into the pathophysiology that underlies the more common idiopathic form of disease; however, no treatment methodologies have developed. Furthermore, for identified common risk alleles, the functional basis underlying risk principally remains unknown. The challenge over the next decade will be to strengthen the findings delivered through genetic discovery by assessing the direct, biological consequences of risk variants in tandem with additional high-content, integrated datasets. This review discusses monogenic risk factors and mechanisms of Mendelian inheritance of Parkinson disease. Highly penetrant mutations in SNCA, Parkin, DJ-1, PINK 1, LRRK2 and VPS35 produce rare, monogenic forms of the disease, while unique variants within LRRK2 and GBA show incomplete penetrance and are strong risk factors for PD. Additionally, over 20 common variants with small effect sizes modulate disease risk. The challenge over the next decade is to strengthen genetic findings by assessing direct, biological consequences of risk variants in tandem with high-content, integrated datasets. This article is part of a special issue on Parkinson disease. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Lessons from the canine Oxtr gene: populations, variants and functional aspects.

PubMed

Bence, M; Marx, P; Szantai, E; Kubinyi, E; Ronai, Z; Banlaki, Z

2017-04-01

Oxytocin receptor (OXTR) acts as a key behavioral modulator of the central nervous system, affecting social behavior, stress, affiliation and cognitive functions. Variants of the Oxtr gene are known to influence behavior both in animals and humans; however, canine Oxtr polymorphisms are less characterized in terms of possible relevance to function, selection criteria in breeding and domestication. In this report, we provide a detailed characterization of common variants of the canine Oxtr gene. In particular (1) novel polymorphisms were identified by direct sequencing of wolf and dog samples, (2) allelic distributions and pairwise linkage disequilibrium patterns of several canine populations were compared, (3) neighbor joining (NJ) tree based on common single nucleotide polymorphisms (SNPs) was constructed, (4) mRNA expression features were assessed, (5) a novel splice variant was detected and (6) in vitro functional assays were performed. Results indicate marked differences regarding Oxtr variations between purebred dogs of different breeds, free-ranging dog populations, wolf subspecies and golden jackals. This, together with existence of explicitly dog-specific alleles and data obtained from the NJ tree implies that Oxtr could indeed have been a target gene during domestication and selection for human preferred aspects of temperament and social behavior. This assumption is further supported by the present observations on gene expression patterns within the brain and luciferase reporter experiments, providing a molecular level link between certain canine Oxtr polymorphisms and differences in nervous system function and behavior. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Application of electrically invisible antennas to the modulated scatterer technique

NASA Astrophysics Data System (ADS)

Crocker, Dylan Andrew

The Modulated Scatterer Technique (MST) has shown promise for applications in microwave imaging, electric field mapping, and materials characterization. Traditionally, MST scatterers consist of dipole antennas centrally loaded with a lumped element capable of modulation (commonly a PIN diode). By modulating the load element, the signal scattered from the MST scatterer is also modulated. However, due to the small size of such scatterers, it can be difficult to reliably detect the modulated signal. Increasing the modulation depth (a parameter related to how well the scatterer modulates the scattered signal) may improve the detectability of the scattered signal. In an effort to improve the modulation depth of scatterers commonly used in MST, the concept of electrically invisible antennas is applied to the design of these scatterers and is the focus of this work. Electrical invisibility of linear antennas, such as loaded dipoles, can be achieved by loading a scatterer in such a way that, when illuminated by an electromagnetic wave, the integral of the current induced along the length of the scatterer (and hence the scattered field as well) approaches zero. By designing a scatterer to be capable of modulation between visible (scattering) and invisible (minimum scattering) states, the modulation depth may be improved. This thesis presents simulations and measurements of new MST scatterers that have been designed to be electrically invisible during the reverse bias state of the modulated element (i.e., a PIN diode). Further, the scattering during the forward bias state remains the same as that of a traditional MST scatterer, resulting in an increase in modulation depth. This new MST scatterer design technique may also have application in improving the performance of similar sensors such as radio frequency identification (RFID) tags.

Module Six: Parallel Circuits; Basic Electricity and Electronics Individualized Learning System.

ERIC Educational Resources Information Center

Bureau of Naval Personnel, Washington, DC.

In this module the student will learn the rules that govern the characteristics of parallel circuits; the relationships between voltage, current, resistance and power; and the results of common troubles in parallel circuits. The module is divided into four lessons: rules of voltage and current, rules for resistance and power, variational analysis,…

Clinical Outcomes and Patterns of Disease Recurrence After Intensity Modulated Proton Therapy for Oropharyngeal Squamous Carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunn, G. Brandon; Blanchard, Pierre; Department of Radiation Oncology, Institut Gustave Roussy, Villejuif

Purpose: A single-institution prospective study was conducted to assess disease control and toxicity of proton therapy for patients with head and neck cancer. Methods and Materials: Disease control, toxicity, functional outcomes, and patterns of failure for the initial cohort of patients with oropharyngeal squamous carcinoma (OPC) treated with intensity modulated proton therapy (IMPT) were prospectively collected in 2 registry studies at a single institution. Locoregional failures were analyzed by using deformable image registration. Results: Fifty patients with OPC treated from March 3, 2011, to July 2014 formed the cohort. Eighty-four percent were male, 50% had never smoked, 98% had stagemore » III/IV disease, 64% received concurrent therapy, and 35% received induction chemotherapy. Forty-four of 45 tumors (98%) tested for p16 were positive. All patients received IMPT (multifield optimization to n=46; single-field optimization to n=4). No Common Terminology Criteria for Adverse Events grade 4 or 5 toxicities were observed. The most common grade 3 toxicities were acute mucositis in 58% of patients and late dysphagia in 12%. Eleven patients had a gastrostomy (feeding) tube placed during therapy, but none had a feeding tube at last follow-up. At a median follow-up time of 29 months, 5 patients had disease recurrence: local in 1, local and regional in 1, regional in 2, and distant in 1. The 2-year actuarial overall and progression-free survival rates were 94.5% and 88.6%. Conclusions: The oncologic, toxicity, and functional outcomes after IMPT for OPC are encouraging and provide the basis for ongoing and future clinical studies.« less

Application of SNMP on CATV

NASA Astrophysics Data System (ADS)

Huang, Hong-bin; Liu, Wei-ping; Chen, Shun-er; Zheng, Liming

2005-02-01

A new type of CATV network management system developed by universal MCU, which supports SNMP, is proposed in this paper. From the point of view in both hardware and software, the function and method of every modules inside the system, which include communications in the physical layer, protocol process, data process, and etc, are analyzed. In our design, the management system takes IP MAN as data transmission channel and every controlled object in the management structure has a SNMP agent. In the SNMP agent developed, there are four function modules, including physical layer communication module, protocol process module, internal data process module and MIB management module. In the paper, the structure and function of every module are designed and demonstrated while the related hardware circuit, software flow as well as the experimental results are tested. Furthermore, by introducing RTOS into the software programming, the universal MCU procedure can conducts such multi-thread management as fast Ethernet controller driving, TCP/IP process, serial port signal monitoring and so on, which greatly improves efficiency of CPU.

Event related desynchronization-modulated functional electrical stimulation system for stroke rehabilitation: a feasibility study.

PubMed

Takahashi, Mitsuru; Takeda, Kotaro; Otaka, Yohei; Osu, Rieko; Hanakawa, Takashi; Gouko, Manabu; Ito, Koji

2012-08-16

We developed an electroencephalogram-based brain computer interface system to modulate functional electrical stimulation (FES) to the affected tibialis anterior muscle in a stroke patient. The intensity of FES current increased in a stepwise manner when the event-related desynchronization (ERD) reflecting motor intent was continuously detected from the primary cortical motor area. We tested the feasibility of the ERD-modulated FES system in comparison with FES without ERD modulation. The stroke patient who presented with severe hemiparesis attempted to perform dorsiflexion of the paralyzed ankle during which FES was applied either with or without ERD modulation. After 20 minutes of training, the range of movement at the ankle joint and the electromyography amplitude of the affected tibialis anterior muscle were significantly increased following the ERD-modulated FES compared with the FES alone. The proposed rehabilitation technique using ERD-modulated FES for stroke patients was feasible. The system holds potentials to improve the limb function and to benefit stroke patients.

Cell Adhesions: Actin-Based Modules that Mediate Cell-Extracellular Matrix and Cell-Cell Interactions

PubMed Central

Bachir, Alexia; Horwitz, Alan Rick; Nelson, W. James; Bianchini, Julie M.

2018-01-01

Cell adhesions link cells to the extracellular matrix (ECM) and to each other, and depend on interactions with the actin cytoskeleton. Both cell-ECM and cell-cell adhesion sites contain discrete, yet overlapping functional modules. These modules establish physical association with the actin cytoskeleton, locally modulate actin organization and dynamics, and trigger intracellular signaling pathways. Interplay between these modules generates distinct actin architectures that underlie different stages, types, and functions of cell-ECM and cell-cell adhesions. Actomyosin contractility is required to generate mature, stable adhesions, as well as sense and translate the mechanical properties of the cellular environment to changes in cell organization and behavior. In this chapter we discuss the organization and function of different adhesion modules and how they interact with the actin cytoskeleton. We highlight the molecular mechanisms of mechanotransduction in adhesions, and how adhesion molecules mediate crosstalk between cell-ECM and cell-cell adhesion sites. PMID:28679638

Multi-functional Electric Module for a Vehicle

NASA Technical Reports Server (NTRS)

Waligora, Thomas M. (Inventor); Fraser-Chanpong, Nathan (Inventor); Figuered, Joshua M. (Inventor); Reed, Ryan (Inventor); Akinyode, Akinjide Akinniyi (Inventor); Spain, Ivan (Inventor); Dawson, Andrew D. (Inventor); Herrera, Eduardo (Inventor); Markee, Mason M. (Inventor); Bluethmann, William J. (Inventor)

2015-01-01

A multi-functional electric module (eModule) is provided for a vehicle having a chassis, a master controller, and a drive wheel having a propulsion-braking module. The eModule includes a steering control assembly, mounting bracket, propulsion control assembly, brake controller, housing, and control arm. The steering control assembly includes a steering motor controlled by steering controllers in response to control signals from the master controller. A mounting feature of the bracket connects to the chassis. The propulsion control assembly and brake controller are in communication with the propulsion-braking module. The control arm connects to the lower portion and contains elements of a suspension system, with the control arm being connectable to the drive wheel via a wheel input/output block. The controllers are responsive to the master controller to control a respective steering, propulsion, and braking function. The steering motor may have a dual-wound stator with windings controlled via the respective steering controllers.

Engineered TAL Effector modulators for the large-scale gain-of-function screening

PubMed Central

Zhang, Hanshuo; Li, Juan; Hou, Sha; Wang, Gancheng; Jiang, Mingjun; Sun, Changhong; Hu, Xiongbing; Zhuang, Fengfeng; Dai, Zhifei; Dai, Junbiao; Xi, Jianzhong Jeff

2014-01-01

Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE–DNA interactions. Here we synthesized more than 200 TALE modulators and identified two determining factors of transcription activity in vivo: chromatin accessibility and the distance from the transcription start site. The implementation of these modulators in a gain-of-function screen was successfully demonstrated for four cell lines in migration/invasion assays and thus has broad relevance in this field. Furthermore, a novel TALE–TALE modulator was developed to transcriptionally inhibit target genes. Together, these findings underscore the huge potential of these TALE modulators in the study of gene function, reprogramming of cellular behaviors, and even clinical investigation. PMID:24939900

Phase Modulator with Terahertz Optical Bandwidth Formed by Multi-Layered Dielectric Stack

NASA Technical Reports Server (NTRS)

Keys, Andrew S. (Inventor); Fork, Richard L. (Inventor)

2005-01-01

An optical phase modulator includes a bandpass multilayer stack, formed by a plurality of dielectric layers, preferably of GaAs and AlAs, and having a transmission function related to the refractive index of the layers of the stack, for receiving an optical input signal to be phase modulated. A phase modulator device produces a nonmechanical change in the refractive index of each layer of the stack by, e.g., the injection of free carrier, to provide shifting of the transmission function so as to produce phase modulation of the optical input signal and to thereby produce a phase modulated output signal.

Methylphenidate has nonlinear dose effects on cued response inhibition in adults but not adolescents

PubMed Central

Simon, Nicholas W.; Moghaddam, Bita

2016-01-01

Ongoing development of the dopamine system during adolescence may provide a partial mechanism for behavioral and psychiatric vulnerabilities. Despite early evidence for a hyperactive adolescent dopaminergic system, recent data suggest that adolescent dopamine may be functionally hypoactive compared to in adults. While this distinction has been established in response to dopaminergic drugs and natural rewards, little is known about age-related differences in cognitive efficacy of dopaminergic drugs. Using a recently established Cued Response Inhibition Task, we tested the effects of acute systemic methylphenidate, commonly known as Ritalin, on response inhibition and response initiation in adolescent and adults rats. First, we replicated previous data that adolescents are able to inhibit a response to a cue on par with adults, but are slower to produce a rewarded response after a stop cue. Next, we observed that methylphenidate modulated response inhibition in adult rats, with low dose (0.3 mg/kg) improving inhibition, and high dose (3 mg/kg) impairing performance. This dose-response pattern is commonly observed with psychostimulant cognitive modulation. In adolescents, however, methylphenidate had no effect on response inhibition at any dose. Latency of response initiation after the stop cue was not affected by methylphenidate in either adult or adolescent rats. These data establish that dose-response of a commonly prescribed psychostimulant medication is different in adolescents and adults. They further demonstrate that healthy adolescent response inhibition is not as sensitive to psychostimulants as in adults, supporting the idea that the dopamine system is hypoactive in adolescence. PMID:27431940

Study participant reported outcomes of mental health interventions: results from a randomized controlled trial among survivors of systematic violence in southern Iraq.

PubMed

Mahmooth, Z; Weiss, W M; Zangana, G A S; Bolton, P

2018-01-01

Common mental health problems experienced by survivors of systematic violence include trauma, depression, and anxiety. A trial of mental health interventions by community mental health workers for survivors of systematic violence in southern Iraq showed benefits from two psychotherapies on trauma, depression, anxiety, and function: Common Elements Treatment Approach (CETA) and cognitive processing therapy (CPT). This study assessed whether other non-predetermined changes reported by intervention participants were more common than in the control group. The trial involved 342 participants (CETA: 99 intervention, 50 control; CPT: 129 intervention, 64 control). Sixteen intervention-related changes since enrollment were identified from free-listing interviews of 15 early therapy completers. The changes were then added as a new quantitative module to the follow-up questionnaire. The changes were organized into eight groupings by thematic analysis - family, social standing, anger management, interest in regular activities, optimism, feeling close to God, avoiding smoking and drugs, and physical health. All participants were interviewed with this module and responses were compared between intervention and control participants. Multi-level, multi-variate regression models showed CETA intervention subjects with significant, positive changes relative to CETA controls on most themes. CPT intervention subjects showed little to no change compared with CPT controls in most themes. Participants receiving CETA reported more positive changes from therapy compared with controls than did participants receiving CPT. This study suggests differential effects of psychotherapy beyond the predetermined clinical outcome measures and that identification of these effects should be part of intervention evaluations.

Action and Perception Are Temporally Coupled by a Common Mechanism That Leads to a Timing Misperception

PubMed Central

Astefanoaei, Corina; Daye, Pierre M.; FitzGibbon, Edmond J.; Creanga, Dorina-Emilia; Rufa, Alessandra; Optican, Lance M.

2015-01-01

We move our eyes to explore the world, but visual areas determining where to look next (action) are different from those determining what we are seeing (perception). Whether, or how, action and perception are temporally coordinated is not known. The preparation time course of an action (e.g., a saccade) has been widely studied with the gap/overlap paradigm with temporal asynchronies (TA) between peripheral target onset and fixation point offset (gap, synchronous, or overlap). However, whether the subjects perceive the gap or overlap, and when they perceive it, has not been studied. We adapted the gap/overlap paradigm to study the temporal coupling of action and perception. Human subjects made saccades to targets with different TAs with respect to fixation point offset and reported whether they perceived the stimuli as separated by a gap or overlapped in time. Both saccadic and perceptual report reaction times changed in the same way as a function of TA. The TA dependencies of the time change for action and perception were very similar, suggesting a common neural substrate. Unexpectedly, in the perceptual task, subjects misperceived lights overlapping by less than ∼100 ms as separated in time (overlap seen as gap). We present an attention-perception model with a map of prominence in the superior colliculus that modulates the stimulus signal's effectiveness in the action and perception pathways. This common source of modulation determines how competition between stimuli is resolved, causes the TA dependence of action and perception to be the same, and causes the misperception. PMID:25632126

Nuclear Technology. Course 30: Mechanical Inspection. Module 30-2, Pump Functional Testing.

ERIC Educational Resources Information Center

Wasel, Ed; Espy, John

This second in a series of eight modules for a course titled Mechanical Inspection describes typical pump functional tests which are performed after pump installation and prior to release of the plant for unrestricted power operation. The module follows a typical format that includes the following sections: (1) introduction, (2) module…

Development and Evaluation of the SUMIT Microcomputer Module Entitled 'Predator Functional Response'.

ERIC Educational Resources Information Center

Shaltz, Mark B.

An experiment was conducted that compared the teaching effectiveness of a computer assisted instructional module and a lecture-discussion. The module, Predator Functional Response (PFR), was developed as part of the SUMIT (Single-concept User-adaptable Microcomputer-based Instructional Technique) project. A class of 30 students was randomly…

Redefining the modular organization of the core Mediator complex.

PubMed

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-07-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.

Redefining the modular organization of the core Mediator complex

PubMed Central

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-01-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation. PMID:24810298

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level.

PubMed

Goswami, Sathi; Sanyal, Sulagna; Chakraborty, Payal; Das, Chandrima; Sarkar, Munna

2017-08-01

NSAIDs are the most common class of painkillers and anti-inflammatory agents. They also show other functions like chemoprevention and chemosuppression for which they act at the protein but not at the genome level since they are mostly anions at physiological pH, which prohibit their approach to the poly-anionic DNA. Complexing the drugs with bioactive metal obliterate their negative charge and allow them to bind to the DNA, thereby, opening the possibility of genome level interaction. To test this hypothesis, we present the interaction of a traditional NSAID, Piroxicam and its copper complex with core histone and chromatin. Spectroscopy, DLS, and SEM studies were applied to see the effect of the interaction on the structure of histone/chromatin. This was coupled with MTT assay, immunoblot analysis, confocal microscopy, micro array analysis and qRT-PCR. The interaction of Piroxicam and its copper complex with histone/chromatin results in structural alterations. Such structural alterations can have different biological manifestations, but to test our hypothesis, we have focused only on the accompanied modulations at the epigenomic/genomic level. The complex, showed alteration of key epigenetic signatures implicated in transcription in the global context, although Piroxicam caused no significant changes. We have correlated such alterations caused by the complex with the changes in global gene expression and validated the candidate gene expression alterations. Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-Term Predictive and Feedback Encoding of Motor Signals in the Simple Spike Discharge of Purkinje Cells

PubMed Central

Popa, Laurentiu S.; Streng, Martha L.

2017-01-01

Abstract Most hypotheses of cerebellar function emphasize a role in real-time control of movements. However, the cerebellum’s use of current information to adjust future movements and its involvement in sequencing, working memory, and attention argues for predicting and maintaining information over extended time windows. The present study examines the time course of Purkinje cell discharge modulation in the monkey (Macaca mulatta) during manual, pseudo-random tracking. Analysis of the simple spike firing from 183 Purkinje cells during tracking reveals modulation up to 2 s before and after kinematics and position error. Modulation significance was assessed against trial shuffled firing, which decoupled simple spike activity from behavior and abolished long-range encoding while preserving data statistics. Position, velocity, and position errors have the most frequent and strongest long-range feedforward and feedback modulations, with less common, weaker long-term correlations for speed and radial error. Position, velocity, and position errors can be decoded from the population simple spike firing with considerable accuracy for even the longest predictive (-2000 to -1500 ms) and feedback (1500 to 2000 ms) epochs. Separate analysis of the simple spike firing in the initial hold period preceding tracking shows similar long-range feedforward encoding of the upcoming movement and in the final hold period feedback encoding of the just completed movement, respectively. Complex spike analysis reveals little long-term modulation with behavior. We conclude that Purkinje cell simple spike discharge includes short- and long-range representations of both upcoming and preceding behavior that could underlie cerebellar involvement in error correction, working memory, and sequencing. PMID:28413823

Inspection system calibration methods

DOEpatents

Deason, Vance A.; Telschow, Kenneth L.

2004-12-28

An inspection system calibration method includes producing two sideband signals of a first wavefront; interfering the two sideband signals in a photorefractive material, producing an output signal therefrom having a frequency and a magnitude; and producing a phase modulated operational signal having a frequency different from the output signal frequency, a magnitude, and a phase modulation amplitude. The method includes determining a ratio of the operational signal magnitude to the output signal magnitude, determining a ratio of a 1st order Bessel function of the operational signal phase modulation amplitude to a 0th order Bessel function of the operational signal phase modulation amplitude, and comparing the magnitude ratio to the Bessel function ratio.

Experience Drives Synchronization: The phase and Amplitude Dynamics of Neural Oscillations to Musical Chords Are Differentially Modulated by Musical Expertise

PubMed Central

Pallesen, Karen Johanne; Bailey, Christopher J.; Brattico, Elvira; Gjedde, Albert; Palva, J. Matias; Palva, Satu

2015-01-01

Musical expertise is associated with structural and functional changes in the brain that underlie facilitated auditory perception. We investigated whether the phase locking (PL) and amplitude modulations (AM) of neuronal oscillations in response to musical chords are correlated with musical expertise and whether they reflect the prototypicality of chords in Western tonal music. To this aim, we recorded magnetoencephalography (MEG) while musicians and non-musicians were presented with common prototypical major and minor chords, and with uncommon, non-prototypical dissonant and mistuned chords, while watching a silenced movie. We then analyzed the PL and AM of ongoing oscillations in the theta (4–8 Hz) alpha (8–14 Hz), beta- (14–30 Hz) and gamma- (30–80 Hz) bands to these chords. We found that musical expertise was associated with strengthened PL of ongoing oscillations to chords over a wide frequency range during the first 300 ms from stimulus onset, as opposed to increased alpha-band AM to chords over temporal MEG channels. In musicians, the gamma-band PL was strongest to non-prototypical compared to other chords, while in non-musicians PL was strongest to minor chords. In both musicians and non-musicians the long-latency (> 200 ms) gamma-band PL was also sensitive to chord identity, and particularly to the amplitude modulations (beats) of the dissonant chord. These findings suggest that musical expertise modulates oscillation PL to musical chords and that the strength of these modulations is dependent on chord prototypicality. PMID:26291324

Modulation of endothelial nitric oxide by plant-derived products.

PubMed

Schmitt, Christoph A; Dirsch, Verena M

2009-09-01

Nitric oxide (NO), produced by endothelial nitric oxide synthase (eNOS), is recognised as a central anti-inflammatory and anti-atherogenic principle in the vasculature. Decreased availability of NO in the vasculature promotes the progression of cardiovascular diseases. Epidemiological and clinical studies have demonstrated that a growing list of natural products, as components of the daily diet or phytomedical preparations, may improve vascular function by enhancing NO bioavailability. In this article we first outline common pathways modulating endothelial NO production or bioavailability to provide a basis for subsequent mechanistic discussions. Then we comprehensively review natural products and plant extracts known to positively influence eNOS activity and/or endothelial function in vitro or in vivo. We will discuss red wine, highlighting polyphenols, oligomeric procyanidins (OPC) and resveratrol as modulators of endothelial NO production. Other dietary products and their active components known to activate eNOS include cocoa (OPC and its monomer (-)-epicatechin), pomegranates (polyphenols), black and green tea (flavanoids, especially epigallocatechin gallate), olive oil (oleic acid and polyphenols), soy (genistein), and quercetin, one of the most abundant flavonoids in plants. In addition, phytomedical preparations made from ginkgo, hawthorn and ginseng, as well as formulations used in traditional Chinese Medicine, have been shown to affect endothelial NO production. Recurring phytochemical patterns among active fractions and purified compounds are discussed. In summary, there is increasing evidence that several single natural products and plant extracts influence endothelial NO production. Identification of such compounds and characterisation of their cellular actions may increase our knowledge of the regulation of endothelial NO production and could provide valuable clues for the prevention or treatment of cardiovascular diseases.

Ammonia impairs glutamatergic communication in astroglial cells: protective role of resveratrol.

PubMed

Bobermin, Larissa Daniele; Hansel, Gisele; Scherer, Emilene B S; Wyse, Angela T S; Souza, Diogo Onofre; Quincozes-Santos, André; Gonçalves, Carlos-Alberto

2015-12-01

Ammonia is a key toxin in the precipitation of hepatic encephalopathy (HE), a neuropsychiatric disorder associated with liver failure. In response to ammonia, various toxic events are triggered in astroglial cells, and alterations in brain glutamate communication are common. Resveratrol is a polyphenolic compound that has been extensively studied in pathological events because it presents several beneficial effects, including some in the central nervous system (CNS). We previously described that resveratrol is able to significantly modulate glial functioning and has a protective effect during ammonia challenge in vitro. In this study, we addressed the mechanisms by which resveratrol can protect C6 astroglial cells from glutamatergic alterations induced by ammonia. Resveratrol was able to prevent all the effects triggered by ammonia: (i) decrease in glutamate uptake activity and expression of the EAAC1 glutamate transporter, the main glutamate transporter present in C6 cells; (ii) increase of glutamate release, which was also dependent on the activation of the Na(+)-K(+)-Cl(-) co-transporter NKCC1; (iii) reduction in GS activity and intracellular GSH content; and (iv) impairment of Na(+)K(+)-ATPase activity. Interestingly, resveratrol, per se, also positively modulated the astroglial functions evaluated. Moreover, we demonstrated that heme oxygenase 1 (HO1), an enzyme that is part of the cellular defense system, mediated some of the effects of resveratrol. In conclusion, the mechanisms of the putative protective role of resveratrol against ammonia toxicity involve the modulation of pathways and molecules related to glutamate communication in astroglial cells. Copyright © 2015 Elsevier B.V. All rights reserved.

Prebiotics: A Potential Treatment Strategy for the Chemotherapy-damaged Gut?

PubMed

Wang, Hanru; Geier, Mark S; Howarth, Gordon S

2016-01-01

Mucositis, characterized by ulcerative lesions along the alimentary tract, is a common consequence of many chemotherapy regimens. Chemotherapy negatively disrupts the intestinal microbiota, resulting in increased numbers of potentially pathogenic bacteria, such as Clostridia and Enterobacteriaceae, and decreased numbers of "beneficial" bacteria, such as Lactobacilli and Bifidobacteria. Agents capable of restoring homeostasis in the bowel microbiota could, therefore, be applicable to mucositis. Prebiotics are indigestible compounds, commonly oligosaccharides, that seek to reverse chemotherapy-induced intestinal dysbiosis through selective colonization of the intestinal microbiota by probiotic bacteria. In addition, evidence is emerging that certain prebiotics contribute to nutrient digestibility and absorption, modulate intestinal barrier function through effects on mucin expression, and also modify mucosal immune responses, possibly via inflammasome-mediated processes. This review examines the known mechanisms of prebiotic action, and explores their potential for reducing the severity of chemotherapy-induced mucositis in the intestine.

Developmental Commonalities between Object and Face Recognition in Adolescence

PubMed Central

Jüttner, Martin; Wakui, Elley; Petters, Dean; Davidoff, Jules

2016-01-01

In the visual perception literature, the recognition of faces has often been contrasted with that of non-face objects, in terms of differences with regard to the role of parts, part relations and holistic processing. However, recent evidence from developmental studies has begun to blur this sharp distinction. We review evidence for a protracted development of object recognition that is reminiscent of the well-documented slow maturation observed for faces. The prolonged development manifests itself in a retarded processing of metric part relations as opposed to that of individual parts and offers surprising parallels to developmental accounts of face recognition, even though the interpretation of the data is less clear with regard to holistic processing. We conclude that such results might indicate functional commonalities between the mechanisms underlying the recognition of faces and non-face objects, which are modulated by different task requirements in the two stimulus domains. PMID:27014176

In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions

NASA Astrophysics Data System (ADS)

Mwaffo, Violet; Butail, Sachit; Porfiri, Maurizio

2017-01-01

Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering.

ePix: a class of architectures for second generation LCLS cameras

DOE PAGES

Dragone, A.; Caragiulo, P.; Markovic, B.; ...

2014-03-31

ePix is a novel class of ASIC architectures, based on a common platform, optimized to build modular scalable detectors for LCLS. The platform architecture is composed of a random access analog matrix of pixel with global shutter, fast parallel column readout, and dedicated sigma-delta analog-to-digital converters per column. It also implements a dedicated control interface and all the required support electronics to perform configuration, calibration and readout of the matrix. Based on this platform a class of front-end ASICs and several camera modules, meeting different requirements, can be developed by designing specific pixel architectures. This approach reduces development time andmore » expands the possibility of integration of detector modules with different size, shape or functionality in the same camera. The ePix platform is currently under development together with the first two integrating pixel architectures: ePix100 dedicated to ultra low noise applications and ePix10k for high dynamic range applications.« less

Conserved pharmacological rescue of hereditary spastic paraplegia-related phenotypes across model organisms

PubMed Central

Julien, Carl; Lissouba, Alexandra; Madabattula, Surya; Fardghassemi, Yasmin; Rosenfelt, Cory; Androschuk, Alaura; Strautman, Joel; Wong, Clement; Bysice, Andrew; O'sullivan, Julia; Rouleau, Guy A.; Drapeau, Pierre; Parker, J. Alex; Bolduc, François V.

2016-01-01

Hereditary spastic paraplegias (HSPs) are a group of neurodegenerative diseases causing progressive gait dysfunction. Over 50 genes have now been associated with HSP. Despite the recent explosion in genetic knowledge, HSP remains without pharmacological treatment. Loss-of-function mutation of the SPAST gene, also known as SPG4, is the most common cause of HSP in patients. SPAST is conserved across animal species and regulates microtubule dynamics. Recent studies have shown that it also modulates endoplasmic reticulum (ER) stress. Here, utilizing null SPAST homologues in C. elegans, Drosophila and zebrafish, we tested FDA-approved compounds known to modulate ER stress in order to ameliorate locomotor phenotypes associated with HSP. We found that locomotor defects found in all of our spastin models could be partially rescued by phenazine, methylene blue, N-acetyl-cysteine, guanabenz and salubrinal. In addition, we show that established biomarkers of ER stress levels correlated with improved locomotor activity upon treatment across model organisms. Our results provide insights into biomarkers and novel therapeutic avenues for HSP. PMID:26744324

STERILE APETALA modulates the stability of a repressor protein complex to control organ size in Arabidopsis thaliana

PubMed Central

Wang, Zhibiao; Ru, Licong; Baekelandt, Alexandra; Goossens, Alain; Xu, Ran; Zhu, Zhengge; Inzé, Dirk; Li, Yunhai

2018-01-01

Organ size control is of particular importance for developmental biology and agriculture, but the mechanisms underlying organ size regulation remain elusive in plants. Meristemoids, which possess stem cell-like properties, have been recognized to play important roles in leaf growth. We have recently reported that the Arabidopsis F-box protein STERILE APETALA (SAP)/SUPPRESSOR OF DA1 (SOD3) promotes meristemoid proliferation and regulates organ size by influencing the stability of the transcriptional regulators PEAPODs (PPDs). Here we demonstrate that KIX8 and KIX9, which function as adaptors for the corepressor TOPLESS and PPD, are novel substrates of SAP. SAP interacts with KIX8/9 and modulates their protein stability. Further results show that SAP acts in a common pathway with KIX8/9 and PPD to control organ growth by regulating meristemoid cell proliferation. Thus, these findings reveal a molecular mechanism by which SAP targets the KIX-PPD repressor complex for degradation to regulate meristemoid cell proliferation and organ size. PMID:29401459

In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions

PubMed Central

Mwaffo, Violet; Butail, Sachit; Porfiri, Maurizio

2017-01-01

Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering. PMID:28071731

Scale invariance in chaotic time series: Classical and quantum examples

NASA Astrophysics Data System (ADS)

Landa, Emmanuel; Morales, Irving O.; Stránský, Pavel; Fossion, Rubén; Velázquez, Victor; López Vieyra, J. C.; Frank, Alejandro

Important aspects of chaotic behavior appear in systems of low dimension, as illustrated by the Map Module 1. It is indeed a remarkable fact that all systems tha make a transition from order to disorder display common properties, irrespective of their exacta functional form. We discuss evidence for 1/f power spectra in the chaotic time series associated in classical and quantum examples, the one-dimensional map module 1 and the spectrum of 48Ca. A Detrended Fluctuation Analysis (DFA) method is applied to investigate the scaling properties of the energy fluctuations in the spectrum of 48Ca obtained with a large realistic shell model calculation (ANTOINE code) and with a random shell model (TBRE) calculation also in the time series obtained with the map mod 1. We compare the scale invariant properties of the 48Ca nuclear spectrum sith similar analyses applied to the RMT ensambles GOE and GDE. A comparison with the corresponding power spectra is made in both cases. The possible consequences of the results are discussed.

Deep supervised dictionary learning for no-reference image quality assessment

NASA Astrophysics Data System (ADS)

Huang, Yuge; Liu, Xuesong; Tian, Xiang; Zhou, Fan; Chen, Yaowu; Jiang, Rongxin

2018-03-01

We propose a deep convolutional neural network (CNN) for general no-reference image quality assessment (NR-IQA), i.e., accurate prediction of image quality without a reference image. The proposed model consists of three components such as a local feature extractor that is a fully CNN, an encoding module with an inherent dictionary that aggregates local features to output a fixed-length global quality-aware image representation, and a regression module that maps the representation to an image quality score. Our model can be trained in an end-to-end manner, and all of the parameters, including the weights of the convolutional layers, the dictionary, and the regression weights, are simultaneously learned from the loss function. In addition, the model can predict quality scores for input images of arbitrary sizes in a single step. We tested our method on commonly used image quality databases and showed that its performance is comparable with that of state-of-the-art general-purpose NR-IQA algorithms.

Temporal modulation transfer functions for listeners with real and simulated hearing loss

PubMed Central

Desloge, Joseph G.; Reed, Charlotte M.; Braida, Louis D.; Perez, Zachary D.; Delhorne, Lorraine A.

2011-01-01

A functional simulation of hearing loss was evaluated in its ability to reproduce the temporal modulation transfer functions (TMTFs) for nine listeners with mild to profound sensorineural hearing loss. Each hearing loss was simulated in a group of three age-matched normal-hearing listeners through spectrally shaped masking noise or a combination of masking noise and multiband expansion. TMTFs were measured for both groups of listeners using a broadband noise carrier as a function of modulation rate in the range 2 to 1024 Hz. The TMTFs were fit with a lowpass filter function that provided estimates of overall modulation-depth sensitivity and modulation cutoff frequency. Although the simulations were capable of accurately reproducing the threshold elevations of the hearing-impaired listeners, they were not successful in reproducing the TMTFs. On average, the simulations resulted in lower sensitivity and higher cutoff frequency than were observed in the TMTFs of the hearing-impaired listeners. Discrepancies in performance between listeners with real and simulated hearing loss are possibly related to inaccuracies in the simulation of recruitment. PMID:21682411

Development of diabetes does not alter behavioral and molecular circadian rhythms in a transgenic rat model of type 2 diabetes mellitus.

PubMed

Qian, Jingyi; Thomas, Anthony P; Schroeder, Analyne M; Rakshit, Kuntol; Colwell, Christopher S; Matveyenko, Aleksey V

2017-08-01

Metabolic state and circadian clock function exhibit a complex bidirectional relationship. Circadian disruption increases propensity for metabolic dysfunction, whereas common metabolic disorders such as obesity and type 2 diabetes (T2DM) are associated with impaired circadian rhythms. Specifically, alterations in glucose availability and glucose metabolism have been shown to modulate clock gene expression and function in vitro; however, to date, it is unknown whether development of diabetes imparts deleterious effects on the suprachiasmatic nucleus (SCN) circadian clock and SCN-driven outputs in vivo. To address this question, we undertook studies in aged diabetic rats transgenic for human islet amyloid polypeptide, an established nonobese model of T2DM (HIP rat), which develops metabolic defects closely recapitulating those present in patients with T2DM. HIP rats were also cross-bred with a clock gene reporter rat model (Per1:luciferase transgenic rat) to permit assessment of the SCN and the peripheral molecular clock function ex vivo. Utilizing these animal models, we examined effects of diabetes on 1 ) behavioral circadian rhythms, 2 ) photic entrainment of circadian activity, 3 ) SCN and peripheral tissue molecular clock function, and 4 ) melatonin secretion. We report that circadian activity, light-induced entrainment, molecular clockwork, as well as melatonin secretion are preserved in the HIP rat model of T2DM. These results suggest that despite the well-characterized ability of glucose to modulate circadian clock gene expression acutely in vitro, SCN clock function and key behavioral and physiological outputs appear to be preserved under chronic diabetic conditions characteristic of nonobese T2DM. Copyright © 2017 the American Physiological Society.

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Descriptive vs. mechanistic network models in plant development in the post-genomic era.

PubMed

Davila-Velderrain, J; Martinez-Garcia, J C; Alvarez-Buylla, E R

2015-01-01

Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals.

Neural mechanisms of oxytocin receptor gene mediating anxiety-related temperament.

PubMed

Wang, Junping; Qin, Wen; Liu, Bing; Zhou, Yuan; Wang, Dawei; Zhang, Yunting; Jiang, Tianzi; Yu, Chunshui

2014-09-01

A common variant (rs53576) of the OXTR gene has been implicated in a number of socio-emotional phenotypes, such as anxiety-related behavior. Previous studies have demonstrated that A-allele carriers have higher levels of physiological and dispositional stress reactivity and depressive symptomatology compared to those with the GG genotype, but the mediating neural mechanisms remain poorly understood. We combined voxel-based morphometry and resting-state functional connectivity analyses in a large cohort of healthy young Chinese Han individuals to test the hypothesis that the OXTR gene polymorphism influences an anxiety-related temperamental trait, as assessed by the harm avoidance subscale from the Tridimensional Personality Questionnaire via modulating the gray matter volume and resting-state functional connectivity of the brain, especially the limbic system. We revealed that female subjects with the AA genotype showed increased harm avoidance scores relative to G-carrier females. We also found that, compared to female individuals with the GG/GA genotype, female individuals with the AA genotype exhibited significantly smaller amygdala volumes bilaterally (especially the centromedial subregion), with a trend of allele-load-dependence. Compared to female individuals with the GG/GA genotype, female subjects with the AA genotype demonstrated reduced resting-state functional coupling between the prefrontal cortex and amygdala bilaterally, also with an allele-load-dependent trend. Furthermore, the magnitude of prefrontal-amygdala coupling in the left hemisphere was positively correlated with harm avoidance scores in female subjects. Our findings highlight a possible neural pathway by which a naturally occurring variation of the OXTR gene may affect an anxiety-related temperamental trait in female subjects by modulating prefrontal-amygdala functional connectivity.

A human functional protein interaction network and its application to cancer data analysis

PubMed Central

2010-01-01

Background One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. Results We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. Conclusions We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases. PMID:20482850

Triggerable electro-optic amplitude modulator bias stabilizer for integrated optical devices

DOEpatents

Conder, A.D.; Haigh, R.E.; Hugenberg, K.F.

1995-09-26

An improved Mach-Zehnder integrated optical electro-optic modulator is achieved by application and incorporation of a DC bias box containing a laser synchronized trigger circuit, a DC ramp and hold circuit, a modulator transfer function negative peak detector circuit, and an adjustable delay circuit. The DC bias box ramps the DC bias along the transfer function curve to any desired phase or point of operation at which point the RF modulation takes place. 7 figs.

Triggerable electro-optic amplitude modulator bias stabilizer for integrated optical devices

DOEpatents

Conder, Alan D.; Haigh, Ronald E.; Hugenberg, Keith F.

1995-01-01

An improved Mach-Zehnder integrated optical electro-optic modulator is achieved by application and incorporation of a DC bias box containing a laser synchronized trigger circuit, a DC ramp and hold circuit, a modulator transfer function negative peak detector circuit, and an adjustable delay circuit. The DC bias box ramps the DC bias along the transfer function curve to any desired phase or point of operation at which point the RF modulation takes place.

Module theoretic zero structures for system matrices

NASA Technical Reports Server (NTRS)

Wyman, Bostwick F.; Sain, Michael K.

1987-01-01

The coordinate-free module-theoretic treatment of transmission zeros for MIMO transfer functions developed by Wyman and Sain (1981) is generalized to include noncontrollable and nonobservable linear dynamical systems. Rational, finitely-generated-modular, and torsion-divisible interpretations of the Rosenbrock system matrix are presented; Gamma-zero and Omega-zero modules are defined and shown to contain the output-decoupling and input-decoupling zero modules, respectively, as submodules; and the cases of left and right invertible transfer functions are considered.

Standardising Assessment to Meet Student Needs in Foreign Language Modules in a University Context: Is Standardisation Possible?

ERIC Educational Resources Information Center

Nunan, Anna

2014-01-01

The Applied Language Centre at University College Dublin offers foreign language modules to students in ten languages at CEFR [Common European Framework of Reference for Languages] levels ranging from A1 to B2. Efforts have been underway in the Centre to standardise the assessment components across languages to ensure parity between module credits…

An Evaluation of Training Modules for Part-Time Workers in Community Education. SCRE Project Report No. 19.

ERIC Educational Resources Information Center

Castelino, Celine; Munn, Pamela

This project evaluated three modules, which were developed to meet key basic training requirements common to part-time workers in different branches of community education (adult education, community development, and youth work). Draft modules were sent to about 40 individuals or organizations in the field for comment on their structure and…

The Math You Need at Baylor University: Improving Quantitative Skills in an Introductory Geology Lab Course

NASA Astrophysics Data System (ADS)

Browning, S.

2014-12-01

The Math You Need (TMYN) modules were introduced at Baylor University in fall 2012 to address issues of math anxiety common among freshmen non-majors completing their lab science requirement, and to reduce lab time spent reviewing basic math concepts. Modules and associated assessment questions commonly use geoscience examples to illustrate the mathematical principles involved, reinforcing topics addressed in lab. Large enrollments in the course selected for these modules necessitate multiple graduate teaching assistants in the lab, making the online nature of the modules and minimal required involvement of the teaching assistants even more valuable. Students completed three selected modules before encountering associated topics in lab, as well as a pre and post-test to gauge improvement. This presentation will review lessons learned and changes made in the first two years of TMYN at Baylor. Results indicate continued increases in mean pre to post test scores (e.g. 3.2% in fall 2012 to 11.9% in spring 2014), percentage of student pre to post- test improvement (59% in fall 2012 to 72% in spring 2014) and student participation (95 in fall 2012 to 186 in spring 2014). Continued use of these modules is anticipated.

A 120kV IGBT modulator for driving a pierce electron gun

DOE Office of Scientific and Technical Information (OSTI.GOV)

Earley, L. M.; Brown, R. W.; Carlson, R. L.

2004-01-01

An IGBT modulator has been developed to drive a 120 kV, 23 A Pierce electron gun. The modulator is capable of producing pulses up to 10 {mu}s in width at repetition rates up to 10Hz with no active reset. The pulse rise time on the electron gun will be approximately 2 {mu}s and the remaining 8 {mu}s of flattop is tuned to have a ripple of less than 1 percent rms. The modulator technology was developed from a previous 50 kV prototype. The modulator consists of six boards, each with one EUPEC IGBT that drives a single common step-up transformermore » wound on METGLAS 2605SC cores. The six transformer cores share a common bi-filar output secondary winding. The modulator uses a fiber optic trigger system and has a high voltage cable output with an epoxy receptacle on the oil end and a ceramic receptacle on the vacuum end. The 120 kV electron gun was manufactured by MDS Co. and will be used to generate sheet electron beams from the standard pencil beam produced by the Pierce electron gun.« less

A distributed control approach for power and energy management in a notional shipboard power system

NASA Astrophysics Data System (ADS)

Shen, Qunying

The main goal of this thesis is to present a power control module (PCON) based approach for power and energy management and to examine its control capability in shipboard power system (SPS). The proposed control scheme is implemented in a notional medium voltage direct current (MVDC) integrated power system (IPS) for electric ship. To realize the control functions such as ship mode selection, generator launch schedule, blackout monitoring, and fault ride-through, a PCON based distributed power and energy management system (PEMS) is developed. The control scheme is proposed as two-layer hierarchical architecture with system level on the top as the supervisory control and zonal level on the bottom as the decentralized control, which is based on the zonal distribution characteristic of the notional MVDC IPS that was proposed as one of the approaches for Next Generation Integrated Power System (NGIPS) by Norbert Doerry. Several types of modules with different functionalities are used to derive the control scheme in detail for the notional MVDC IPS. Those modules include the power generation module (PGM) that controls the function of generators, the power conversion module (PCM) that controls the functions of DC/DC or DC/AC converters, etc. Among them, the power control module (PCON) plays a critical role in the PEMS. It is the core of the control process. PCONs in the PEMS interact with all the other modules, such as power propulsion module (PPM), energy storage module (ESM), load shedding module (LSHED), and human machine interface (HMI) to realize the control algorithm in PEMS. The proposed control scheme is implemented in real time using the real time digital simulator (RTDS) to verify its validity. To achieve this, a system level energy storage module (SESM) and a zonal level energy storage module (ZESM) are developed in RTDS to cooperate with PCONs to realize the control functionalities. In addition, a load shedding module which takes into account the reliability of power supply (in terms of quality of service) is developed. This module can supply uninterruptible power to the mission critical loads. In addition, a multi-agent system (MAS) based framework is proposed to implement the PCON based PEMS through a hardware setup that is composed of MAMBA boards and FPGA interface. Agents are implemented using Java Agent DEvelopment Framework (JADE). Various test scenarios were tested to validate the approach.

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia

2014-08-28

The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigatedmore » preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results.« less

Optical pulse synthesis using brillouin selective sideband amplification

NASA Technical Reports Server (NTRS)

Yao, X. Steve (Inventor)

2002-01-01

Techniques for producing optical pulses based on Brillouin selective sideband amplification by using a common modulation control signal to modulate both a signal beam to produce multiple sideband signals and a single pump beam to produce multiple pump beams.

Prediction of missing common genes for disease pairs using network based module separation on incomplete human interactome.

PubMed

Akram, Pakeeza; Liao, Li

2017-12-06

Identification of common genes associated with comorbid diseases can be critical in understanding their pathobiological mechanism. This work presents a novel method to predict missing common genes associated with a disease pair. Searching for missing common genes is formulated as an optimization problem to minimize network based module separation from two subgraphs produced by mapping genes associated with disease onto the interactome. Using cross validation on more than 600 disease pairs, our method achieves significantly higher average receiver operating characteristic ROC Score of 0.95 compared to a baseline ROC score 0.60 using randomized data. Missing common genes prediction is aimed to complete gene set associated with comorbid disease for better understanding of biological intervention. It will also be useful for gene targeted therapeutics related to comorbid diseases. This method can be further considered for prediction of missing edges to complete the subgraph associated with disease pair.

A characterization of low luminance static and dynamic modulation transfer function curves for P-1, P-43, and P-53 phosphorus

NASA Astrophysics Data System (ADS)

Beasley, Howard H.; Martin, John S.; Klymenko, Victor; Harding, Thomas H.; Verona, Robert W.; Rash, Clarence E.

1995-07-01

A counterphase modulation technique is used to measure the static and dynamic modulation transfer functions for three phosphorus of current interest to U.S. Army aviation helmet-mounted displays (P-1, P-43, and P-53). A family of modulation transfer curves, one for each temporal frequency, is presented for each phosphorus. The measured MFT curves generally support the supposition that phosphorus persistence is a critical parameter in the ability of a CRT display to accurately reproduce contrast modulation transfer in dynamic environments.

Aberrant functional connectivity for diagnosis of major depressive disorder: a discriminant analysis.

PubMed

Cao, Longlong; Guo, Shuixia; Xue, Zhimin; Hu, Yong; Liu, Haihong; Mwansisya, Tumbwene E; Pu, Weidan; Yang, Bo; Liu, Chang; Feng, Jianfeng; Chen, Eric Y H; Liu, Zhening

2014-02-01

Aberrant brain functional connectivity patterns have been reported in major depressive disorder (MDD). It is unknown whether they can be used in discriminant analysis for diagnosis of MDD. In the present study we examined the efficiency of discriminant analysis of MDD by individualized computer-assisted diagnosis. Based on resting-state functional magnetic resonance imaging data, a new approach was adopted to investigate functional connectivity changes in 39 MDD patients and 37 well-matched healthy controls. By using the proposed feature selection method, we identified significant altered functional connections in patients. They were subsequently applied to our analysis as discriminant features using a support vector machine classification method. Furthermore, the relative contribution of functional connectivity was estimated. After subset selection of high-dimension features, the support vector machine classifier reached up to approximately 84% with leave-one-out training during the discrimination process. Through summarizing the classification contribution of functional connectivities, we obtained four obvious contribution modules: inferior orbitofrontal module, supramarginal gyrus module, inferior parietal lobule-posterior cingulated gyrus module and middle temporal gyrus-inferior temporal gyrus module. The experimental results demonstrated that the proposed method is effective in discriminating MDD patients from healthy controls. Functional connectivities might be useful as new biomarkers to assist clinicians in computer auxiliary diagnosis of MDD. © 2013 The Authors. Psychiatry and Clinical Neurosciences © 2013 Japanese Society of Psychiatry and Neurology.

The IMPORTance of the Nucleus during Flavivirus Replication

PubMed Central

Lopez-Denman, Adam J.; Mackenzie, Jason M.

2017-01-01

Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation. In this review, we discuss the current understanding of flavivirus nuclear localisation, and the function it has during flavivirus infection. We also describe—while closely related—the functional differences between similar viral proteins in their nuclear translocation. PMID:28106839

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

NASA Astrophysics Data System (ADS)

Wiebusch, Martin

2015-10-01

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools.

Optimized Signaling Method for High-Speed Transmission Channels with Higher Order Transfer Function

NASA Astrophysics Data System (ADS)

Ševčík, Břetislav; Brančík, Lubomír; Kubíček, Michal

2017-08-01

In this paper, the selected results from testing of optimized CMOS friendly signaling method for high-speed communications over cables and printed circuit boards (PCBs) are presented and discussed. The proposed signaling scheme uses modified concept of pulse width modulated (PWM) signal which enables to better equalize significant channel losses during data high-speed transmission. Thus, the very effective signaling method to overcome losses in transmission channels with higher order transfer function, typical for long cables and multilayer PCBs, is clearly analyzed in the time and frequency domain. Experimental results of the measurements include the performance comparison of conventional PWM scheme and clearly show the great potential of the modified signaling method for use in low power CMOS friendly equalization circuits, commonly considered in modern communication standards as PCI-Express, SATA or in Multi-gigabit SerDes interconnects.