Performance Reviews for the Orchestral Musician

ERIC Educational Resources Information Center

Watson, Amanda; Forrest, David

2014-01-01

Musicians are appointed to positions in professional symphony orchestras--both rank and file and section principals--following a blind audition process. They perform set repertoire works and orchestral excerpts behind a screen. In many higher education programs, musicians focus on learning the orchestral excerpts and instrumental repertoire that…

An Exploratory Comparison of Novice, Intermediate, and Expert Orchestral Conductors

ERIC Educational Resources Information Center

Bergee, Martin J.

2005-01-01

This study compared novice, "intermediate" (graduate student), and expert orchestral conductors. Two novice conductors, one graduate student in orchestral conducting, and one expert conductor led a university symphony orchestra in part of the first movement of Brahms's Symphony No. 2. Wired for sound, conductors attempted to verbalize their…

Orchestral Performance and the Footprint of Mindfulness

ERIC Educational Resources Information Center

Langer, Ellen; Russell, Timothy; Eisenkraft, Noah

2009-01-01

Two studies were designed to test the hypothesis that actively creating novel distinctions and sonically portraying them during the performance of orchestral music is preferable to attempting to re-create a past performance. The data suggest that orchestral musicians preferred creating music when they were encouraged to mindfully incorporate…

A Young Person's Guide to the Orchestral Profession

ERIC Educational Resources Information Center

Corkhill, David

2005-01-01

Through interviews with ten conservatoire students and ten professional orchestral musicians teaching at conservatoires, this paper seeks to establish whether young people regard the orchestral music profession as a worthwhile ambition. If so, are teachers preparing students sufficiently for their careers and passing on the benefits of their…

The Effects of Orchestration on Musicians' and Nonmusicians' Perception of Musical Tension

ERIC Educational Resources Information Center

Silvey, Brian A.

2011-01-01

The purpose of this study was to examine the effects of orchestration on musicians' and nonmusicians' (N = 40) perception of musical tension. Participants were asked to register their perceptions of tension using the Continuous Response Digital Interface dial while listening to three orchestrations (full orchestra, brass quintet, and solo piano)…

Technology-Supported Orchestration Matters: Outperforming Paper-Based Scripting in a Jigsaw Classroom

ERIC Educational Resources Information Center

Balestrini, Mara; Hernandez-Leo, Davinia; Nieves, Raul; Blat, Josep

2014-01-01

Under the umbrella of ubiquitous technologies, many computational artifacts have been designed to enhance the learning experience in physical settings such as classrooms or playgrounds, but few of them focus on aiding orchestration. This paper presents a systematic evaluation of the signal orchestration system (SOS) used by students for a jigsaw…

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model.

PubMed

Woltering, Joost M; Duboule, Denis

2015-11-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

A Study of Master's Degrees in Orchestral Conducting in the United States

ERIC Educational Resources Information Center

St. John, Brian Allen

2010-01-01

In order to learn to be an orchestra conductor in the United States of America, students often begins their formal education by seeking to earn a master's degree in orchestral conducting. This project compiled a listing of American universities which offer a master's degree in orchestral conducting and categorized the component parts of their…

Engaging with Mathematics in the Kindergarten. Orchestrating a Fairy Tale through Questioning and Use of Tools

ERIC Educational Resources Information Center

Carlsen, Martin

2013-01-01

The aim of this study is to analyse how a kindergarten teacher orchestrated a mathematical activity involving a fairy tale. Taking a sociocultural perspective on learning and development, naturally occurring talk-in-interaction has been analysed in order to scrutinise the subtleties of the orchestration. The fairy tale "Goldilocks and the…

Optimization of Orchestral Layouts Based on Instrument Directivity Patterns

NASA Astrophysics Data System (ADS)

Stroud, Nathan Paul

The experience of hearing an exceptional symphony orchestra perform in an excel- lent concert hall can be profound and moving, causing a level of excitement not often reached for listeners. Romantic period style orchestral music, recognized for validating the use of intense emotion for aesthetic pleasure, was the last significant development in the history of the orchestra. In an age where orchestral popularity is waning, the possibil- ity of evolving the orchestral sound in our modern era exists through the combination of our current understanding of instrument directivity patterns and their interaction with architectural acoustics. With the aid of wave field synthesis (WFS), newly proposed variations on orchestral layouts are tested virtually using a 64-channel WFS array. Each layout is objectively and subjectively compared for determination of which layout could optimize the sound of the orchestra and revitalize the excitement of the performance.

A Descriptive Study of High School and University Students' Focus of Attention in Fast and Slow Orchestral Excerpts

ERIC Educational Resources Information Center

MacLeod, Rebecca B.; Geringer, John M.; Scott, Laurie

2009-01-01

The purpose of this study was to investigate listener discrimination of orchestral performances and to ascertain focus of listener attention to technical and expressive music elements of those performances. High School (n = 84) and University (n = 84) music students listened to four orchestral excerpts: two slow/soft excerpts and two fast/loud…

Challenge of Supporting Vocational Learning: Empowering Collaboration in a Scripted 3D Game--How Does Teachers' Real-Time Orchestration Make a Difference?

ERIC Educational Resources Information Center

Hamalainen, Raija; Oksanen, Kimmo

2012-01-01

Along with the development of new technologies, orchestrating computer-supported collaborative learning (CSCL) has become a topic of discussion because new learning spaces challenge teacher to support collaborative learning in new ways. However, despite the optimistic notions of teachers' orchestration in CSCL situations, there are still no…

Workflow Design Using Fragment Composition

NASA Astrophysics Data System (ADS)

Mosser, Sébastien; Blay-Fornarino, Mireille; France, Robert

The Service-Oriented Architecture (Soa) paradigm supports the assembly of atomic services to create applications that implement complex business processes. Assembly can be accomplished by service orchestrations defined by Soa architects. The Adore method allows Soa architects to model complex orchestrations of services by composing models of smaller orchestrations called orchestration fragments. The Adore method can also be used to weave fragments that address new concerns into existing application models. In this paper we illustrate how the Adore method can be used to separate and compose process aspects in a Soa design of the Car Crash Crisis Management System. The paper also includes a discussion of the benefits and limitations of the Adore method.

Nature of orchestral noise.

PubMed

O'Brien, Ian; Wilson, Wayne; Bradley, Andrew

2008-08-01

Professional orchestral musicians are at risk of exposure to excessive noise when at work. This is an industry-wide problem that threatens not only the hearing of orchestral musicians but also the way orchestras operate. The research described in this paper recorded noise levels within a professional orchestra over three years in order to provide greater insight to the orchestral noise environment; to guide future research into orchestral noise management and hearing conservation strategies; and to provide a basis for the future education of musicians and their managers. Every rehearsal, performance, and recording from May 2004 to May 2007 was monitored, with the woodwind, brass, and percussion sections monitored in greatest detail. The study recorded dBALEQ and dBC peak data, which are presented in graphical form with accompanying summarized data tables. The findings indicate that the principal trumpet, first and third horns, and principal trombone are at greatest risk of exposure to excessive sustained noise levels and that the percussion and timpani are at greatest risk of exposure to excessive peak noise levels. However, the findings also strongly support the notion that the true nature of orchestral noise is a great deal more complex than this simple statement would imply.

Electro-mechanical probe positioning system for large volume plasma device

NASA Astrophysics Data System (ADS)

Sanyasi, A. K.; Sugandhi, R.; Srivastava, P. K.; Srivastav, Prabhakar; Awasthi, L. M.

2018-05-01

An automated electro-mechanical system for the positioning of plasma diagnostics has been designed and implemented in a Large Volume Plasma Device (LVPD). The system consists of 12 electro-mechanical assemblies, which are orchestrated using the Modbus communication protocol on 4-wire RS485 communications to meet the experimental requirements. Each assembly has a lead screw-based mechanical structure, Wilson feed-through-based vacuum interface, bipolar stepper motor, micro-controller-based stepper drive, and optical encoder for online positioning correction of probes. The novelty of the system lies in the orchestration of multiple drives on a single interface, fabrication and installation of the system for a large experimental device like the LVPD, in-house developed software, and adopted architectural practices. The paper discusses the design, description of hardware and software interfaces, and performance results in LVPD.

Integrated Business Process Adaptation towards Friction-Free Business-to-Business Collaboration

ERIC Educational Resources Information Center

Shan, Zhe

2011-01-01

One key issue in process-aware E-commerce collaboration is the orchestration of business processes of multiple business partners throughout a supply chain network in an automated and seamless way. Since each partner has its own internal processes with different control flow structures and message interfaces, the real challenge lies in verifying…

Instructional Implications of Listening Comprehension Research. Reading Education Report No. 39.

ERIC Educational Resources Information Center

Pearson, P. David; Fielding, Linda

While listening comprehension is perhaps the most ignored area of the language arts, a review of the literature suggests that it is deserving of more classroom instructional time. Involving the simultaneous orchestration of skills in phonology, syntax, semantics, and knowledge of text structure, listening comprehension seems to be controlled by…

Robotic Intelligence Kernel: Driver

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

The INL Robotic Intelligence Kernel-Driver is built on top of the RIK-A and implements a dynamic autonomy structure. The RIK-D is used to orchestrate hardware for sensing and action as well as software components for perception, communication, behavior and world modeling into a single cognitive behavior kernel that provides intrinsic intelligence for a wide variety of unmanned ground vehicle systems.

Design of Control Plane Architecture Based on Cloud Platform and Experimental Network Demonstration for Multi-domain SDON

NASA Astrophysics Data System (ADS)

Li, Ming; Yin, Hongxi; Xing, Fangyuan; Wang, Jingchao; Wang, Honghuan

2016-02-01

With the features of network virtualization and resource programming, Software Defined Optical Network (SDON) is considered as the future development trend of optical network, provisioning a more flexible, efficient and open network function, supporting intraconnection and interconnection of data centers. Meanwhile cloud platform can provide powerful computing, storage and management capabilities. In this paper, with the coordination of SDON and cloud platform, a multi-domain SDON architecture based on cloud control plane has been proposed, which is composed of data centers with database (DB), path computation element (PCE), SDON controller and orchestrator. In addition, the structure of the multidomain SDON orchestrator and OpenFlow-enabled optical node are proposed to realize the combination of centralized and distributed effective management and control platform. Finally, the functional verification and demonstration are performed through our optical experiment network.

The orchestration of occupation: the dance of mothers.

PubMed

Larson, E A

2000-01-01

This article describes the relationship of mothers' orchestration of daily occupations, the specialized maternal work of parenting a child with a disability, and the mother's subjective well-being. Mothers' daily occupations and subjective well-being were studied using multiple in-depth interviews, participant observation of a day's round of occupations, and scales of well-being. Data were treated to a recursive analysis, which included theoretical notes generated during transcriptions that identified important themes and additional points of inquiry, line-by-line coding of transcripts, and theoretical sorting of codes and regrouping, recoding. To account for patterns in the data, a relational analysis was conducted that included the generation of metaphors. Emergent findings of this analysis identified the mothers' guiding occupational motif and eight processes of orchestration in their daily routines. The occupational motif, the embrace of paradox, directed the mother's orchestration of daily occupations. The orchestration processes included planning, organizing, balancing, anticipating, interpreting, forecasting, perspective shifting, and meaning making. Examples illustrate the maternally driven and child-sensitive nature of these processes. In their daily rounds, the mothers studied were attentive to the manner and method with which they interacted with their children to produce child-contingent occupations commensurate with their values of being a good mother. Using these orchestration processes, mothers made sense of their past, designed their present, and planned for their future within their daily occupational rounds for themselves and family members.

Organizational Implications of the U.S. Army’s Increasing Demand for Explosive Ordnance Disposal Capabilities

DTIC Science & Technology

2008-05-22

Washington D.C: Government Printing Office, 1976), 1-1 to 1-5. 43 Ibid, 2-1 to 2-32. 16 “orchestrated ballet of farm implements.”44 The Army’s...Orchestrated Ballet of Farm Implements”, Engineer Bulletin, August 1996, http://fas.org/man/dod 101/sys/land/docs /960800-greene2.htm (accessed 5 April...An Alternative to the Orchestrated Ballet of Farm Implements” Engineer Bulletin (August 1996), http://fas.org/man/dod_101/sys/land/docs/960800

The Conceptual Structure of IMS Learning Design Does Not Impede Its Use for Authoring

ERIC Educational Resources Information Center

Derntl, M.; Neumann, S.; Griffiths, D.; Oberhuemer, P.

2012-01-01

IMS Learning Design (LD) is the only available interoperability specification in the area of technology enhanced learning that allows the definition and orchestration of complex activity flows and resource environments in a multirole setting. IMS LD has been available since 2003, and yet it has not been widely adopted either by practitioners or by…

Three’s company: The fission yeast actin cytoskeleton

PubMed Central

Kovar, David R.; Sirotkin, Vladimir; Lord, Matthew

2010-01-01

How the actin cytoskeleton assembles into different structures to drive diverse cellular processes is a fundamental cell biological question. In addition to orchestrating the appropriate combination of regulators and actin-binding proteins, different actin-based structures must insulate themselves from one another to maintain specificity within a crowded cytoplasm. Actin specification is particularly vexing in complex eukaryotes where a multitude of protein isoforms and actin structures operate within the same cell. Fission yeast Schizosaccharomyces pombe possesses a single actin isoform that functions in three distinct structures throughout the cell cycle. In this review, we explore recent studies in fission yeast that help unravel how different actin structures operate in cells. PMID:21145239

Architecting for Large Scale Agile Software Development: A Risk-Driven Approach

DTIC Science & Technology

2013-05-01

addressed aspect of scale in agile software development. Practices such as Scrum of Scrums are meant to address orchestration of multiple development...owner, Scrum master) have differing responsibilities from the roles in the existing phase-based waterfall program structures. Such differences may... Scrum . Communication with both internal and external stakeholders must be open and documentation should not be used as a substitute for communication

Music, emotion, and time perception: the influence of subjective emotional valence and arousal?

PubMed Central

Droit-Volet, Sylvie; Ramos, Danilo; Bueno, José L. O.; Bigand, Emmanuel

2013-01-01

The present study used a temporal bisection task with short (<2 s) and long (>2 s) stimulus durations to investigate the effect on time estimation of several musical parameters associated with emotional changes in affective valence and arousal. In order to manipulate the positive and negative valence of music, Experiments 1 and 2 contrasted the effect of musical structure with pieces played normally and backwards, which were judged to be pleasant and unpleasant, respectively. This effect of valence was combined with a subjective arousal effect by changing the tempo of the musical pieces (fast vs. slow) (Experiment 1) or their instrumentation (orchestral vs. piano pieces). The musical pieces were indeed judged more arousing with a fast than with a slow tempo and with an orchestral than with a piano timbre. In Experiment 3, affective valence was also tested by contrasting the effect of tonal (pleasant) vs. atonal (unpleasant) versions of the same musical pieces. The results showed that the effect of tempo in music, associated with a subjective arousal effect, was the major factor that produced time distortions with time being judged longer for fast than for slow tempi. When the tempo was held constant, no significant effect of timbre on the time judgment was found although the orchestral music was judged to be more arousing than the piano music. Nevertheless, emotional valence did modulate the tempo effect on time perception, the pleasant music being judged shorter than the unpleasant music. PMID:23882233

Transposable elements as genetic regulatory substrates in early development.

PubMed

Gifford, Wesley D; Pfaff, Samuel L; Macfarlan, Todd S

2013-05-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. Published by Elsevier Ltd.

Transposable elements as genetic regulatory substrates in early development

PubMed Central

Gifford, Wesley D.; Pfaff, Samuel L.; Macfarlan, Todd S.

2014-01-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. PMID:23411159

A Decrease in Ambient Temperature Induces Post-Mitotic Enlargement of Palisade Cells in North American Lake Cress.

PubMed

Amano, Rumi; Nakayama, Hokuto; Morohoshi, Yurika; Kawakatsu, Yaichi; Ferjani, Ali; Kimura, Seisuke

2015-01-01

In order to maintain organs and structures at their appropriate sizes, multicellular organisms orchestrate cell proliferation and post-mitotic cell expansion during morphogenesis. Recent studies using Arabidopsis leaves have shown that compensation, which is defined as post-mitotic cell expansion induced by a decrease in the number of cells during lateral organ development, is one example of such orchestration. Some of the basic molecular mechanisms underlying compensation have been revealed by genetic and chimeric analyses. However, to date, compensation had been observed only in mutants, transgenics, and γ-ray-treated plants, and it was unclear whether it occurs in plants under natural conditions. Here, we illustrate that a shift in ambient temperature could induce compensation in Rorippa aquatica (Brassicaceae), a semi-aquatic plant found in North America. The results suggest that compensation is a universal phenomenon among angiosperms and that the mechanism underlying compensation is shared, in part, between Arabidopsis and R. aquatica.

A Decrease in Ambient Temperature Induces Post-Mitotic Enlargement of Palisade Cells in North American Lake Cress

PubMed Central

Morohoshi, Yurika; Kawakatsu, Yaichi; Ferjani, Ali; Kimura, Seisuke

2015-01-01

In order to maintain organs and structures at their appropriate sizes, multicellular organisms orchestrate cell proliferation and post-mitotic cell expansion during morphogenesis. Recent studies using Arabidopsis leaves have shown that compensation, which is defined as post-mitotic cell expansion induced by a decrease in the number of cells during lateral organ development, is one example of such orchestration. Some of the basic molecular mechanisms underlying compensation have been revealed by genetic and chimeric analyses. However, to date, compensation had been observed only in mutants, transgenics, and γ-ray–treated plants, and it was unclear whether it occurs in plants under natural conditions. Here, we illustrate that a shift in ambient temperature could induce compensation in Rorippa aquatica (Brassicaceae), a semi-aquatic plant found in North America. The results suggest that compensation is a universal phenomenon among angiosperms and that the mechanism underlying compensation is shared, in part, between Arabidopsis and R. aquatica. PMID:26569502

Implications of Metaphors in Defining Technical Communication.

ERIC Educational Resources Information Center

Beck, Charles E.

1991-01-01

Identifies four metaphors that appear dominant in current studies in the field of technical communication: transmitter, channel, balance, and bridge. Suggests limitations upon each of the metaphors. Discusses the alternative metaphors of lock, translator, transformer, synthesizer, conductor, and orchestrator. Proposes orchestration as a fruitful…

Direct or Directed: Orchestrating a More Harmonious Approach to Teaching Technology within an Art & Design Higher Education Curriculum with Special Reference to Visual Communications Courses

ERIC Educational Resources Information Center

Marshall, Lindsey; Meachem, Lester

2007-01-01

In this scoping study we have investigated the integration of subject-specific software into the structure of visual communications courses. There is a view that the response within visual communications courses to the rapid developments in technology has been linked to necessity rather than by design. Through perceptions of staff with day-to-day…

Orchestrating the Tumor Microenvironment to Improve Survival for Patients With Pancreatic Cancer: Normalization, Not Destruction.

PubMed

Whatcott, Clifford J; Han, Haiyong; Von Hoff, Daniel D

2015-01-01

Pancreatic cancer is the fourth leading cause of cancer death in the United States. The microenvironment of pancreatic cancer could be one of the "perfect storms" that support the growth of a cancer. Indeed, pancreatic cancer may be the poster child of a problem with the microenvironment. In this article, we review the rationale and attempts to date on modifying or targeting structural proteins in the microenvironment including hyaluronan (HA) (in primary and metastases), collagen, and SPARC (secreted protein, acidic, and rich in cysteine). Indeed, working in this area has produced a regimen that improves survival for patients with advanced pancreatic cancer (nab-paclitaxel + gemcitabine). In addition, in initial clinical trials, PEGylated hyaluronidase appears promising. We also review a new approach that is different than targeting/destroying the microenvironment and that is orchestrating, reengineering, reprogramming, or normalizing the microenvironment (including normalizing structural proteins, normalizing an immunologically tumor-friendly environment to a less friendly environment, reversing epithelial-to-mesenchymal transition, and so on). We believe this will be most effectively done by agents that have global effects on transcription. There is initial evidence that this can be done by agents such as vitamin D derivatives and other new agents. There is no doubt these opportunities can now be tried in the clinic with hopefully beneficial effects.

The evolution of cortical development: the synapsid-diapsid divergence.

PubMed

Goffinet, Andre M

2017-11-15

The cerebral cortex covers the rostral part of the brain and, in higher mammals and particularly humans, plays a key role in cognition and consciousness. It is populated with neuronal cell bodies distributed in radially organized layers. Understanding the common and lineage-specific molecular mechanisms that orchestrate cortical development and evolution are key issues in neurobiology. During evolution, the cortex appeared in stem amniotes and evolved divergently in two main branches of the phylogenetic tree: the synapsids (which led to present day mammals) and the diapsids (reptiles and birds). Comparative studies in organisms that belong to those two branches have identified some common principles of cortical development and organization that are possibly inherited from stem amniotes and regulated by similar molecular mechanisms. These comparisons have also highlighted certain essential features of mammalian cortices that are absent or different in diapsids and that probably evolved after the synapsid-diapsid divergence. Chief among these is the size and multi-laminar organization of the mammalian cortex, and the propensity to increase its area by folding. Here, I review recent data on cortical neurogenesis, neuronal migration and cortical layer formation and folding in this evolutionary perspective, and highlight important unanswered questions for future investigation. © 2017. Published by The Company of Biologists Ltd.

WWWinda Orchestrator: a mechanism for coordinating distributed flocks of Java Applets

NASA Astrophysics Data System (ADS)

Gutfreund, Yechezkal-Shimon; Nicol, John R.

1997-01-01

The WWWinda Orchestrator is a simple but powerful tool for coordinating distributed Java applets. Loosely derived from the Linda programming language developed by David Gelernter and Nicholas Carriero of Yale, WWWinda implements a distributed shared object space called TupleSpace where applets can post, read, or permanently store arbitrary Java objects. In this manner, applets can easily share information without being aware of the underlying communication mechanisms. WWWinda is a very useful for orchestrating flocks of distributed Java applets. Coordination event scan be posted to WWWinda TupleSpace and used to orchestrate the actions of remote applets. Applets can easily share information via the TupleSpace. The technology combines several functions in one simple metaphor: distributed web objects, remote messaging between applets, distributed synchronization mechanisms, object- oriented database, and a distributed event signaling mechanisms. WWWinda can be used a s platform for implementing shared VRML environments, shared groupware environments, controlling remote devices such as cameras, distributed Karaoke, distributed gaming, and shared audio and video experiences.

DDA3 associates with microtubule plus ends and orchestrates microtubule dynamics and directional cell migration

PubMed Central

Zhang, Liangyu; Shao, Hengyi; Zhu, Tongge; Xia, Peng; Wang, Zhikai; Liu, Lifang; Yan, Maomao; Hill, Donald L.; Fang, Guowei; Chen, Zhengjun; Wang, Dongmei; Yao, Xuebiao

2013-01-01

Cell motility and adhesion involve orchestrated interaction of microtubules (MTs) with their plus-end tracking proteins (+TIPs). However, the mechanisms underlying regulations of MT dynamics and directional cell migration are still elusive. Here, we show that DDA3-EB1 interaction orchestrates MT plus-end dynamics and facilitates directional cell migration. Biochemical characterizations reveal that DDA3 interacts with EB1 via its SxIP motif within the C-terminal Pro/Ser-rich region. Time-lapse and total internal reflection fluorescence (TIRF) microscopic assays demonstrate that DDA3 exhibits EB1-dependent, MT plus-end loading and tracking. The EB1-based loading of DDA3 is responsible for MT plus-ends stabilization at the cell cortex, which in turn orchestrates directional cell migration. Interestingly, the DDA3-EB1 interaction is potentially regulated by EB1 acetylation, which may account for physiological regulation underlying EGF-elicited cell migration. Thus, the EB1-based function of DDA3 links MT dynamics to directional cell migration. PMID:23652583

A Model of Evolution of Development Based on Germline Penetration of New “No-Junk” DNA

PubMed Central

Fontana, Alessandro; Wróbel, Borys

2012-01-01

There is a mounting body of evidence that somatic transposition may be involved in normal development of multicellular organisms and in pathology, especially cancer. Epigenetic Tracking (ET) is an abstract model of multicellular development, able to generate complex 3-dimensional structures. Its aim is not to model the development of a particular organism nor to merely summarise mainstream knowledge on genetic regulation of development. Rather, the goal of ET is to provide a theoretical framework to test new postulated genetic mechanisms, not fully established yet in mainstream biology. The first proposal is that development is orchestrated through a subset of cells which we call driver cells. In these cells, the cellular state determines a specific pattern of gene activation which leads to the occurrence of developmental events. The second proposal is that evolution of development is affected by somatic transposition events. We postulate that when the genome of a driver cell does not specify what developmental event should be undertaken when the cell is in a particular cellular state, somatic transposition events can reshape the genome, build new regulatory regions, and lead to a new pattern of gene activation in the cell. Our third hypothesis, not supported yet by direct evidence, but consistent with some experimental observations, is that these new “no-junk” sequences—regulatory regions created by transposable elements at new positions in the genome—can exit the cell and enter the germline, to be incorporated in the genome of the progeny. We call this mechanism germline penetration. This process allows heritable incorporation of novel developmental events in the developmental trajectory. In this paper we will present the model and link these three postulated mechanisms to biological observations. PMID:24704981

Long-Term Teacher Orchestration of Technology-Mediated Collaborative Inquiry

ERIC Educational Resources Information Center

Viilo, Marjut; Seitamaa-Hakkarainen, Pirita; Hakkarainen, Kai

2018-01-01

This explorative case study longitudinally examines teacher orchestration of an inquiry learning process in a technology-enhanced elementary classroom. A 13-month investigative study on cultural artifacts was conducted on 32 fourth grade students who progressed to the fifth grade during the project. The activities were mediated and documented…

Secure NFV Orchestration Over an SDN-Controlled Optical Network With Time-Shared Quantum Key Distribution Resources

NASA Astrophysics Data System (ADS)

Aguado, Alejandro; Hugues-Salas, Emilio; Haigh, Paul Anthony; Marhuenda, Jaume; Price, Alasdair B.; Sibson, Philip; Kennard, Jake E.; Erven, Chris; Rarity, John G.; Thompson, Mark Gerard; Lord, Andrew; Nejabati, Reza; Simeonidou, Dimitra

2017-04-01

We demonstrate, for the first time, a secure optical network architecture that combines NFV orchestration and SDN control with quantum key distribution (QKD) technology. A novel time-shared QKD network design is presented as a cost-effective solution for practical networks.

Incorporating Wind Excerpts in the School Band Curriculum

ERIC Educational Resources Information Center

Bruns, Robert

2010-01-01

Professional musicians and college students commonly study orchestral excerpts, but a similar practice has yet to be implemented in the band field. Due to their widespread use in orchestral auditions, excerpts have been incorporated as a tool for musical development. Many college professors regularly assign excerpt study as part of their…

Orchestration of Social Modes in E-Learning

ERIC Educational Resources Information Center

Weinberger, Armin; Papadopoulos, Pantelis M.

2016-01-01

The concept of orchestration has recently emerged as a useful metaphor in technology-enhanced learning research communities, because of its explanatory power and appeal in describing how different learning activities, tools, and arrangements could be combined to promote learning. More than a buffet of tools offering possibilities to the teachers,…

Orchestration in Learning Technology Research: Evaluation of a Conceptual Framework

ERIC Educational Resources Information Center

Prieto, Luis P.; Dimitriadis, Yannis; Asensio-Pérez, Juan I.; Looi, Chee-Kit

2015-01-01

The term "orchestrating learning" is being used increasingly often, referring to the coordination activities performed while applying learning technologies to authentic settings. However, there is little consensus about how this notion should be conceptualised, and what aspects it entails. In this paper, a conceptual framework for…

Webbing and Orchestration. Two Interrelated Views on Digital Tools in Mathematics Education

ERIC Educational Resources Information Center

Trouche, Luc; Drijvers, Paul

2014-01-01

The integration of digital tools in mathematics education is considered both promising and problematic. To deal with this issue, notions of "webbing" and "instrumental orchestration" are developed. However, the two seemed to be disconnected, and having different cultural and theoretical roots. In this article, we investigate…

The Principal as Orchestral Conductor.

ERIC Educational Resources Information Center

Luce, David R.

1992-01-01

A new way of viewing the principal is to think of the principal as an orchestral conductor. Insights gained from this perspective may help in progressing toward more healthy and productive school organizations. Both the conductor and the principal are highly visible by virtue of their positions and function as intermediaries in their respective…

Roles of Teachers in Orchestrating Learning in Elementary Science Classrooms

ERIC Educational Resources Information Center

Zhai, Junqing; Tan, Aik-Ling

2015-01-01

This study delves into the different roles that elementary science teachers play in the classroom to orchestrate science learning opportunities for students. Examining the classroom practices of three elementary science teachers in Singapore, we found that teachers shuttle between four key roles in enabling student learning in science. Teachers…

Approaches to Learning and Study Orchestrations in High School Students

ERIC Educational Resources Information Center

Cano, Francisco

2007-01-01

In the framework of the SAL (Students' approaches to learning) position, the learning experience (approaches to learning and study orchestrations) of 572 high school students was explored, examining its interrelationships with some personal and familial variables. Three major results emerged. First, links were found between family's intellectual…

Orchestrating emotion and action in an evolutionary framework. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Arbib, Michael A.

2015-06-01

The lead author of the Quartet Theory [10] is, appropriately enough, an expert on the neuroscience linking music and emotion, and examples of this linkage are a welcome feature of the article. Actually, the article charts two quartets: A structural quartet of affect systems centered on (i) brainstem, (ii) diencephalon, (iii) hippocampus and (iv) orbitofrontal cortex.

The Congenital Heart Surgeons Society Datacenter: unique attributes as a research organization.

PubMed

Caldarone, Christopher A; Williams, William G

2010-01-01

Over the last 25 years, the Congenital Heart Surgeons Society (CHSS) has evolved from an informal club to a mature organization. A central feature of the CHSS has been dedication to evaluating outcomes of congenital heart surgery across a wide array of clinical diagnoses. These research activities have been orchestrated through the CHSS Datacenter, which has developed a unique organizational structure that has strengths and weaknesses in comparison to other research organizational structures (e.g., prospective randomized trials, registries, etc). This review will highlight the unique attributes of the CHSS Datacenter with emphasis on the Datacenter's strengths and weaknesses in comparison to other organizational structures. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Multimodal Teaching Analytics: Automated Extraction of Orchestration Graphs from Wearable Sensor Data

ERIC Educational Resources Information Center

Prieto, L. P.; Sharma, K.; Kidzinski, L.; Rodríguez-Triana, M. J.; Dillenbourg, P.

2018-01-01

The pedagogical modelling of everyday classroom practice is an interesting kind of evidence, both for educational research and teachers' own professional development. This paper explores the usage of wearable sensors and machine learning techniques to automatically extract orchestration graphs (teaching activities and their social plane over time)…

Generic Service Integration in Adaptive Learning Experiences Using IMS Learning Design

ERIC Educational Resources Information Center

de-la-Fuente-Valentin, Luis; Pardo, Abelardo; Kloos, Carlos Delgado

2011-01-01

IMS Learning Design is a specification to capture the orchestration taking place in a learning scenario. This paper presents an extension called Generic Service Integration. This paradigm allows a bidirectional communication between the course engine in charge of the orchestration and conventional Web 2.0 tools. This communication allows the…

Instructional Design or School Politics? A Discussion of "Orchestration" in TEL Research

ERIC Educational Resources Information Center

Perrotta, C.; Evans, M. A.

2013-01-01

This paper argues that the emphasis on orchestration as a metaphor for teaching in technology-enhanced learning (TEL) environments, featured in recent academic discussions, is an opportunity to broaden the scope of the inquiry into educational technology. Drawing on sociological literature and research that investigated the systemic factors that…

Kindergarten Teachers' Orchestration of Mathematical Activities Afforded by Technology: Agency and Mediation

ERIC Educational Resources Information Center

Carlsen, Martin; Erfjord, Ingvald; Hundeland, Per Sigurd; Monaghan, John

2016-01-01

This paper focuses on kindergarten teachers' interactions with young children during mathematical learning activities involving the use of digital tools. We aim to characterise the teachers' roles and actions in these activities and extend considerations of teachers' orchestrations current in the research literature with regard to agency and…

Architectural Principles for Orchestration of Cross-Organizational Service Delivery: Case Studies from the Netherlands

NASA Astrophysics Data System (ADS)

van Veenstra, Anne Fleur; Janssen, Marijn

One of the main challenges for e-government is to create coherent services for citizens and businesses. Realizing Integrated Service Delivery (ISD) requires government agencies to collaborate across their organizational boundaries. The coordination of processes across multiple organizations to realize ISD is called orchestration. One way of achieving orchestration is to formalize processes using architecture. In this chapter we identify architectural principles for orchestration by looking at three case studies of cross-organizational service delivery chain formation in the Netherlands. In total, six generic principles were formulated and subsequently validated in two workshops with experts. These principles are: (i) build an intelligent front office, (ii) give processes a clear starting point and end, (iii) build a central workflow application keeping track of the process, (iv) differentiate between simple and complex processes, (v) ensure that the decision-making responsibility and the overview of the process are not performed by the same process role, and (vi) create a central point where risk profiles are maintained. Further research should focus on how organizations can adapt these principles to their own situation.

Proceedings of the Annual Mechanics of Composites Review (12th) Held in Wright-Patterson AFB, Ohio on 16-17 October 1987

DTIC Science & Technology

1988-01-01

ignored but the Volkersen model is extended to include adherend deformations will be discussed. STATISTICAL METHODOLOGY FOR DESIGN ALLOWABLES [15-17...structure. In the certification methodology , the development test program and the calculation of composite design allowables is orchestrated to support...Development of design methodology of thick composites and their test methods. (b) Role of interface in emerging composite systems. *CONTRACTS IMPROVED DAMAGE

RNA structures as mediators of neurological diseases and as drug targets

PubMed Central

Bernat, Viachaslau; Disney, Matthew D.

2015-01-01

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics. PMID:26139368

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord

PubMed Central

José-Edwards, Diana S.; Oda-Ishii, Izumi; Kugler, Jamie E.; Passamaneck, Yale J.; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-01-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs. PMID:26684323

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.

PubMed

José-Edwards, Diana S; Oda-Ishii, Izumi; Kugler, Jamie E; Passamaneck, Yale J; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-12-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.

Thermal tolerance in the keystone species Daphnia magna-a candidate gene and an outlier analysis approach.

PubMed

Jansen, M; Geerts, A N; Rago, A; Spanier, K I; Denis, C; De Meester, L; Orsini, L

2017-04-01

Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long-term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm- and cold-adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST-linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna. © 2017 John Wiley & Sons Ltd.

GITEWS, an extensible and open integration platform for manifold sensor systems and processing components based on Sensor Web Enablement and the principles of Service Oriented Architectures

NASA Astrophysics Data System (ADS)

Haener, Rainer; Waechter, Joachim; Fleischer, Jens; Herrnkind, Stefan; Schwarting, Herrmann

2010-05-01

The German Indonesian Tsunami Early Warning System (GITEWS) is a multifaceted system consisting of various sensor types like seismometers, sea level sensors or GPS stations, and processing components, all with their own system behavior and proprietary data structure. To operate a warning chain, beginning from measurements scaling up to warning products, all components have to interact in a correct way, both syntactically and semantically. Designing the system great emphasis was laid on conformity to the Sensor Web Enablement (SWE) specification by the Open Geospatial Consortium (OGC). The technical infrastructure, the so called Tsunami Service Bus (TSB) follows the blueprint of Service Oriented Architectures (SOA). The TSB is an integration concept (SWE) where functionality (observe, task, notify, alert, and process) is grouped around business processes (Monitoring, Decision Support, Sensor Management) and packaged as interoperable services (SAS, SOS, SPS, WNS). The benefits of using a flexible architecture together with SWE lead to an open integration platform: • accessing and controlling heterogeneous sensors in a uniform way (Functional Integration) • assigns functionality to distinct services (Separation of Concerns) • allows resilient relationship between systems (Loose Coupling) • integrates services so that they can be accessed from everywhere (Location Transparency) • enables infrastructures which integrate heterogeneous applications (Encapsulation) • allows combination of services (Orchestration) and data exchange within business processes Warning systems will evolve over time: New sensor types might be added, old sensors will be replaced and processing components will be improved. From a collection of few basic services it shall be possible to compose more complex functionality essential for specific warning systems. Given these requirements a flexible infrastructure is a prerequisite for sustainable systems and their architecture must be tailored for evolution. The use of well-known techniques and widely used open source software implementing industrial standards reduces the impact of service modifications allowing the evolution of a system as a whole. GITEWS implemented a solution to feed sensor raw data from any (remote) system into the infrastructure. Specific dispatchers enable plugging in sensor-type specific processing without changing the architecture. Client components don't need to be adjusted if new sensor-types or individuals are added to the system, because they access them via standardized services. One of the outstanding features of service-oriented architectures is the possibility to compose new services from existing ones. The so called orchestration, allows the definition of new warning processes which can be adapted easily to new requirements. This approach has following advantages: • With implementing SWE it is possible to establish the "detection" and integration of sensors via the internet. Thus a system of systems combining early warning functionality at different levels of detail is feasible. • Any institution could add both its own components as well as components from third parties if they are developed in conformance to SOA principles. In a federation an institution keeps the ownership of its data and decides which data are provided by a service and when. • A system can be deployed at minor costs as a core for own development at any institution and thus enabling autonomous early warning- or monitoring systems. The presentation covers both design and various instantiations (live demonstration) of the GITEWS architecture. Experiences concerning the design and complexity of SWE will be addressed in detail. A substantial amount of attention is laid on the techniques and methods of extending the architecture, adapting proprietary components to SWE services and encoding, and their orchestration in high level workflows and processes. Furthermore the potential of the architecture concerning adaptive behavior, collaboration across boundaries and semantic interoperability will be addressed.

Fighting Viral Infections and Virus-Driven Tumors with Cytotoxic CD4+ T Cells

PubMed Central

Muraro, Elena; Merlo, Anna; Martorelli, Debora; Cangemi, Michela; Dalla Santa, Silvia; Dolcetti, Riccardo; Rosato, Antonio

2017-01-01

CD4+ T cells have been and are still largely regarded as the orchestrators of immune responses, being able to differentiate into distinct T helper cell populations based on differentiation signals, transcription factor expression, cytokine secretion, and specific functions. Nonetheless, a growing body of evidence indicates that CD4+ T cells can also exert a direct effector activity, which depends on intrinsic cytotoxic properties acquired and carried out along with the evolution of several pathogenic infections. The relevant role of CD4+ T cell lytic features in the control of such infectious conditions also leads to their exploitation as a new immunotherapeutic approach. This review aims at summarizing currently available data about functional and therapeutic relevance of cytotoxic CD4+ T cells in the context of viral infections and virus-driven tumors. PMID:28289418

Agile IT: Thinking in User-Centric Models

NASA Astrophysics Data System (ADS)

Margaria, Tiziana; Steffen, Bernhard

We advocate a new teaching direction for modern CS curricula: extreme model-driven development (XMDD), a new development paradigm designed to continuously involve the customer/application expert throughout the whole systems' life cycle. Based on the `One-Thing Approach', which works by successively enriching and refining one single artifact, system development becomes in essence a user-centric orchestration of intuitive service functionality. XMDD differs radically from classical software development, which, in our opinion is no longer adequate for the bulk of application programming - in particular when it comes to heterogeneous, cross organizational systems which must adapt to rapidly changing market requirements. Thus there is a need for new curricula addressing this model-driven, lightweight, and cooperative development paradigm that puts the user process in the center of the development and the application expert in control of the process evolution.

First field demonstration of cloud datacenter workflow automation employing dynamic optical transport network resources under OpenStack and OpenFlow orchestration.

PubMed

Szyrkowiec, Thomas; Autenrieth, Achim; Gunning, Paul; Wright, Paul; Lord, Andrew; Elbers, Jörg-Peter; Lumb, Alan

2014-02-10

For the first time, we demonstrate the orchestration of elastic datacenter and inter-datacenter transport network resources using a combination of OpenStack and OpenFlow. Programmatic control allows a datacenter operator to dynamically request optical lightpaths from a transport network operator to accommodate rapid changes of inter-datacenter workflows.

STTEPping in the Right Direction? Western Classical Music in an Orchestral Programme for Disadvantaged African Youth

ERIC Educational Resources Information Center

van Niekerk, Caroline; Salminen, Sanna

2008-01-01

This article looks at STTEP, an outreach project currently housed at the University of Pretoria, which concentrates on the teaching of western orchestral instruments, plus background areas such as music theory, to disadvantaged children and youth from a variety of townships around Pretoria, South Africa. STTEP's direction can well be described as…

Genomic control of patterning

PubMed Central

Peter, Isabelle S.; Davidson, Eric H.

2014-01-01

The development of multicellular organisms involves the partitioning of the organism into territories of cells of specific structure and function. The information for spatial patterning processes is directly encoded in the genome. The genome determines its own usage depending on stage and position, by means of interactions that constitute gene regulatory networks (GRNs). The GRN driving endomesoderm development in sea urchin embryos illustrates different regulatory strategies by which developmental programs are initiated, orchestrated, stabilized or excluded to define the pattern of specified territories in the developing embryo. PMID:19378258

Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate.

PubMed

Nandakumar, Jayakrishnan; Nair, Pravin A; Shuman, Stewart

2007-04-27

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelopes the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

Using Differential Evolution to Optimize Learning from Signals and Enhance Network Security

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

Harmer, Paul K; Temple, Michael A; Buckner, Mark A

2011-01-01

Computer and communication network attacks are commonly orchestrated through Wireless Access Points (WAPs). This paper summarizes proof-of-concept research activity aimed at developing a physical layer Radio Frequency (RF) air monitoring capability to limit unauthorizedWAP access and mprove network security. This is done using Differential Evolution (DE) to optimize the performance of a Learning from Signals (LFS) classifier implemented with RF Distinct Native Attribute (RF-DNA) fingerprints. Performance of the resultant DE-optimized LFS classifier is demonstrated using 802.11a WiFi devices under the most challenging conditions of intra-manufacturer classification, i.e., using emissions of like-model devices that only differ in serial number. Using identicalmore » classifier input features, performance of the DE-optimized LFS classifier is assessed relative to a Multiple Discriminant Analysis / Maximum Likelihood (MDA/ML) classifier that has been used for previous demonstrations. The comparative assessment is made using both Time Domain (TD) and Spectral Domain (SD) fingerprint features. For all combinations of classifier type, feature type, and signal-to-noise ratio considered, results show that the DEoptimized LFS classifier with TD features is uperior and provides up to 20% improvement in classification accuracy with proper selection of DE parameters.« less

Frogs as integrative models for understanding digestive organ development and evolution

PubMed Central

Womble, Mandy; Pickett, Melissa; Nascone-Yoder, Nanette

2016-01-01

The digestive system comprises numerous cells, tissues and organs that are essential for the proper assimilation of nutrients and energy. Many aspects of digestive organ function are highly conserved among vertebrates, yet the final anatomical configuration of the gut varies widely between species, especially those with different diets. Improved understanding of the complex molecular and cellular events that orchestrate digestive organ development is pertinent to many areas of biology and medicine, including the regeneration or replacement of diseased organs, the etiology of digestive organ birth defects, and the evolution of specialized features of digestive anatomy. In this review, we highlight specific examples of how investigations using Xenopus laevis frog embryos have revealed insight into the molecular and cellular dynamics of digestive organ patterning and morphogenesis that would have been difficult to obtain in other animal models. Additionally, we discuss recent studies of gut development in non-model frog species with unique feeding strategies, such as Lepidobatrachus laev is and Eleutherodactylouscoqui, which are beginning to provide glimpses of the evolutionary mechanisms that may generate morphological variation in the digestive tract. The unparalleled experimental versatility of frog embryos make them excellent, integrative models for studying digestive organ development across multiple disciplines. PMID:26851628

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.

PubMed

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

2008-04-25

With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.

In-Space Cryogenic Propellant Depot Stepping Stone

NASA Technical Reports Server (NTRS)

Howell, Joe T.; Mankins, John C.; Fikes, John C.

2005-01-01

An In-Space Cryogenic Propellant Depot (ISCPD) is an important stepping stone to provide the capability to preposition, store, manufacture, and later use the propellants for Earth-Neighborhood campaigns and beyond. An in-space propellant depot will provide affordable propellants and other similar consumables to support the development of sustainable and affordable exploration strategies as well as commercial space activities. An in-space propellant depot not only requires technology development in key areas such as zero boil-off storage and fluid transfer, but in other areas such as lightweight structures, highly reliable connectors, and autonomous operations. These technologies can be applicable to a broad range of propellant depot concepts or specific to a certain design. In addition, these technologies are required for spacecraft and orbit transfer vehicle propulsion and power systems, and space life support. Generally, applications of this technology require long-term storage, on-orbit fluid transfer and supply, cryogenic propellant production from water, unique instrumentation and autonomous operations. This paper discusses the reasons why such advances are important to future affordable and sustainable operations in space. This paper also discusses briefly R&D objectives comprising a promising approach to the systems planning and evolution into a meaningful stepping stone design, development, and implementation of an In-Space Cryogenic Propellant Depot. The success of a well-planned and orchestrated approach holds great promise for achieving innovation and revolutionary technology development for supporting future exploration and development of space.

Drosophila Hox and Sex-Determination Genes Control Segment Elimination through EGFR and extramacrochetae Activity

PubMed Central

Foronda, David; Martín, Paloma; Sánchez-Herrero, Ernesto

2012-01-01

The formation or suppression of particular structures is a major change occurring in development and evolution. One example of such change is the absence of the seventh abdominal segment (A7) in Drosophila males. We show here that there is a down-regulation of EGFR activity and fewer histoblasts in the male A7 in early pupae. If this activity is elevated, cell number increases and a small segment develops in the adult. At later pupal stages, the remaining precursors of the A7 are extruded under the epithelium. This extrusion requires the up-regulation of the HLH protein Extramacrochetae and correlates with high levels of spaghetti-squash, the gene encoding the regulatory light chain of the non-muscle myosin II. The Hox gene Abdominal-B controls both the down-regulation of spitz, a ligand of the EGFR pathway, and the up-regulation of extramacrochetae, and also regulates the transcription of the sex-determining gene doublesex. The male Doublesex protein, in turn, controls extramacrochetae and spaghetti-squash expression. In females, the EGFR pathway is also down-regulated in the A7 but extramacrochetae and spaghetti-squash are not up-regulated and extrusion of precursor cells is almost absent. Our results show the complex orchestration of cellular and genetic events that lead to this important sexually dimorphic character change. PMID:22912593

RING-Domain E3 Ligase-Mediated Host–Virus Interactions: Orchestrating Immune Responses by the Host and Antagonizing Immune Defense by Viruses

PubMed Central

Zhang, Yuexiu; Li, Lian-Feng; Munir, Muhammad; Qiu, Hua-Ji

2018-01-01

The RING-domain E3 ligases (RING E3s), a group of E3 ligases containing one or two RING finger domains, are involved in various cellular processes such as cell proliferation, immune regulation, apoptosis, among others. In the host, a substantial number of the RING E3s have been implicated to inhibit viral replication through regulating immune responses, including activation and inhibition of retinoic acid-inducible gene I-like receptors, toll-like receptors, and DNA receptor signaling pathways, modulation of cell-surface expression of major histocompatibility complex, and co-stimulatory molecules. During the course of evolution and adaptation, viruses encode RING E3s to antagonize host immune defense, such as the infected cell protein 0 of herpes simplex virus type 1, the non-structural protein 1 of rotavirus, and the K3 and K5 of Kaposi’s sarcoma-associated herpesvirus. In addition, recent studies suggest that viruses can hijack the host RING E3s to facilitate viral replication. Based on emerging and interesting discoveries, the RING E3s present novel links among the host and viruses. Herein, we focus on the latest research progresses in the RING E3s-mediated host–virus interactions and discuss the outlooks of the RING E3s for future research. PMID:29872431

INTEGRATING GENETIC AND STRUCTURAL DATA ON HUMAN PROTEIN KINOME IN NETWORK-BASED MODELING OF KINASE SENSITIVITIES AND RESISTANCE TO TARGETED AND PERSONALIZED ANTICANCER DRUGS.

PubMed

Verkhivker, Gennady M

2016-01-01

The human protein kinome presents one of the largest protein families that orchestrate functional processes in complex cellular networks, and when perturbed, can cause various cancers. The abundance and diversity of genetic, structural, and biochemical data underlies the complexity of mechanisms by which targeted and personalized drugs can combat mutational profiles in protein kinases. Coupled with the evolution of system biology approaches, genomic and proteomic technologies are rapidly identifying and charactering novel resistance mechanisms with the goal to inform rationale design of personalized kinase drugs. Integration of experimental and computational approaches can help to bring these data into a unified conceptual framework and develop robust models for predicting the clinical drug resistance. In the current study, we employ a battery of synergistic computational approaches that integrate genetic, evolutionary, biochemical, and structural data to characterize the effect of cancer mutations in protein kinases. We provide a detailed structural classification and analysis of genetic signatures associated with oncogenic mutations. By integrating genetic and structural data, we employ network modeling to dissect mechanisms of kinase drug sensitivities to oncogenic EGFR mutations. Using biophysical simulations and analysis of protein structure networks, we show that conformational-specific drug binding of Lapatinib may elicit resistant mutations in the EGFR kinase that are linked with the ligand-mediated changes in the residue interaction networks and global network properties of key residues that are responsible for structural stability of specific functional states. A strong network dependency on high centrality residues in the conformation-specific Lapatinib-EGFR complex may explain vulnerability of drug binding to a broad spectrum of mutations and the emergence of drug resistance. Our study offers a systems-based perspective on drug design by unravelling complex relationships between robustness of targeted kinase genes and binding specificity of targeted kinase drugs. We discuss how these approaches can exploit advances in chemical biology and network science to develop novel strategies for rationally tailored and robust personalized drug therapies.

Interactive Whiteboards and All that Jazz: The Contribution of Musical Metaphors to the Analysis of Classroom Activity with Interactive Technologies

ERIC Educational Resources Information Center

Beauchamp, Gary; Kennewell, Steve; Tanner, Howard; Jones, Sonia

2010-01-01

The teacher's role has often been described as one of "orchestration", and this musical analogy is a powerful one in characterising the manipulation of features in the classroom setting in order to generate activity or "performance" which leads to learning. However, a classical view of orchestration would fail to recognise the extent to which…

Orchestrating BMD Control in Extended BPEL

DTIC Science & Technology

2008-05-21

Orchestration of secure WebMail , Technical Report ISE-TR-06-08, George Mason University, Fairfax, VA, August 2006. [9] E. Christensen, F. Curbera...methods to access and dissemination control, securing circuit switched (SS7) and IP based telecommunication (VoIP) systems, multimedia, security ...decorating the Business Process Execution Language (BPEL) with Quality of Service (QoS), Measures of Performance (MoP), Measures of Effectiveness (MoE

The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

PubMed

Agarwal, Poonam; Miller, Kyle M

2016-10-01

DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective

PubMed Central

Barrada, Adam; Montané, Marie-Hélène; Robaglia, Christophe; Menand, Benoît

2015-01-01

Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth. PMID:26295391

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

PubMed Central

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

2008-01-01

Background With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Methods Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. Conclusions As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way. PMID:18460173

Load-sensitive dynamic workflow re-orchestration and optimisation for faster patient healthcare.

PubMed

Meli, Christopher L; Khalil, Ibrahim; Tari, Zahir

2014-01-01

Hospital waiting times are considerably long, with no signs of reducing any-time soon. A number of factors including population growth, the ageing population and a lack of new infrastructure are expected to further exacerbate waiting times in the near future. In this work, we show how healthcare services can be modelled as queueing nodes, together with healthcare service workflows, such that these workflows can be optimised during execution in order to reduce patient waiting times. Services such as X-ray, computer tomography, and magnetic resonance imaging often form queues, thus, by taking into account the waiting times of each service, the workflow can be re-orchestrated and optimised. Experimental results indicate average waiting time reductions are achievable by optimising workflows using dynamic re-orchestration. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Theory-Led Design of Instruments and Representations in Learning Analytics: Developing a Novel Tool for Orchestration of Online Collaborative Learning

ERIC Educational Resources Information Center

Kelly, Nick; Thompson, Kate; Yeoman, Pippa

2015-01-01

This paper describes theory-led design as a way of developing novel tools for learning analytics (LA). It focuses upon the domain of automated discourse analysis (ADA) of group learning activities to help an instructor to orchestrate online groups in real-time. The paper outlines the literature on the development of LA tools within the domain of…

Spatiotemporal dynamics of Aurora B-PLK1-MCAK signaling axis orchestrates kinetochore bi-orientation and faithful chromosome segregation

PubMed Central

Shao, Hengyi; Huang, Yuejia; Zhang, Liangyu; Yuan, Kai; Chu, Youjun; Dou, Zhen; Jin, Changjiang; Garcia-Barrio, Minerva; Liu, Xing; Yao, Xuebiao

2015-01-01

Chromosome segregation in mitosis is orchestrated by the dynamic interactions between the kinetochore and spindle microtubules. The microtubule depolymerase mitotic centromere-associated kinesin (MCAK) is a key regulator for an accurate kinetochore-microtubule attachment. However, the regulatory mechanism underlying precise MCAK depolymerase activity control during mitosis remains elusive. Here, we describe a novel pathway involving an Aurora B-PLK1 axis for regulation of MCAK activity in mitosis. Aurora B phosphorylates PLK1 on Thr210 to activate its kinase activity at the kinetochores during mitosis. Aurora B-orchestrated PLK1 kinase activity was examined in real-time mitosis using a fluorescence resonance energy transfer-based reporter and quantitative analysis of native PLK1 substrate phosphorylation. Active PLK1, in turn, phosphorylates MCAK at Ser715 which promotes its microtubule depolymerase activity essential for faithful chromosome segregation. Importantly, inhibition of PLK1 kinase activity or expression of a non-phosphorylatable MCAK mutant prevents correct kinetochore-microtubule attachment, resulting in abnormal anaphase with chromosome bridges. We reason that the Aurora B-PLK1 signaling at the kinetochore orchestrates MCAK activity, which is essential for timely correction of aberrant kinetochore attachment to ensure accurate chromosome segregation during mitosis. PMID:26206521

Structure of the intact ATM/Tel1 kinase

NASA Astrophysics Data System (ADS)

Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen, Xuetong; Wang, Weiwu; Cai, Gang

2016-05-01

The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents.

Visualizing the semantic structure in classical music works.

PubMed

Chan, Wing-Yi; Qu, Huamin; Mak, Wai-Ho

2010-01-01

A major obstacle in the appreciation of classical music is that extensive training is required to understand musical structure and compositional techniques toward comprehending the thoughts behind the musical work. In this paper, we propose an innovative visualization solution to reveal the semantic structure in classical orchestral works such that users can gain insights into musical structure and appreciate the beauty of music. We formulate the semantic structure into macrolevel layer interactions, microlevel theme variations, and macro-micro relationships between themes and layers to abstract the complicated construction of a musical composition. The visualization has been applied with success in understanding some classical music works as supported by highly promising user study results with the general audience and very positive feedback from music students and experts, demonstrating its effectiveness in conveying the sophistication and beauty of classical music to novice users with informative and intuitive displays.

At the Edge of Translation – Materials to Program Cells for Directed Differentiation

PubMed Central

Arany, Praveen R; Mooney, David J

2010-01-01

The rapid advancement in basic biology knowledge, especially in the stem cell field, has created new opportunities to develop biomaterials capable of orchestrating the behavior of transplanted and host cells. Based on our current understanding of cellular differentiation, a conceptual framework for the use of materials to program cells in situ is presented, namely a domino versus a switchboard model, to highlight the use of single versus multiple cues in a controlled manner to modulate biological processes. Further, specific design principles of material systems to present soluble and insoluble cues that are capable of recruiting, programming and deploying host cells for various applications are presented. The evolution of biomaterials from simple inert substances used to fill defects, to the recent development of sophisticated material systems capable of programming cells in situ is providing a platform to translate our understanding of basic biological mechanisms to clinical care. PMID:20860763

Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae.

PubMed

Kobayashi, Junya; Matsuura, Yoshiyuki

2017-10-01

In the budding yeast Saccharomyces cerevisiae, the protein phosphatase Cdc14p orchestrates various events essential for mitotic exit. We have determined the X-ray crystal structures at 1.85 Å resolution of the catalytic domain of Cdc14p in both the apo state, and as a complex with S160-phosphorylated Swi6p peptide. Each asymmetric unit contains two Cdc14p chains arranged in an intimately associated homodimer, consistent with its oligomeric state in solution. The dimerization interface is located on the backside of the substrate-binding cleft. Structure-based mutational analyses indicate that the dimerization of Cdc14p is required for normal growth of yeast cells. © 2017 The Protein Society.

RNA Structures as Mediators of Neurological Diseases and as Drug Targets.

PubMed

Bernat, Viachaslau; Disney, Matthew D

2015-07-01

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish

PubMed Central

Kratochwil, Claudius F.; Geissler, Laura; Irisarri, Iker; Meyer, Axel

2015-01-01

Abstract Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates. PMID:26475317

Inter-Cellular Forces Orchestrate Contact Inhibition of Locomotion

PubMed Central

Davis, John R.; Luchici, Andrei; Mosis, Fuad; Thackery, James; Salazar, Jesus A.; Mao, Yanlan; Dunn, Graham A.; Betz, Timo; Miodownik, Mark; Stramer, Brian M.

2015-01-01

Summary Contact inhibition of locomotion (CIL) is a multifaceted process that causes many cell types to repel each other upon collision. During development, this seemingly uncoordinated reaction is a critical driver of cellular dispersion within embryonic tissues. Here, we show that Drosophila hemocytes require a precisely orchestrated CIL response for their developmental dispersal. Hemocyte collision and subsequent repulsion involves a stereotyped sequence of kinematic stages that are modulated by global changes in cytoskeletal dynamics. Tracking actin retrograde flow within hemocytes in vivo reveals synchronous reorganization of colliding actin networks through engagement of an inter-cellular adhesion. This inter-cellular actin-clutch leads to a subsequent build-up in lamellar tension, triggering the development of a transient stress fiber, which orchestrates cellular repulsion. Our findings reveal that the physical coupling of the flowing actin networks during CIL acts as a mechanotransducer, allowing cells to haptically sense each other and coordinate their behaviors. PMID:25799385

A Hardware-Supported Algorithm for Self-Managed and Choreographed Task Execution in Sensor Networks.

PubMed

Bordel, Borja; Miguel, Carlos; Alcarria, Ramón; Robles, Tomás

2018-03-07

Nowadays, sensor networks are composed of a great number of tiny resource-constraint nodes, whose management is increasingly more complex. In fact, although collaborative or choreographic task execution schemes are which fit in the most perfect way with the nature of sensor networks, they are rarely implemented because of the high resource consumption of these algorithms (especially if networks include many resource-constrained devices). On the contrary, hierarchical networks are usually designed, in whose cusp it is included a heavy orchestrator with a remarkable processing power, being able to implement any necessary management solution. However, although this orchestration approach solves most practical management problems of sensor networks, a great amount of the operation time is wasted while nodes request the orchestrator to address a conflict and they obtain the required instructions to operate. Therefore, in this paper it is proposed a new mechanism for self-managed and choreographed task execution in sensor networks. The proposed solution considers only a lightweight gateway instead of traditional heavy orchestrators and a hardware-supported algorithm, which consume a negligible amount of resources in sensor nodes. The gateway avoids the congestion of the entire sensor network and the hardware-supported algorithm enables a choreographed task execution scheme, so no particular node is overloaded. The performance of the proposed solution is evaluated through numerical and electronic ModelSim-based simulations.

A Hardware-Supported Algorithm for Self-Managed and Choreographed Task Execution in Sensor Networks

PubMed Central

2018-01-01

Nowadays, sensor networks are composed of a great number of tiny resource-constraint nodes, whose management is increasingly more complex. In fact, although collaborative or choreographic task execution schemes are which fit in the most perfect way with the nature of sensor networks, they are rarely implemented because of the high resource consumption of these algorithms (especially if networks include many resource-constrained devices). On the contrary, hierarchical networks are usually designed, in whose cusp it is included a heavy orchestrator with a remarkable processing power, being able to implement any necessary management solution. However, although this orchestration approach solves most practical management problems of sensor networks, a great amount of the operation time is wasted while nodes request the orchestrator to address a conflict and they obtain the required instructions to operate. Therefore, in this paper it is proposed a new mechanism for self-managed and choreographed task execution in sensor networks. The proposed solution considers only a lightweight gateway instead of traditional heavy orchestrators and a hardware-supported algorithm, which consume a negligible amount of resources in sensor nodes. The gateway avoids the congestion of the entire sensor network and the hardware-supported algorithm enables a choreographed task execution scheme, so no particular node is overloaded. The performance of the proposed solution is evaluated through numerical and electronic ModelSim-based simulations. PMID:29518986

Evolving marine biomimetics for regenerative dentistry.

PubMed

Green, David W; Lai, Wing-Fu; Jung, Han-Sung

2014-05-13

New products that help make human tissue and organ regeneration more effective are in high demand and include materials, structures and substrates that drive cell-to-tissue transformations, orchestrate anatomical assembly and tissue integration with biology. Marine organisms are exemplary bioresources that have extensive possibilities in supporting and facilitating development of human tissue substitutes. Such organisms represent a deep and diverse reserve of materials, substrates and structures that can facilitate tissue reconstruction within lab-based cultures. The reason is that they possess sophisticated structures, architectures and biomaterial designs that are still difficult to replicate using synthetic processes, so far. These products offer tantalizing pre-made options that are versatile, adaptable and have many functions for current tissue engineers seeking fresh solutions to the deficiencies in existing dental biomaterials, which lack the intrinsic elements of biofunctioning, structural and mechanical design to regenerate anatomically correct dental tissues both in the culture dish and in vivo.

Evolving Marine Biomimetics for Regenerative Dentistry

PubMed Central

Green, David W.; Lai, Wing-Fu; Jung, Han-Sung

2014-01-01

New products that help make human tissue and organ regeneration more effective are in high demand and include materials, structures and substrates that drive cell-to-tissue transformations, orchestrate anatomical assembly and tissue integration with biology. Marine organisms are exemplary bioresources that have extensive possibilities in supporting and facilitating development of human tissue substitutes. Such organisms represent a deep and diverse reserve of materials, substrates and structures that can facilitate tissue reconstruction within lab-based cultures. The reason is that they possess sophisticated structures, architectures and biomaterial designs that are still difficult to replicate using synthetic processes, so far. These products offer tantalizing pre-made options that are versatile, adaptable and have many functions for current tissue engineers seeking fresh solutions to the deficiencies in existing dental biomaterials, which lack the intrinsic elements of biofunctioning, structural and mechanical design to regenerate anatomically correct dental tissues both in the culture dish and in vivo. PMID:24828293

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

PubMed Central

Sheng, Gang; Zhao, Hongtu; Wang, Jiuyu; Rao, Yu; Tian, Wenwen; Swarts, Daan C.; van der Oost, John; Patel, Dinshaw J.; Wang, Yanli

2014-01-01

We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5′-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand. PMID:24374628

AP-2α and AP-2β cooperatively orchestrate homeobox gene expression during branchial arch patterning.

PubMed

Van Otterloo, Eric; Li, Hong; Jones, Kenneth L; Williams, Trevor

2018-01-25

The evolution of a hinged moveable jaw with variable morphology is considered a major factor behind the successful expansion of the vertebrates. DLX homeobox transcription factors are crucial for establishing the positional code that patterns the mandible, maxilla and intervening hinge domain, but how the genes encoding these proteins are regulated remains unclear. Herein, we demonstrate that the concerted action of the AP-2α and AP-2β transcription factors within the mouse neural crest is essential for jaw patterning. In the absence of these two proteins, the hinge domain is lost and there are alterations in the size and patterning of the jaws correlating with dysregulation of homeobox gene expression, with reduced levels of Emx, Msx and Dlx paralogs accompanied by an expansion of Six1 expression. Moreover, detailed analysis of morphological features and gene expression changes indicate significant overlap with various compound Dlx gene mutants. Together, these findings reveal that the AP-2 genes have a major function in mammalian neural crest development, influencing patterning of the craniofacial skeleton via the DLX code, an effect that has implications for vertebrate facial evolution, as well as for human craniofacial disorders. © 2018. Published by The Company of Biologists Ltd.

Frogs as integrative models for understanding digestive organ development and evolution.

PubMed

Womble, Mandy; Pickett, Melissa; Nascone-Yoder, Nanette

2016-03-01

The digestive system comprises numerous cells, tissues and organs that are essential for the proper assimilation of nutrients and energy. Many aspects of digestive organ function are highly conserved among vertebrates, yet the final anatomical configuration of the gut varies widely between species, especially those with different diets. Improved understanding of the complex molecular and cellular events that orchestrate digestive organ development is pertinent to many areas of biology and medicine, including the regeneration or replacement of diseased organs, the etiology of digestive organ birth defects, and the evolution of specialized features of digestive anatomy. In this review, we highlight specific examples of how investigations using Xenopus laevis frog embryos have revealed insight into the molecular and cellular dynamics of digestive organ patterning and morphogenesis that would have been difficult to obtain in other animal models. Additionally, we discuss recent studies of gut development in non-model frog species with unique feeding strategies, such as Lepidobatrachus laevis and Eleutherodactylous coqui, which are beginning to provide glimpses of the evolutionary mechanisms that may generate morphological variation in the digestive tract. The unparalleled experimental versatility of frog embryos make them excellent, integrative models for studying digestive organ development across multiple disciplines. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

PubMed Central

Baslé, Arnaud; Gray, Joseph; Venditto, Immacolata; Briggs, Jonathon; Zhang, Xiaoyang; Labourel, Aurore; Terrapon, Nicolas; Buffetto, Fanny; Nepogodiev, Sergey; Xiao, Yao; Field, Robert A.; Zhu, Yanping; O’Neil, Malcolm A.; Urbanowicz, Breeana R.; York, William S.; Davies, Gideon J.; Abbott, D. Wade; Ralet, Marie-Christine; Martens, Eric C.; Henrissat, Bernard; Gilbert, Harry J.

2017-01-01

Carbohydrate polymers drive microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron utilizes the most structurally complex glycan known; the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but one of its 21 distinct glycosidic linkages. We show that rhamnogalacturonan-II side-chain and backbone deconstruction are coordinated, to overcome steric constraints, and that degradation reveals previously undiscovered enzyme families and novel catalytic activities. The degradome informs revision of the current structural model of RG-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycans in the human diet. PMID:28329766

Jasmonate-triggered plant immunity.

PubMed

Campos, Marcelo L; Kang, Jin-Ho; Howe, Gregg A

2014-07-01

The plant hormone jasmonate (JA) exerts direct control over the production of chemical defense compounds that confer resistance to a remarkable spectrum of plant-associated organisms, ranging from microbial pathogens to vertebrate herbivores. The underlying mechanism of JA-triggered immunity (JATI) can be conceptualized as a multi-stage signal transduction cascade involving: i) pattern recognition receptors (PRRs) that couple the perception of danger signals to rapid synthesis of bioactive JA; ii) an evolutionarily conserved JA signaling module that links fluctuating JA levels to changes in the abundance of transcriptional repressor proteins; and iii) activation (de-repression) of transcription factors that orchestrate the expression of myriad chemical and morphological defense traits. Multiple negative feedback loops act in concert to restrain the duration and amplitude of defense responses, presumably to mitigate potential fitness costs of JATI. The convergence of diverse plant- and non-plant-derived signals on the core JA module indicates that JATI is a general response to perceived danger. However, the modular structure of JATI may accommodate attacker-specific defense responses through evolutionary innovation of PRRs (inputs) and defense traits (outputs). The efficacy of JATI as a defense strategy is highlighted by its capacity to shape natural populations of plant attackers, as well as the propensity of plant-associated organisms to subvert or otherwise manipulate JA signaling. As both a cellular hub for integrating informational cues from the environment and a common target of pathogen effectors, the core JA module provides a focal point for understanding immune system networks and the evolution of chemical diversity in the plant kingdom.

Glycans: bioactive signals decoded by lectins.

PubMed

Gabius, Hans-Joachim

2008-12-01

The glycan part of cellular glycoconjugates affords a versatile means to build biochemical signals. These oligosaccharides have an exceptional talent in this respect. They surpass any other class of biomolecule in coding capacity within an oligomer (code word). Four structural factors account for this property: the potential for variability of linkage points, anomeric position and ring size as well as the aptitude for branching (first and second dimensions of the sugar code). Specific intermolecular recognition is favoured by abundant potential for hydrogen/co-ordination bonds and for C-H/pi-interactions. Fittingly, an array of protein folds has developed in evolution with the ability to select certain glycans from the natural diversity. The thermodynamics of this reaction profits from the occurrence of these ligands in only a few energetically favoured conformers, comparing favourably with highly flexible peptides (third dimension of the sugar code). Sequence, shape and local aspects of glycan presentation (e.g. multivalency) are key factors to regulate the avidity of lectin binding. At the level of cells, distinct glycan determinants, a result of enzymatic synthesis and dynamic remodelling, are being defined as biomarkers. Their presence gains a functional perspective by co-regulation of the cognate lectin as effector, for example in growth regulation. The way to tie sugar signal and lectin together is illustrated herein for two tumour model systems. In this sense, orchestration of glycan and lectin expression is an efficient means, with far-reaching relevance, to exploit the coding potential of oligosaccharides physiologically and medically.

Orchestration: The Movement and Vocal Behavior of Free-Ranging Norwegian Killer Whales (Orcinus Orca)

DTIC Science & Technology

2008-06-01

MIT/WHOI 2008-08 Massachusetts Institute of Technology Woods Hole Oceanographic Institution 0" joint Program in Oceanography/ 0 OFTtcy Applied Ocean...Biology Paola Malanotte-Rizzoli James A. Yoder MIT Director of Joint Program WHOI Dean of Graduate Studies ORCHESTRATION: THE MOVEMENT AND VOCAL BEHAVIOR...Steve Young and Syd Lewis, have mentored and believed in me, a gift that I cherish. Stacy DeRuiter and I have been labmates since we began the Joint

Inter-cellular forces orchestrate contact inhibition of locomotion.

PubMed

Davis, John R; Luchici, Andrei; Mosis, Fuad; Thackery, James; Salazar, Jesus A; Mao, Yanlan; Dunn, Graham A; Betz, Timo; Miodownik, Mark; Stramer, Brian M

2015-04-09

Contact inhibition of locomotion (CIL) is a multifaceted process that causes many cell types to repel each other upon collision. During development, this seemingly uncoordinated reaction is a critical driver of cellular dispersion within embryonic tissues. Here, we show that Drosophila hemocytes require a precisely orchestrated CIL response for their developmental dispersal. Hemocyte collision and subsequent repulsion involves a stereotyped sequence of kinematic stages that are modulated by global changes in cytoskeletal dynamics. Tracking actin retrograde flow within hemocytes in vivo reveals synchronous reorganization of colliding actin networks through engagement of an inter-cellular adhesion. This inter-cellular actin-clutch leads to a subsequent build-up in lamellar tension, triggering the development of a transient stress fiber, which orchestrates cellular repulsion. Our findings reveal that the physical coupling of the flowing actin networks during CIL acts as a mechanotransducer, allowing cells to haptically sense each other and coordinate their behaviors. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Complexity of Danger: The Diverse Nature of Damage-associated Molecular Patterns*

PubMed Central

Schaefer, Liliana

2014-01-01

In reply to internal or external danger stimuli, the body orchestrates an inflammatory response. The endogenous triggers of this process are the damage-associated molecular patterns (DAMPs). DAMPs represent a heterogeneous group of molecules that draw their origin either from inside the various compartments of the cell or from the extracellular space. Following interaction with pattern recognition receptors in cross-talk with various non-immune receptors, DAMPs determine the downstream signaling outcome of septic and aseptic inflammatory responses. In this review, the diverse nature, structural characteristics, and signaling pathways elicited by DAMPs will be critically evaluated. PMID:25391648

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

PubMed Central

Bebel, Aleksandra; Karaca, Ezgi; Kumar, Banushree; Stark, W Marshall; Barabas, Orsolya

2016-01-01

Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division. DOI: http://dx.doi.org/10.7554/eLife.19706.001 PMID:28009253

Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

PubMed

Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

2017-03-07

Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Windows Terminal Servers Orchestration

NASA Astrophysics Data System (ADS)

Bukowiec, Sebastian; Gaspar, Ricardo; Smith, Tim

2017-10-01

Windows Terminal Servers provide application gateways for various parts of the CERN accelerator complex, used by hundreds of CERN users every day. The combination of new tools such as Puppet, HAProxy and Microsoft System Center suite enable automation of provisioning workflows to provide a terminal server infrastructure that can scale up and down in an automated manner. The orchestration does not only reduce the time and effort necessary to deploy new instances, but also facilitates operations such as patching, analysis and recreation of compromised nodes as well as catering for workload peaks.

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

PubMed

Chen, Chun-Kan; Blanco, Mario; Jackson, Constanza; Aznauryan, Erik; Ollikainen, Noah; Surka, Christine; Chow, Amy; Cerase, Andrea; McDonel, Patrick; Guttman, Mitchell

2016-10-28

The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription. Copyright © 2016, American Association for the Advancement of Science.

Microtubules move the nucleus to quiescence.

PubMed

Laporte, Damien; Sagot, Isabelle

2014-01-01

The nucleus is a cellular compartment that hosts several macro-molecular machines displaying a highly complex spatial organization. This tight architectural orchestration determines not only DNA replication and repair but also regulates gene expression. In budding yeast microtubules play a key role in structuring the nucleus since they condition the Rabl arrangement in G1 and chromosome partitioning during mitosis through their attachment to centromeres via the kinetochore proteins. Recently, we have shown that upon quiescence entry, intranuclear microtubules emanating from the spindle pole body elongate to form a highly stable bundle that spans the entire nucleus. Here, we examine some molecular mechanisms that may underlie the formation of this structure. As the intranuclear microtubule bundle causes a profound re-organization of the yeast nucleus and is required for cell survival during quiescence, we discuss the possibility that the assembly of such a structure participates in quiescence establishment.

Architectural Analysis of Systems Based on the Publisher-Subscriber Style

NASA Technical Reports Server (NTRS)

Ganesun, Dharmalingam; Lindvall, Mikael; Ruley, Lamont; Wiegand, Robert; Ly, Vuong; Tsui, Tina

2010-01-01

Architectural styles impose constraints on both the topology and the interaction behavior of involved parties. In this paper, we propose an approach for analyzing implemented systems based on the publisher-subscriber architectural style. From the style definition, we derive a set of reusable questions and show that some of them can be answered statically whereas others are best answered using dynamic analysis. The paper explains how the results of static analysis can be used to orchestrate dynamic analysis. The proposed method was successfully applied on the NASA's Goddard Mission Services Evolution Center (GMSEC) software product line. The results show that the GMSEC has a) a novel reusable vendor-independent middleware abstraction layer that allows the NASA's missions to configure the middleware of interest without changing the publishers' or subscribers' source code, and b) some high priority bugs due to behavioral discrepancies, which were eluded during testing and code reviews, among different implementations of the same APIs for different vendors.

Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a.

PubMed

Yelin-Bekerman, Laura; Elbaz, Idan; Diber, Alex; Dahary, Dvir; Gibbs-Bar, Liron; Alon, Shahar; Lerer-Goldshtein, Tali; Appelbaum, Lior

2015-10-01

Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron-specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron-specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a(-/-)) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.

Human breast milk: A review on its composition and bioactivity.

PubMed

Andreas, Nicholas J; Kampmann, Beate; Mehring Le-Doare, Kirsty

2015-11-01

Breast milk is the perfect nutrition for infants, a result of millions of years of evolution, finely attuning it to the requirements of the infant. Breast milk contains many complex proteins, lipids and carbohydrates, the concentrations of which alter dramatically over a single feed, as well as over lactation, to reflect the infant's needs. In addition to providing a source of nutrition for infants, breast milk contains a myriad of biologically active components. These molecules possess diverse roles, both guiding the development of the infants immune system and intestinal microbiota. Orchestrating the development of the microbiota are the human milk oligosaccharides, the synthesis of which are determined by the maternal genotype. In this review, we discuss the composition of breast milk and the factors that affect it during the course of breast feeding. Understanding the components of breast milk and their functions will allow for the improvement of clinical practices, infant feeding and our understanding of immune responses to infection and vaccination in infants. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

SIGNALS AND REGULATORS THAT GOVERN STREPTOMYCES DEVELOPMENT

PubMed Central

McCormick, Joseph R.; Flärdh, Klas

2012-01-01

Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the Gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex, and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae, first to form specialized aerial hyphae, and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from “-omics” studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve. PMID:22092088

Concurrent Timbres in Orchestration: a Perceptual Study of Factors Determining "blend"

NASA Astrophysics Data System (ADS)

Sandell, Gregory John

Orchestration often involves selecting instruments for concurrent presentation, as in melodic doubling or chords. One evaluation of the aural outcome of such choices is along the continuum of "blend": whether the instruments fuse into a single composite timbre, segregate into distinct timbral entities, or fall somewhere in between the two extremes. This study investigates, through perceptual experimentation, the acoustical correlates of blend for 15 natural-sounding orchestral instruments presented in concurrently-sounding pairs (e.g. flute-cello, trumpet -oboe, etc.). Ratings of blend showed primary effects for centroid (the location of the midpoint of the spectral energy distribution) and duration of the onset for the tones. Lower average values of both centroid and onset duration for a pair of tones led to increased blends, as did closeness in value for the two factors. Blend decreased (instruments segregated) with higher average values or increased difference in value for the two factors. The musical interval of presentation slightly affected the relative importance of these two mechanisms, with unison intervals determined more by lower average centroid, and minor thirds determined more by closeness in centroid. The contribution of onset in general was slightly more pronounced in the unison conditions than in the minor third condition. Additional factors contributing to blend were correlation of amplitude and centroid envelopes (blend increased as temporal patterns rose and fell in synchrony) and similarity in the overall amount of fundamental frequency perturbation (decreased blend with increasing jitter from both tones). To confirm the importance of centroid as an independent factor determining blend, pairs of tones including instruments with artificially changed centroids were rated for blend. Judgments for several versions of the same instrument pair showed that blend decreased as the altered instrument increased in centroid, corroborating the earlier experiments. Other factors manipulated were amplitude level and the degree of inharmonicity. A survey of orchestration manuals showed many illustrations of "blending" combinations of instruments that were consistent with the results of these experiments. This study's acoustically-based guidelines for blend augment instance-based methods of traditional orchestration teaching, providing underlying abstractions helpful for evaluating the blend of arbitrary combinations of instruments.

Meteorological phenomena in Western classical orchestral music

NASA Astrophysics Data System (ADS)

Williams, P. D.; Aplin, K. L.

2012-12-01

The creative output of composers, writers, and artists is often influenced by their surroundings. To give a literary example, it has been claimed recently that some of the characters in Oliver Twist and A Christmas Carol were based on real-life people who lived near Charles Dickens in London. Of course, an important part of what we see and hear is not only the people with whom we interact, but also our geophysical surroundings. Of all the geophysical phenomena to influence us, the weather is arguably the most significant, because we are exposed to it directly and daily. The weather was a great source of inspiration for Monet, Constable, and Turner, who are known for their scientifically accurate paintings of the skies. But to what extent does weather inspire composers? The authors of this presentation, who are atmospheric scientists by day but amateur classical musicians by night, have been contemplating this question. We have built a systematic musical database, which has allowed us to catalogue and analyze the frequencies with which weather is depicted in a sample of classical orchestral music. The depictions vary from explicit mimicry using traditional and specialized orchestral instruments, through to subtle suggestions. We have found that composers are generally influenced by their own environment in the type of weather they choose to represent. As befits the national stereotype, British composers seem disproportionately keen to depict the UK's variable weather patterns and stormy coastline. Reference: Aplin KL and Williams PD (2011) Meteorological phenomena in Western classical orchestral music. Weather, 66(11), pp 300-306. doi:10.1002/wea.765

Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.

PubMed

Ren, Zhong

2016-09-06

DNA polymerases in family B are workhorses of DNA replication that carry out the bulk of the job at a high speed with high accuracy. A polymerase in this family relies on a built-in exonuclease for proofreading. It has not been observed at the atomic resolution how the polymerase advances one nucleotide space on the DNA template strand after a correct nucleotide is incorporated, that is, a process known as translocation. It is even more puzzling how translocation is avoided after the primer strand is excised by the exonuclease and returned back to the polymerase active site once an error occurs. The structural events along the bifurcate pathways of translocation and proofreading have been unwittingly captured by hundreds of structures in Protein Data Bank. This study analyzes all available structures of a representative member in family B and reveals the orchestrated event sequence during translocation and proofreading. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Anticipating students' reasoning and planning prompts in structured problem-solving lessons

NASA Astrophysics Data System (ADS)

Vale, Colleen; Widjaja, Wanty; Doig, Brian; Groves, Susie

2018-02-01

Structured problem-solving lessons are used to explore mathematical concepts such as pattern and relationships in early algebra, and regularly used in Japanese Lesson Study research lessons. However, enactment of structured problem-solving lessons which involves detailed planning, anticipation of student solutions and orchestration of whole-class discussion of solutions is an ongoing challenge for many teachers. Moreover, primary teachers have limited experience in teaching early algebra or mathematical reasoning actions such as generalising. In this study, the critical factors of enacting the structured problem-solving lessons used in Japanese Lesson Study to elicit and develop primary students' capacity to generalise are explored. Teachers from three primary schools participated in two Japanese Lesson Study teams for this study. The lesson plans and video recordings of teaching and post-lesson discussion of the two research lessons along with students' responses and learning are compared to identify critical factors. The anticipation of students' reasoning together with preparation of supporting and challenging prompts was critical for scaffolding students' capacity to grasp and communicate generality.

Milk—A Nutrient System of Mammalian Evolution Promoting mTORC1-Dependent Translation

PubMed Central

Melnik, Bodo C.

2015-01-01

Based on own translational research of the biochemical and hormonal effects of cow’s milk consumption in humans, this review presents milk as a signaling system of mammalian evolution that activates the nutrient-sensitive kinase mechanistic target of rapamycin complex 1 (mTORC1), the pivotal regulator of translation. Milk, a mammary gland-derived secretory product, is required for species-specific gene-nutrient interactions that promote appropriate growth and development of the newborn mammal. This signaling system is highly conserved and tightly controlled by the lactation genome. Milk is sufficient to activate mTORC1, the crucial regulator of protein, lipid, and nucleotide synthesis orchestrating anabolism, cell growth and proliferation. To fulfill its mTORC1-activating function, milk delivers four key metabolic messengers: (1) essential branched-chain amino acids (BCAAs); (2) glutamine; (3) palmitic acid; and (4) bioactive exosomal microRNAs, which in a synergistical fashion promote mTORC1-dependent translation. In all mammals except Neolithic humans, postnatal activation of mTORC1 by milk intake is restricted to the postnatal lactation period. It is of critical concern that persistent hyperactivation of mTORC1 is associated with aging and the development of age-related disorders such as obesity, type 2 diabetes mellitus, cancer, and neurodegenerative diseases. Persistent mTORC1 activation promotes endoplasmic reticulum (ER) stress and drives an aimless quasi-program, which promotes aging and age-related diseases. PMID:26225961

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

NASA Technical Reports Server (NTRS)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

Information Integration and Communication in Plant Growth Regulation.

PubMed

Chaiwanon, Juthamas; Wang, Wenfei; Zhu, Jia-Ying; Oh, Eunkyoo; Wang, Zhi-Yong

2016-03-10

Plants are equipped with the capacity to respond to a large number of diverse signals, both internal ones and those emanating from the environment, that are critical to their survival and adaption as sessile organisms. These signals need to be integrated through highly structured intracellular networks to ensure coherent cellular responses, and in addition, spatiotemporal actions of hormones and peptides both orchestrate local cell differentiation and coordinate growth and physiology over long distances. Further, signal interactions and signaling outputs vary significantly with developmental context. This review discusses our current understanding of the integrated intracellular and intercellular signaling networks that control plant growth. Copyright © 2016 Elsevier Inc. All rights reserved.

Regulation of dendritic cell function through toll-like receptors.

PubMed

Kaisho, Tsuneyasu; Akira, Shizuo

2003-12-01

Higher animals establish host defense by orchestrating innate and adaptive immunity. This is mediated by professional antigen presenting cells, i.e. dendritic cells (DCs). DCs can incorporate pathogens, produce a variety of cytokines, maturate, and present pathogen-derived peptides to T cells, thereby inducing T cell activation and differentiation. These responses are triggered by microbial recognition through type I transmembrane proteins, Toll-like receptors (TLRs) on DCs. TLRs consist of ten members and each TLR is involved in recognizing a variety of microorganism-derived molecular structures. TLR ligands include cell wall components, proteins, nucleic acids, and synthetic chemical compounds, all of which can activate DCs as immune adjuvants.

On the road to bioartificial organs.

PubMed

Ren, X; Ott, H C

2014-10-01

Biological organs are highly orchestrated systems with well-coordinated positioning, grouping, and interaction of different cell types within their specialized extracellular environment. Bioartificial organs are intended to be functional replacements of native organs generated through bioengineering techniques and hold the potential to alleviate donor organ shortage for transplantation. The development, production, and evaluation of such bioartificial organs require synergistic efforts of biology, material science, engineering, and medicine. In this review, we highlight the emerging platforms enabling structured assembly of multiple cell types into functional grafts and discuss recent advances and challenges in the development of bioartificial organs, including cell sources, in vitro organ culture, in vivo evaluation, and clinical considerations.

Information Integration and Communication in Plant Growth Regulation

PubMed Central

Chaiwanon, Juthamas; Wang, Wenfei; Zhu, Jia-Ying; Oh, Eunkyoo; Wang, Zhi-Yong

2016-01-01

Plants are equipped with the capacity to respond to a large number of diverse signals, both internal ones and those emanating from the environment, that are critical to their survival and adaption as sessile organisms. These signals need to be integrated through highly structured intracellular networks to ensure coherent cellular responses, and in addition, spatiotemporal actions of hormones and peptides both orchestrate local cell differentiation and coordinate growth and physiology over long distances. Further, signal interactions and signaling outputs vary significantly with developmental context. This review discusses our current understanding of the integrated intracellular and intercellular signaling networks that control plant growth. PMID:26967291

Switching of the substrate specificity of protein tyrosine phosphatase N12 by cyclin-dependent kinase 2 phosphorylation orchestrating 2 oncogenic pathways.

PubMed

Li, Hui; Yang, Duxiao; Ning, Shanglei; Xu, Yinghui; Yang, Fan; Yin, Rusha; Feng, Taihu; Han, Shouqing; Guo, Lu; Zhang, Pengju; Qu, Wenjie; Guo, Renbo; Song, Chen; Xiao, Peng; Zhou, Chengjun; Xu, Zhigang; Sun, Jin-Peng; Yu, Xiao

2018-01-01

The protein tyrosine phosphatase nonreceptor type 12 (PTPN12) is a multifunctional protein and has elicited much research attention because its decreased protein level has been associated with poor prognosis of several types of cancers. Recently, we have solved the crystal structure of the phosphatase domain of PTPN12, which disclosed a specific PTPN12-insert-loop harboring a cyclin-dependent kinase 2 (CDK2) phosphorylation site. However, the functional significance of this phosphorylation is undefined. In the present study, we found that S19 site phosphorylation of PTPN12 by CDK2 discharged its antitumor activity by down-regulation of its inhibitory role in cell migration, but not affecting its other regulatory functions. Phosphorylation of PTPN12 at the S19 site changed its substrate interface, and by doing so, selectively decreased its activity toward the human epidermal growth factor receptor 2 (HER2)- pY 1196 site, but not other HER2 phosphorylation sites or other known PTPN12 substrates. A further in-depth mechanism study revealed that the phosphorylation of PTPN12 by CDK2 impaired recruitment of the serine/threonine-protein kinase 1 (PAK1) to HER2, resulted in the blockade of the HER2-pY 1196 -PAK1-T 423 signaling pathway, thus increased tumor cell motility. Taken together, our results identified a new phosphorylation-based substrate recognition mechanism of PTPN12 by CDK2, which orchestrated signaling crosstalk between the oncogenic CDK2 and HER2 pathways. The newly identified governing mechanism of the substrate selectivity of a particular phosphatase was previously unappreciated and exemplifies how a phospho-network is precisely controlled in different cellular contexts.-Li, H., Yang, D., Ning, S., Xu, Y., Yang, F., Yin, R., Feng, T., Han, S., Guo, L., Zhang, P., Qu, W., Guo, R., Song, C., Xiao, P., Zhou, C., Xu, Z., Sun, J.-P., Yu, X. Switching of the substrate specificity of protein tyrosine phosphatase N12 by cyclin-dependent kinase 2 phosphorylation orchestrating 2 oncogenic pathways. © FASEB.

Supporting Collective Inquiry: A Technology Framework for Distributed Learning

NASA Astrophysics Data System (ADS)

Tissenbaum, Michael

This design-based study describes the implementation and evaluation of a technology framework to support smart classrooms and Distributed Technology Enhanced Learning (DTEL) called SAIL Smart Space (S3). S3 is an open-source technology framework designed to support students engaged in inquiry investigations as a knowledge community. To evaluate the effectiveness of S3 as a generalizable technology framework, a curriculum named PLACE (Physics Learning Across Contexts and Environments) was developed to support two grade-11 physics classes (n = 22; n = 23) engaged in a multi-context inquiry curriculum based on the Knowledge Community and Inquiry (KCI) pedagogical model. This dissertation outlines three initial design studies that established a set of design principles for DTEL curricula, and related technology infrastructures. These principles guided the development of PLACE, a twelve-week inquiry curriculum in which students drew upon their community-generated knowledge base as a source of evidence for solving ill-structured physics problems based on the physics of Hollywood movies. During the culminating smart classroom activity, the S3 framework played a central role in orchestrating student activities, including managing the flow of materials and students using real-time data mining and intelligent agents that responded to emergent class patterns. S3 supported students' construction of knowledge through the use individual, collective and collaborative scripts and technologies, including tablets and interactive large-format displays. Aggregate and real-time ambient visualizations helped the teacher act as a wondering facilitator, supporting students in their inquiry where needed. A teacher orchestration tablet gave the teacher some control over the flow of the scripted activities, and alerted him to critical moments for intervention. Analysis focuses on S3's effectiveness in supporting students' inquiry across multiple learning contexts and scales of time, and in making timely and effective use of the community's knowledge base, towards producing solutions to sophisticated, ill defined problems in the domain of physics. Video analysis examined whether S3 supported teacher orchestration, freeing him to focus less on classroom management and more on students' inquiry. Three important outcomes of this research are a set of design principles for DTEL environments, a specific technology infrastructure (S3), and a DTEL research framework.

Evolution in Stage-Structured Populations

PubMed Central

Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

2016-01-01

For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

PubMed Central

de los Reyes, Pedro; Romero-Campero, Francisco J.; Ruiz, M. Teresa; Romero, José M.; Valverde, Federico

2017-01-01

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions. PMID:28751903

Orchestrating care: nursing practice with hospitalised older adults.

PubMed

Dahlke, Sherry Ann; Phinney, Alison; Hall, Wendy Ann; Rodney, Patricia; Baumbusch, Jennifer

2015-12-01

The increased incidence of health challenges with aging means that nurses are increasingly caring for older adults, often in hospital settings. Research about the complexity of nursing practice with this population remains limited. To seek an explanation of nursing practice with hospitalised older adults. Design. A grounded theory study guided by symbolic interactionism was used to explore nursing practice with hospitalised older adults from a nursing perspective. Glaserian grounded theory methods were used to develop a mid-range theory after analysis of 375 hours of participant observation, 35 interviews with 24 participants and review of selected documents. The theory of orchestrating care was developed to explain how nurses are continuously trying to manage their work environments by understanding the status of the patients, their unit, mobilising the assistance of others and stretching available resources to resolve their problem of providing their older patients with what they perceived as 'good care' while sustaining themselves as 'good' nurses. They described their practice environments as hard and under-resourced. Orchestrating care is comprised of two subprocesses: building synergy and minimising strain. These two processes both facilitated and constrained each other and nurses' abilities to orchestrate care. Although system issues presented serious constraints to nursing practice, the ways in which nurses were making meaning of their work environment both aided them in managing their challenges and constrained their agency. Nurses need to be encouraged to share their important perspective about older adult care. Administrators have a role to play in giving nurses voice in workplace committees and in forums. Further research is needed to better understand how multidisciplinary teams influence care of hospitalized older adults. © 2014 John Wiley & Sons Ltd.

Abstracting application deployment on Cloud infrastructures

NASA Astrophysics Data System (ADS)

Aiftimiei, D. C.; Fattibene, E.; Gargana, R.; Panella, M.; Salomoni, D.

2017-10-01

Deploying a complex application on a Cloud-based infrastructure can be a challenging task. In this contribution we present an approach for Cloud-based deployment of applications and its present or future implementation in the framework of several projects, such as “!CHAOS: a cloud of controls” [1], a project funded by MIUR (Italian Ministry of Research and Education) to create a Cloud-based deployment of a control system and data acquisition framework, “INDIGO-DataCloud” [2], an EC H2020 project targeting among other things high-level deployment of applications on hybrid Clouds, and “Open City Platform”[3], an Italian project aiming to provide open Cloud solutions for Italian Public Administrations. We considered to use an orchestration service to hide the complex deployment of the application components, and to build an abstraction layer on top of the orchestration one. Through Heat [4] orchestration service, we prototyped a dynamic, on-demand, scalable platform of software components, based on OpenStack infrastructures. On top of the orchestration service we developed a prototype of a web interface exploiting the Heat APIs. The user can start an instance of the application without having knowledge about the underlying Cloud infrastructure and services. Moreover, the platform instance can be customized by choosing parameters related to the application such as the size of a File System or the number of instances of a NoSQL DB cluster. As soon as the desired platform is running, the web interface offers the possibility to scale some infrastructure components. In this contribution we describe the solution design and implementation, based on the application requirements, the details of the development of both the Heat templates and of the web interface, together with possible exploitation strategies of this work in Cloud data centers.

Actin Out: Regulation of the Synaptic Cytoskeleton

PubMed Central

Spence, Erin F.; Soderling, Scott H.

2015-01-01

The small size of dendritic spines belies the elaborate role they play in excitatory synaptic transmission and ultimately complex behaviors. The cytoskeletal architecture of the spine is predominately composed of actin filaments. These filaments, which at first glance might appear simple, are also surprisingly complex. They dynamically assemble into different structures and serve as a platform for orchestrating the elaborate responses of the spine during spinogenesis and experience-dependent plasticity. Multiple mutations associated with human neurodevelopmental and psychiatric disorders involve genes that encode regulators of the synaptic cytoskeleton. A major, unresolved question is how the disruption of specific actin filament structures leads to the onset and progression of complex synaptic and behavioral phenotypes. This review will cover established and emerging mechanisms of actin cytoskeletal remodeling and how this influences specific aspects of spine biology that are implicated in disease. PMID:26453304

Active and passive vibration suppression for space structures

NASA Technical Reports Server (NTRS)

Hyland, David C.

1991-01-01

The relative benefits of passive and active vibration suppression for large space structures (LSS) are discussed. The intent is to sketch the true ranges of applicability of these approaches using previously published technical results. It was found that the distinction between active and passive vibration suppression approaches is not as sharp as might be thought at first. The relative simplicity, reliability, and cost effectiveness touted for passive measures are vitiated by 'hidden costs' bound up with detailed engineering implementation issues and inherent performance limitations. At the same time, reliability and robustness issues are often cited against active control. It is argued that a continuum of vibration suppression measures offering mutually supporting capabilities is needed. The challenge is to properly orchestrate a spectrum of methods to reap the synergistic benefits of combined advanced materials, passive damping, and active control.

The concurrent evolution of cooperation and the population structures that support it.

PubMed

Powers, Simon T; Penn, Alexandra S; Watson, Richard A

2011-06-01

The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

CENP-E Kinesin Interacts with SKAP Protein to Orchestrate Accurate Chromosome Segregation in Mitosis*

PubMed Central

Huang, Yuejia; Wang, Wenwen; Yao, Phil; Wang, Xiwei; Liu, Xing; Zhuang, Xiaoxuan; Yan, Feng; Zhou, Jinhua; Du, Jian; Ward, Tarsha; Zou, Hanfa; Zhang, Jiancun; Fang, Guowei; Ding, Xia; Dou, Zhen; Yao, Xuebiao

2012-01-01

Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochore. Although previous studies show that the mitotic kinesin CENP-E forms a link between attachment of the spindle microtubule to the kinetochore and the mitotic checkpoint signaling cascade, the molecular mechanism underlying dynamic kinetochore-microtubule interactions in mammalian cells remains elusive. Here, we identify a novel interaction between CENP-E and SKAP that functions synergistically in governing dynamic kinetochore-microtubule interactions. SKAP binds to the C-terminal tail of CENP-E in vitro and is essential for an accurate kinetochore-microtubule attachment in vivo. Immunoelectron microscopic analysis indicates that SKAP is a constituent of the kinetochore corona fibers of mammalian centromeres. Depletion of SKAP or CENP-E by RNA interference results in a dramatic reduction of inter-kinetochore tension, which causes chromosome mis-segregation with a prolonged delay in achieving metaphase alignment. Importantly, SKAP binds to microtubules in vitro, and this interaction is synergized by CENP-E. Based on these findings, we propose that SKAP cooperates with CENP-E to orchestrate dynamic kinetochore-microtubule interaction for faithful chromosome segregation. PMID:22110139

TRIO: Burst Buffer Based I/O Orchestration

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

Wang, Teng; Oral, H Sarp; Pritchard, Michael

The growing computing power on leadership HPC systems is often accompanied by ever-escalating failure rates. Checkpointing is a common defensive mechanism used by scientific applications for failure recovery. However, directly writing the large and bursty checkpointing dataset to parallel filesystem can incur significant I/O contention on storage servers. Such contention in turn degrades the raw bandwidth utilization of storage servers and prolongs the average job I/O time of concurrent applications. Recently burst buffer has been proposed as an intermediate layer to absorb the bursty I/O traffic from compute nodes to storage backend. But an I/O orchestration mechanism is still desiredmore » to efficiently move checkpointing data from bursty buffers to storage backend. In this paper, we propose a burst buffer based I/O orchestration framework, named TRIO, to intercept and reshape the bursty writes for better sequential write traffic to storage severs. Meanwhile, TRIO coordinates the flushing orders among concurrent burst buffers to alleviate the contention on storage server bandwidth. Our experimental results reveal that TRIO can deliver 30.5% higher bandwidth and reduce the average job I/O time by 37% on average for data-intensive applications in various checkpointing scenarios.« less

FOXP3 Orchestrates H4K16 Acetylation and H3K4 Tri-Methylation for Activation of Multiple Genes through Recruiting MOF and Causing Displacement of PLU-1

PubMed Central

Katoh, Hiroto; Qin, Zhaohui S.; Liu, Runhua; Wang, Lizhong; Li, Weiquan; Li, Xiangzhi; Wu, Lipeng; Du, Zhanwen; Lyons, Robert; Liu, Chang-Gong; Liu, Xiuping; Dou, Yali; Zheng, Pan; Liu, Yang

2011-01-01

SUMMARY Both H4K16 acetylation and H3K4 tri-methylation are required for gene activation. However, it is still largely unclear how these modifications are orchestrated by transcriptional factors. Here we analyzed the mechanism of the transcriptional activation by FOXP3, an X-linked suppressor of autoimmune diseases and cancers. FOXP3 binds near transcriptional start sites of its target genes. By recruiting MOF and displacing histone H3K4 demethylase PLU-1, FOXP3 increases both H4K16 acetylation and H3K4 tri-methylation at the FOXP3-associated chromatins of multiple FOXP3-activated genes. RNAi-mediated silencing of MOF reduced both gene activation and tumor suppression by FOXP3, while both somatic mutations in clinical cancer samples and targeted mutation of FOXP3 in mouse prostate epithelial disrupted nuclear localization of MOF. Our data demonstrate a pull-push model in which a single transcription factor orchestrates two epigenetic alterations necessary for gene activation and provide a mechanism for somatic inactivation of the FOXP3 protein function in cancer cells. PMID:22152480

Cell-accurate optical mapping across the entire developing heart.

PubMed

Weber, Michael; Scherf, Nico; Meyer, Alexander M; Panáková, Daniela; Kohl, Peter; Huisken, Jan

2017-12-29

Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca 2+ -mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs.

Cell-accurate optical mapping across the entire developing heart

PubMed Central

Meyer, Alexander M; Panáková, Daniela; Kohl, Peter

2017-01-01

Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca2+-mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs. PMID:29286002

Electromagnetic fields as structure-function zeitgebers in biological systems: environmental orchestrations of morphogenesis and consciousness.

PubMed

Rouleau, Nicolas; Dotta, Blake T

2014-01-01

Within a cell system structure dictates function. Any interaction between cells, or a cell and its environment, has the potential to have long term implications on the function of a given cell and emerging cell aggregates. The structure and function of cells are continuously subjected to modification by electrical and chemical stimuli. However, biological systems are also subjected to an ever-present influence: the electromagnetic (EM) environment. Biological systems have the potential to be influenced by subtle energies which are exchanged at atomic and subatomic scales as EM phenomena. These energy exchanges have the potential to manifest at higher orders of discourse and affect the output (behavior) of a biological system. Here we describe theoretical and experimental evidence of EM influence on cells and the integration of whole systems. Even weak interactions between EM energies and biological systems display the potential to affect a developing system. We suggest the growing literature of EM effects on biological systems has significant implications to the cell and its functional aggregates.

Structure-Templated Predictions of Novel Protein Interactions from Sequence Information

PubMed Central

Betel, Doron; Breitkreuz, Kevin E; Isserlin, Ruth; Dewar-Darch, Danielle; Tyers, Mike; Hogue, Christopher W. V

2007-01-01

The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain–motif interactions from structural topology (D-MIST) for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information. PMID:17892321

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

PubMed

Dominguez, Daniel; Freese, Peter; Alexis, Maria S; Su, Amanda; Hochman, Myles; Palden, Tsultrim; Bazile, Cassandra; Lambert, Nicole J; Van Nostrand, Eric L; Pratt, Gabriel A; Yeo, Gene W; Graveley, Brenton R; Burge, Christopher B

2018-06-07

RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by deep sequencing of bound RNAs. These data enable construction of "RNA maps" of RBP activity without requiring crosslinking-based assays. We found an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, however, we observed extensive preferences for contextual features distinct from short linear RNA motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. Our results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Slow oscillations orchestrating fast oscillations and memory consolidation.

PubMed

Mölle, Matthias; Born, Jan

2011-01-01

Slow-wave sleep (SWS) facilitates the consolidation of hippocampus-dependent declarative memory. Based on the standard two-stage memory model, we propose that memory consolidation during SWS represents a process of system consolidation which is orchestrated by the neocortical <1Hz electroencephalogram (EEG) slow oscillation and involves the reactivation of newly encoded representations and their subsequent redistribution from temporary hippocampal to neocortical long-term storage sites. Indeed, experimental induction of slow oscillations during non-rapid eye movement (non-REM) sleep by slowly alternating transcranial current stimulation distinctly improves consolidation of declarative memory. The slow oscillations temporally group neuronal activity into up-states of strongly enhanced neuronal activity and down-states of neuronal silence. In a feed-forward efferent action, this grouping is induced not only in the neocortex but also in other structures relevant to consolidation, namely the thalamus generating 10-15Hz spindles, and the hippocampus generating sharp wave-ripples, with the latter well known to accompany a replay of newly encoded memories taking place in hippocampal circuitries. The feed-forward synchronizing effect of the slow oscillation enables the formation of spindle-ripple events where ripples and accompanying reactivated hippocampal memory information become nested into the single troughs of spindles. Spindle-ripple events thus enable reactivated memory-related hippocampal information to be fed back to neocortical networks in the excitable slow oscillation up-state where they can induce enduring plastic synaptic changes underlying the effective formation of long-term memories. Copyright © 2011 Elsevier B.V. All rights reserved.

Ectoenzymes and innate immunity: the role of human CD157 in leukocyte trafficking.

PubMed

Funaro, Ada; Ortolan, Erika; Bovino, Paola; Lo Buono, Nicola; Nacci, Giulia; Parrotta, Rossella; Ferrero, Enza; Malavasi, Fabio

2009-01-01

CD157 is a glycosylphosphatidylinositol-anchored molecule encoded by a member of the CD38/ADP-ribosyl cyclase gene family, involved in the metabolism of NAD. Expressed mainly by cells of the myeloid lineage and by vascular endothelial cells, CD157 has a dual nature behaving both as an ectoenzyme and as a receptor. Although it lacks a cytoplasmic domain, and cannot transduce signals on its own, the molecule compensates for this structural limit by interacting with conventional receptors. Recent experimental evidence suggests that CD157 orchestrates critical functions of human neutrophils. Indeed, CD157-mediated signals promote cell polarization, regulate chemotaxis induced through the high affinity fMLP receptor and control transendothelial migration.

Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork.

PubMed

Choe, Katherine N; Moldovan, George-Lucian

2017-02-02

Proliferating cell nuclear antigen (PCNA) lies at the center of the faithful duplication of eukaryotic genomes. With its distinctive doughnut-shaped molecular structure, PCNA was originally studied for its role in stimulating DNA polymerases. However, we now know that PCNA does much more than promote processive DNA synthesis. Because of the complexity of the events involved, cellular DNA replication poses major threats to genomic integrity. Whatever predicament lies ahead for the replication fork, PCNA is there to orchestrate the events necessary to handle it. Through its many protein interactions and various post-translational modifications, PCNA has far-reaching impacts on a myriad of cellular functions. Copyright © 2017 Elsevier Inc. All rights reserved.

Open-Source, Distributed Computational Environment for Virtual Materials Exploration

DTIC Science & Technology

2015-01-01

compromising structural integrity.  For  example, advanced designs could specify advanced materials processing techniques such as heat  treatments  in specific...orchestration of execution of multiple standalone codes at varying  length scales will need advanced  high ‐performance computing (HPC) integration in...possible hooks that could be used to  coordinate larger  workflows spanning tools developed by different groups.    The  high  level approach explored

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

NASA Technical Reports Server (NTRS)

Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

2004-01-01

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

NASA Astrophysics Data System (ADS)

Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

2004-09-01

This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

PubMed Central

Lavagnino, Nicolás; Serra, François; Arbiza, Leonardo; Dopazo, Hernán; Hasson, Esteban

2012-01-01

Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved. PMID:22346339

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.

PubMed

Migliori, Amy D; Keller, Nicholas; Alam, Tanfis I; Mahalingam, Marthandan; Rao, Venigalla B; Arya, Gaurav; Smith, Douglas E

2014-06-17

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

NASA Astrophysics Data System (ADS)

Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E.

2014-06-01

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.

Regulation of the mammalian heat shock factor 1.

PubMed

Dayalan Naidu, Sharadha; Dinkova-Kostova, Albena T

2017-06-01

Living organisms are endowed with the capability to tackle various forms of cellular stress due to the presence of molecular chaperone machinery complexes that are ubiquitous throughout the cell. During conditions of proteotoxic stress, the transcription factor heat shock factor 1 (HSF1) mediates the elevation of heat shock proteins, which are crucial components of the chaperone complex machinery and function to ameliorate protein misfolding and aggregation and restore protein homeostasis. In addition, HSF1 orchestrates a versatile transcriptional programme that includes genes involved in repair and clearance of damaged macromolecules and maintenance of cell structure and metabolism, and provides protection against a broad range of cellular stress mediators, beyond heat shock. Here, we discuss the structure and function of the mammalian HSF1 and its regulation by post-translational modifications (phosphorylation, sumoylation and acetylation), proteasomal degradation, and small-molecule activators and inhibitors. © 2017 Federation of European Biochemical Societies.

New frontiers: discovering cilia-independent functions of cilia proteins.

PubMed

Vertii, Anastassiia; Bright, Alison; Delaval, Benedicte; Hehnly, Heidi; Doxsey, Stephen

2015-10-01

In most vertebrates, mitotic spindles and primary cilia arise from a common origin, the centrosome. In non-cycling cells, the centrosome is the template for primary cilia assembly and, thus, is crucial for their associated sensory and signaling functions. During mitosis, the duplicated centrosomes mature into spindle poles, which orchestrate mitotic spindle assembly, chromosome segregation, and orientation of the cell division axis. Intriguingly, both cilia and spindle poles are centrosome-based, functionally distinct structures that require the action of microtubule-mediated, motor-driven transport for their assembly. Cilia proteins have been found at non-cilia sites, where they have distinct functions, illustrating a diverse and growing list of cellular processes and structures that utilize cilia proteins for crucial functions. In this review, we discuss cilia-independent functions of cilia proteins and re-evaluate their potential contributions to "cilia" disorders. © 2015 The Authors.

Quantitative mass imaging of single biological macromolecules.

PubMed

Young, Gavin; Hundt, Nikolas; Cole, Daniel; Fineberg, Adam; Andrecka, Joanna; Tyler, Andrew; Olerinyova, Anna; Ansari, Ayla; Marklund, Erik G; Collier, Miranda P; Chandler, Shane A; Tkachenko, Olga; Allen, Joel; Crispin, Max; Billington, Neil; Takagi, Yasuharu; Sellers, James R; Eichmann, Cédric; Selenko, Philipp; Frey, Lukas; Riek, Roland; Galpin, Martin R; Struwe, Weston B; Benesch, Justin L P; Kukura, Philipp

2018-04-27

The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars. These capabilities enabled us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry allows spatiotemporally resolved measurement of a broad range of biomolecular interactions, one molecule at a time. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Bridging experiment and theory: A template for unifying NMR data and electronic structure calculations

DOE PAGES

Brown, David M. L.; Cho, Herman; de Jong, Wibe A.

2016-02-09

Here, the testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashionmore » would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists.« less

Zinc and Zinc Transporters: Novel Regulators of Ventricular Myocardial Development.

PubMed

Lin, Wen; Li, Deqiang

2018-06-01

Ventricular myocardial development is a well-orchestrated process involving different cardiac structures, multiple signal pathways, and myriad proteins. Dysregulation of this important developmental event can result in cardiomyopathies, such as left ventricle non-compaction, which affect the pediatric population and the adults. Human and mouse studies have shed light upon the etiology of some cardiomyopathy cases and highlighted the contribution of both genetic and environmental factors. However, the regulation of ventricular myocardial development remains incompletely understood. Zinc is an essential trace metal with structural, enzymatic, and signaling function. Perturbation of zinc homeostasis has resulted in developmental and physiological defects including cardiomyopathy. In this review, we summarize several mechanisms by which zinc and zinc transporters can impact the regulation of ventricular myocardial development. Based on our review, we propose that zinc deficiency and mutations of zinc transporters may underlie some cardiomyopathy cases especially those involving ventricular myocardial development defects.

Virtually Out of This World!

NASA Technical Reports Server (NTRS)

2002-01-01

Ames Research Center granted Reality Capture Technologies (RCT), Inc., a license to further develop NASA's Mars Map software platform. The company incorporated NASA#s innovation into software that uses the Virtual Plant Model (VPM)(TM) to structure, modify, and implement the construction sites of industrial facilities, as well as develop, validate, and train operators on procedures. The VPM orchestrates the exchange of information between engineering, production, and business transaction systems. This enables users to simulate, control, and optimize work processes while increasing the reliability of critical business decisions. Engineers can complete the construction process and test various aspects of it in virtual reality before building the actual structure. With virtual access to and simulation of the construction site, project personnel can manage, access control, and respond to changes on complex constructions more effectively. Engineers can also create operating procedures, training, and documentation. Virtual Plant Model(TM) is a trademark of Reality Capture Technologies, Inc.

Polyaniline nanotubes coated with TiO2&γ-Fe2O3@graphene oxide as a novel and effective visible light photocatalyst for removal of rhodamine B from water

NASA Astrophysics Data System (ADS)

Ghavami, Monireh; Kassaee, Mohammad Zaman; Mohammadi, Reza; Koohi, Maryam; Haerizadeh, Bibi Narjes

2014-12-01

Synthesis of polyaniline-nanotubes (PANI-NT), in the presence of TiO2 and γ-Fe2O3 functionalized graphene oxide (GO), gives a green and magnetically recyclable photocatalyst, TiO2&γ-Fe2O3@GO/PANI-NT. The later orchestrates 94% photocatalytic efficiency in removal of rhodamine B (RB) from water, under simulated solar light irradiation. This is far higher than the 36% observed in the presence of TiO2&γ-Fe2O3@GO alone, where PANI-NT is excluded from the structure. Morphology, composition, and structural properties of our economically sound photocatalyst are characterized by X-ray diffraction, energy-dispersive X-ray spectroscopy, thermo-gravimetric, transmission electron microscopy, inductively coupled plasma, RAMAN and Fourier-transform infrared spectroscopy.

Bridging experiment and theory: A template for unifying NMR data and electronic structure calculations

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

Brown, David M. L.; Cho, Herman; de Jong, Wibe A.

Here, the testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashionmore » would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists.« less

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

PubMed Central

Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E

2014-01-01

How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here, we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force, and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free energy profile of motor conformational states with that of the ATP hydrolysis cycle. PMID:24937091

The evolution of lycopsid rooting structures: conservatism and disparity.

PubMed

Hetherington, Alexander J; Dolan, Liam

2017-07-01

Contents 538 I. 538 II. 539 III. 541 IV. 542 543 References 543 SUMMARY: The evolution of rooting structures was a crucial event in Earth's history, increasing the ability of plants to extract water, mine for nutrients and anchor above-ground shoot systems. Fossil evidence indicates that roots evolved at least twice among vascular plants, in the euphyllophytes and independently in the lycophytes. Here, we review the anatomy and evolution of lycopsid rooting structures. Highlighting recent discoveries made with fossils we suggest that the evolution of lycopsid rooting structures displays two contrasting patterns - conservatism and disparity. The structures termed roots have remained structurally similar despite hundreds of millions of years of evolution - an example of remarkable conservatism. By contrast, and over the same time period, the organs that give rise to roots have diversified, resulting in the evolution of numerous novel and disparate organs. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Orchestrating liver development.

PubMed

Gordillo, Miriam; Evans, Todd; Gouon-Evans, Valerie

2015-06-15

The liver is a central regulator of metabolism, and liver failure thus constitutes a major health burden. Understanding how this complex organ develops during embryogenesis will yield insights into how liver regeneration can be promoted and how functional liver replacement tissue can be engineered. Recent studies of animal models have identified key signaling pathways and complex tissue interactions that progressively generate liver progenitor cells, differentiated lineages and functional tissues. In addition, progress in understanding how these cells interact, and how transcriptional and signaling programs precisely coordinate liver development, has begun to elucidate the molecular mechanisms underlying this complexity. Here, we review the lineage relationships, signaling pathways and transcriptional programs that orchestrate hepatogenesis. © 2015. Published by The Company of Biologists Ltd.

Directivity measurements of the violin during performance

NASA Astrophysics Data System (ADS)

Hardy, Jean-François; Migneron, Jean-Gabriel

2005-04-01

Many studies have shown that directivity of musical instruments is significant for the perceived sound within the hall and for performer's ease of hearing each other. The directivity patterns explain in part the differences between many common or special orchestral stage plots. Measurements of the violin's directivity have been performed using an acoustical intensimetry procedure. The precise directivity characteristics of isolated tones have been compared with the mean directivity resulting from performance of four extracts chosen among the orchestral repertoire. Results, which were measured in both horizontal and vertical planes, show interesting differences between the average directivity of each test. They lead to links with few important distinctions in the traditional violin's positions inside the orchestra.

Functional diversification and specialization of cytosolic 70-kDa heat shock proteins.

PubMed

McCallister, Chelsea; Siracusa, Matthew C; Shirazi, Farzaneh; Chalkia, Dimitra; Nikolaidis, Nikolas

2015-03-20

A fundamental question in molecular evolution is how protein functional differentiation alters the ability of cells and organisms to cope with stress and survive. To answer this question we used two paralogous Hsp70s from mouse and explored whether these highly similar cytosolic molecular chaperones, which apart their temporal expression have been considered functionally interchangeable, are differentiated with respect to their lipid-binding function. We demonstrate that the two proteins bind to diverse lipids with different affinities and therefore are functionally specialized. The observed lipid-binding patterns may be related with the ability of both Hsp70s to induce cell death by binding to a particular plasma-membrane lipid, and the potential of only one of them to promote cell survival by binding to a specific lysosomal-membrane lipid. These observations reveal that two seemingly identical proteins differentially modulate cellular adaptation and survival by having acquired specialized functions via sequence divergence. Therefore, this study provides an evolutionary paradigm, where promiscuity, specificity, sub- and neo-functionalization orchestrate one of the most conserved systems in nature, the cellular stress-response.

The Rise of SN 2014J in the Nearby Galaxy M 82

NASA Technical Reports Server (NTRS)

A.Goobar; Johansson, J.; Amanullah, R.; Cao, Y.; Perley, D.A.; Kasliwal, M. M.; Ferreti, R.; Nugent, P. E.; Harris, C.; Cenko, S. B.

2014-01-01

We report on the discovery of SN 2014J in the nearby galaxy M 82. Given its proximity, it offers the best opportunity to date to study a thermonuclear supernova over a wide range of the electromagnetic spectrum. Optical, near-IR and mid-IR observations on the rising lightcurve, orchestrated by the intermediate Palomar Transient Factory (iPTF), show that SN 2014J is a spectroscopically normal Type Ia supernova, albeit exhibiting high-velocity features in its spectrum and heavily reddened by dust in the host galaxy. Our earliest detections start just hours after the fitted time of explosion. We use high-resolution optical spectroscopy to analyze the dense intervening material and do not detect any evolution in the resolved absorption features during the lightcurve rise. Similarly to other highly reddened Type Ia supernovae, a low value of total-to-selective extinction, R (sub V) less than or approximately equal to 2, provides the best match to our observations. We also study pre-explosion optical and near-IR images from HST with special emphasis on the sources nearest to the SN location.

Experimental demonstration of fronthaul flexibility for enhanced CoMP service in 5G radio and optical access networks.

PubMed

Zhang, Jiawei; Ji, Yuefeng; Yu, Hao; Huang, Xingang; Li, Han

2017-09-04

The RAN architecture towards mobile 5G and beyond is undergoing a fundamental evolution, which brings optics into the radio world. Fronthaul is a new segment that leverages on the advantages of optical communication for RAN transport. However, the current fronthaul architecture shows a fixed connection between an RRH and a BBU, which leads to inefficient resource utilization. In this paper, we focus on the fronthaul flexibility that allows "any-RRH to any-BBU" connection. In particular, we consider a CoMP service and discuss how flexible optical fronthaul helps to improve its performance. To achieve this goal, we propose an SDN-enabled orchestration for coordinating radio and optical access networks. Under this unified control manner, the agile RRH-BBU mapping can be reached through lightpath reconfiguration. To further verify the benefits of flexibility, we experiment the CoMP service in the cloud radio over flexible optical fronthaul (CRoFlex) testbed. Experimental results demonstrate the proposed SDN-enabled flexible optical fronthaul can improve the CoMP performance by optimizing the RRH-BBU mapping.

Communicative Mediation by Adults in the Construction of Symbolic Uses by Infants.

PubMed

Palacios, Pedro; Rodríguez, Cintia; Méndez-Sánchez, Cecilia

2018-06-01

Adult semiotic mediation in the origin and evolution of the first symbolic uses of objects by infants in contexts of triadic interactions was investigated. Six infant-parent dyads interacting together with ten objects were observed longitudinally from 9 to 15 months of age, with an interval of three months between each observation. The communicative mediators used by adults, in the form of demonstrations and ostensive gestures, decrease as infants grow up. The orchestration of these semiotic mediators also decreases and the functions of the demonstrations change. At the beginning, the adults use them merely to demonstrate the symbolic uses of object, but later they use them to evaluate, complete or correct the symbolic uses by the infants. The semiotic mediators are first used to guide the child at the level of attention and later at the level of cultural practices of symbolic uses of objects. These changes in communicative mediators and their functions reveal the educational role of adults through adjustment in communication, always in tune with the infant's knowledge and performance.

Architecture of a Service-Enabled Sensing Platform for the Environment

PubMed Central

Kotsev, Alexander; Pantisano, Francesco; Schade, Sven; Jirka, Simon

2015-01-01

Recent technological advancements have led to the production of arrays of miniaturized sensors, often embedded in existing multitasking devices (e.g., smartphones, tablets) and using a wide range of radio standards (e.g., Bluetooth, Wi-Fi, 4G cellular networks). Altogether, these technological evolutions coupled with the diffusion of ubiquitous Internet connectivity provide the base-line technology for the Internet of Things (IoT). The rapid increase of IoT devices is enabling the definition of new paradigms of data collection and introduces the concept of mobile crowd-sensing. In this respect, new sensing methodologies promise to extend the current understanding of the environment and social behaviors by leveraging citizen-contributed data for a wide range of applications. Environmental sensing can however only be successful if all the heterogeneous technologies and infrastructures work smoothly together. As a result, the interconnection and orchestration of devices is one of the central issues of the IoT paradigm. With this in mind, we propose an approach for improving the accessibility of observation data, based on interoperable standards and on-device web services. PMID:25688593

Architecture of a service-enabled sensing platform for the environment.

PubMed

Kotsev, Alexander; Pantisano, Francesco; Schade, Sven; Jirka, Simon

2015-02-13

Recent technological advancements have led to the production of arrays of miniaturized sensors, often embedded in existing multitasking devices (e.g., smartphones, tablets) and using a wide range of radio standards (e.g., Bluetooth, Wi-Fi, 4G cellular networks). Altogether, these technological evolutions coupled with the diffusion of ubiquitous Internet connectivity provide the base-line technology for the Internet of Things (IoT). The rapid increase of IoT devices is enabling the definition of new paradigms of data collection and introduces the concept of mobile crowd-sensing. In this respect, new sensing methodologies promise to extend the current understanding of the environment and social behaviors by leveraging citizen-contributed data for a wide range of applications. Environmental sensing can however only be successful if all the heterogeneous technologies and infrastructures work smoothly together. As a result, the interconnection and orchestration of devices is one of the central issues of the IoT paradigm. With this in mind, we propose an approach for improving the accessibility of observation data, based on interoperable standards and on-device web services.

Helminth Infections: Recognition and Modulation of the Immune Response by Innate Immune Cells

PubMed Central

Motran, Claudia Cristina; Silvane, Leonardo; Chiapello, Laura Silvina; Theumer, Martin Gustavo; Ambrosio, Laura Fernanda; Volpini, Ximena; Celias, Daiana Pamela; Cervi, Laura

2018-01-01

The survival of helminths in the host over long periods of time is the result of a process of adaptation or dynamic co-evolution between the host and the parasite. However, infection with helminth parasites causes damage to the host tissues producing the release of danger signals that induce the recruitment of various cells, including innate immune cells such as macrophages (Mo), dendritic cells (DCs), eosinophils, basophils, and mast cells. In this scenario, these cells are able to secrete soluble factors, which orchestrate immune effector mechanisms that depend on the different niches these parasites inhabit. Here, we focus on recent advances in the knowledge of excretory-secretory products (ESP), resulting from helminth recognition by DCs and Mo. Phagocytes and other cells types such as innate lymphocyte T cells 2 (ILC2), when activated by ESP, participate in an intricate cytokine network to generate innate and adaptive Th2 responses. In this review, we also discuss the mechanisms of innate immune cell-induced parasite killing and the tissue repair necessary to assure helminth survival over long periods of time. PMID:29670630

The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

PubMed

Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2016-06-01

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

Constructal Law of Vascular Trees for Facilitation of Flow

PubMed Central

Razavi, Mohammad S.; Shirani, Ebrahim; Salimpour, Mohammad Reza; Kassab, Ghassan S.

2014-01-01

Diverse tree structures such as blood vessels, branches of a tree and river basins exist in nature. The constructal law states that the evolution of flow structures in nature has a tendency to facilitate flow. This study suggests a theoretical basis for evaluation of flow facilitation within vascular structure from the perspective of evolution. A novel evolution parameter (Ev) is proposed to quantify the flow capacity of vascular structures. Ev is defined as the ratio of the flow conductance of an evolving structure (configuration with imperfection) to the flow conductance of structure with least imperfection. Attaining higher Ev enables the structure to expedite flow circulation with less energy dissipation. For both Newtonian and non-Newtonian fluids, the evolution parameter was developed as a function of geometrical shape factors in laminar and turbulent fully developed flows. It was found that the non-Newtonian or Newtonian behavior of fluid as well as flow behavior such as laminar or turbulent behavior affects the evolution parameter. Using measured vascular morphometric data of various organs and species, the evolution parameter was calculated. The evolution parameter of the tree structures in biological systems was found to be in the range of 0.95 to 1. The conclusion is that various organs in various species have high capacity to facilitate flow within their respective vascular structures. PMID:25551617

Examining Teachers' Instructional Moves Aimed at Developing Students' Ideas and Questions in Learner-Centered Science Classrooms

NASA Astrophysics Data System (ADS)

Harris, Christopher J.; Phillips, Rachel S.; Penuel, William R.

2012-11-01

Prior research has shown that orchestrating scientific discourse in classrooms is difficult and takes a great deal of effort on the part of teachers. In this study, we examined teachers' instructional moves to elicit and develop students' ideas and questions as they orchestrated discourse with their fifth grade students during a learner-centered environmental biology unit. The unit materials included features meant to support teachers in eliciting and working with students' ideas and questions as a source for student-led investigations. We present three contrasting cases of teachers to highlight evidence that shows teachers' differing strategies for eliciting students' ideas and questions, and for developing their ideas, questions and questioning skills. Results from our cross case analysis provide insight into the ways in which teachers' enactments enabled them to work with students' ideas and questions to help advance learning. Consistent with other studies, we found that teachers could readily elicit ideas and questions but experienced challenges in helping students develop them. Findings suggest a need for more specified supports, such as specific discourse strategies, to help teachers attend to student thinking. We explore implications for curricular tools and discuss a need for more examples of effective discourse moves for use by teachers in orchestrating scientific discourse.

Population-Area Relationship for Medieval European Cities

PubMed Central

Lobo, José; Bettencourt, Luís M. A.; Ortman, Scott G.; Smith, Michael E.

2016-01-01

Medieval European urbanization presents a line of continuity between earlier cities and modern European urban systems. Yet, many of the spatial, political and economic features of medieval European cities were particular to the Middle Ages, and subsequently changed over the Early Modern Period and Industrial Revolution. There is a long tradition of demographic studies estimating the population sizes of medieval European cities, and comparative analyses of these data have shed much light on the long-term evolution of urban systems. However, the next step—to systematically relate the population size of these cities to their spatial and socioeconomic characteristics—has seldom been taken. This raises a series of interesting questions, as both modern and ancient cities have been observed to obey area-population relationships predicted by settlement scaling theory. To address these questions, we analyze a new dataset for the settled area and population of 173 European cities from the early fourteenth century to determine the relationship between population and settled area. To interpret this data, we develop two related models that lead to differing predictions regarding the quantitative form of the population-area relationship, depending on the level of social mixing present in these cities. Our empirical estimates of model parameters show a strong densification of cities with city population size, consistent with patterns in contemporary cities. Although social life in medieval Europe was orchestrated by hierarchical institutions (e.g., guilds, church, municipal organizations), our results show no statistically significant influence of these institutions on agglomeration effects. The similarities between the empirical patterns of settlement relating area to population observed here support the hypothesis that cities throughout history share common principles of organization that self-consistently relate their socioeconomic networks to structured urban spaces. PMID:27706192

Population-Area Relationship for Medieval European Cities.

PubMed

Cesaretti, Rudolf; Lobo, José; Bettencourt, Luís M A; Ortman, Scott G; Smith, Michael E

2016-01-01

Medieval European urbanization presents a line of continuity between earlier cities and modern European urban systems. Yet, many of the spatial, political and economic features of medieval European cities were particular to the Middle Ages, and subsequently changed over the Early Modern Period and Industrial Revolution. There is a long tradition of demographic studies estimating the population sizes of medieval European cities, and comparative analyses of these data have shed much light on the long-term evolution of urban systems. However, the next step-to systematically relate the population size of these cities to their spatial and socioeconomic characteristics-has seldom been taken. This raises a series of interesting questions, as both modern and ancient cities have been observed to obey area-population relationships predicted by settlement scaling theory. To address these questions, we analyze a new dataset for the settled area and population of 173 European cities from the early fourteenth century to determine the relationship between population and settled area. To interpret this data, we develop two related models that lead to differing predictions regarding the quantitative form of the population-area relationship, depending on the level of social mixing present in these cities. Our empirical estimates of model parameters show a strong densification of cities with city population size, consistent with patterns in contemporary cities. Although social life in medieval Europe was orchestrated by hierarchical institutions (e.g., guilds, church, municipal organizations), our results show no statistically significant influence of these institutions on agglomeration effects. The similarities between the empirical patterns of settlement relating area to population observed here support the hypothesis that cities throughout history share common principles of organization that self-consistently relate their socioeconomic networks to structured urban spaces.

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Using container orchestration to improve service management at the RAL Tier-1

NASA Astrophysics Data System (ADS)

Lahiff, Andrew; Collier, Ian

2017-10-01

In recent years container orchestration has been emerging as a means of gaining many potential benefits compared to a traditional static infrastructure, such as increased utilisation through multi-tenancy, improved availability due to self-healing, and the ability to handle changing loads due to elasticity and auto-scaling. To this end we have been investigating migrating services at the RAL Tier-1 to an Apache Mesos cluster. In this model the concept of individual machines is abstracted away and services are run in containers on a cluster of machines, managed by schedulers, enabling a high degree of automation. Here we describe Mesos, the infrastructure deployed at RAL, and describe in detail the explicit example of running a batch farm on Mesos.

Hospitals' strategies for orchestrating selection of physician preference items.

PubMed

Montgomery, Kathleen; Schneller, Eugene S

2007-06-01

This article analyzes hospitals' strategies to shape physicians' behavior and counter suppliers' power in purchasing physician preference items. Two models of standardization are limitations on the range of manufacturers or products (the "formulary" model) and price ceilings for particular item categories (the "payment-cap" model), both requiring processes to define product equivalencies often with inadequate product comparison data. The formulary model is more difficult to implement because of physicians' resistance to top-down dictates. The payment-cap model is more feasible because it preserves physicians' choice while also restraining manufacturers' power. Hospitals may influence physicians' involvement through a process of orchestration that includes committing to improve clinical facilities, scheduling, and training and fostering a culture of mutual trust and respect.

From the ECM to the Cytoskeleton and Back: How Integrins Orchestrate T Cell Action

PubMed Central

Epler, Jennifer A.; Liu, Rugao

2000-01-01

T lymphocytes constitute a highly dynamic tissue type. During the course of their lives, they travel through a variety of physiological environments and experience a multitude of interactions with extracellular matrix components and other cells. In order to do this, they must receive many environmental cues, and translate these signals into the appropriate biological actions. Particularly dramatic are the cytoskeletal shape changes a T cell must undergo during the processes of leaving the bloodstream, migrating through tissues, and encountering antigen. In this review, we highlight the role of integrins in providing a link between the extracellular environment and cytoskeletal regulation and how these receptors help to orchestrate T cell migration and antigen recognition. PMID:11097209

Hospitals' Strategies for Orchestrating Selection of Physician Preference Items

PubMed Central

Montgomery, Kathleen; Schneller, Eugene S

2007-01-01

This article analyzes hospitals' strategies to shape physicians' behavior and counter suppliers' power in purchasing physician preference items. Two models of standardization are limitations on the range of manufacturers or products (the “formulary” model) and price ceilings for particular item categories (the “payment-cap” model), both requiring processes to define product equivalencies often with inadequate product comparison data. The formulary model is more difficult to implement because of physicians' resistance to top-down dictates. The payment-cap model is more feasible because it preserves physicians' choice while also restraining manufacturers' power. Hospitals may influence physicians' involvement through a process of orchestration that includes committing to improve clinical facilities, scheduling, and training and fostering a culture of mutual trust and respect. PMID:17517118

Biochemistry and neuroscience: the twain need to meet.

PubMed

Kennedy, Mary B

2017-04-01

Neuroscience has come to mean the study of electrophysiology of neurons and synapses, micro and macro-scale neuroanatomy, and the functional organization of brain areas. The molecular axis of the field, as reflected in textbooks, often includes only descriptions of the structure and function of individual channels and receptor proteins, and the extracellular signals that guide development and repair. Studies of cytosolic 'molecular machines', large assemblies of proteins that orchestrate regulation of neuronal functions, have been neglected. However, a complete understanding of brain function that will enable new strategies for treatment of the most intractable neural disorders will require that in vitro biochemical studies of molecular machines be reintegrated into the field of neuroscience. Copyright © 2017 Elsevier Ltd. All rights reserved.

Introduction to the Thematic Minireview Series: Green biological chemistry.

PubMed

Jez, Joseph M

2018-04-06

Plants and their green cousins cyanobacteria and algae use sunlight to drive the chemistry that lets them grow, survive, and perform an amazing range of biochemical reactions. The ability of these organisms to use a freely available energy source makes them attractive as sustainable and renewable platforms for more than just food production. They are also a source of metabolic tools for engineering microbes for "green" chemistry. This Thematic Minireview Series discusses how green organisms capture light and protect their photosynthetic machinery from too much light; new structural snapshots of the clock complex that orchestrates signaling during the light/dark cycle; challenges for improving stress responses in crops; harnessing cyanobacteria as biofactories; and efforts to engineer microbes for "green" biopolymer production. © 2018 Jez.

An integrative theory of prefrontal cortex function.

PubMed

Miller, E K; Cohen, J D

2001-01-01

The prefrontal cortex has long been suspected to play an important role in cognitive control, in the ability to orchestrate thought and action in accordance with internal goals. Its neural basis, however, has remained a mystery. Here, we propose that cognitive control stems from the active maintenance of patterns of activity in the prefrontal cortex that represent goals and the means to achieve them. They provide bias signals to other brain structures whose net effect is to guide the flow of activity along neural pathways that establish the proper mappings between inputs, internal states, and outputs needed to perform a given task. We review neurophysiological, neurobiological, neuroimaging, and computational studies that support this theory and discuss its implications as well as further issues to be addressed

Influences of dopamine and glutamate in the medial preoptic area on male sexual behavior.

PubMed

Will, Ryan G; Hull, Elaine M; Dominguez, Juan M

2014-06-01

Several brain nuclei interact to orchestrate the appetitive and consummatory aspects of male sexual behavior. Of these structures, the medial preoptic area (mPOA) of the hypothalamus is of particular interest, as it receives input from all sensory modalities, and damage to this region disrupts copulation in a wide variety of taxa. Furthermore, the mPOA is both responsive to gonadal hormones and involved in endocrine regulation. Neurochemical studies have demonstrated that both dopamine and glutamate levels rise in the mPOA in response to sexual activity, while antagonism of these neurotransmitters impairs male sexual response. Here we review how dopamine and glutamate act in the mPOA to modulate male sexual behavior. Copyright © 2014 Elsevier Inc. All rights reserved.

Justification of automated decision-making: medical explanations as medical arguments.

PubMed Central

Shankar, R. D.; Musen, M. A.

1999-01-01

People use arguments to justify their claims. Computer systems use explanations to justify their conclusions. We are developing WOZ, an explanation framework that justifies the conclusions of a clinical decision-support system. WOZ's central component is the explanation strategy that decides what information justifies a claim. The strategy uses Toulmin's argument structure to define pieces of information and to orchestrate their presentation. WOZ uses explicit models that abstract the core aspects of the framework such as the explanation strategy. In this paper, we present the use of arguments, the modeling of explanations, and the explanation process used in WOZ. WOZ exploits the wealth of naturally occurring arguments, and thus can generate convincing medical explanations. Images Figure 5 PMID:10566388

Alleviation of acquired stuttering with human centremedian thalamic stimulation.

PubMed Central

Bhatnagar, S C; Andy, O J

1989-01-01

Despite many investigations, the cerebral mechanism for stuttering remains unknown. Recently, increased attention has been paid to acquired stuttering of adult onset in the hope that the events associated with it might provide clues to the biological mechanism underlying stuttering. This attention has focused exclusively on the cortical substrates. We present our observations of acquired dysfluency, presumably of subcortical origin in a neurosurgical subject with intractable pain. The stuttering was relieved by thalamic electric stimulation. The effect of thalamic stimulation on the stuttering suggests that the pathophysiology of transient asynchronisation in the balancing and sequencing of multiple impulses is amenable to a diffusely orchestrated functional tuning of the thalamic and brainstem implicated subcortical structures and pathways. Images PMID:2795045

A Generative Angular Model of Protein Structure Evolution

PubMed Central

Golden, Michael; García-Portugués, Eduardo; Sørensen, Michael; Mardia, Kanti V.; Hamelryck, Thomas; Hein, Jotun

2017-01-01

Abstract Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modeled using a novel angular diffusion process on the two-dimensional torus. Coupling sequence and structure evolution in our model allows for modeling both “smooth” conformational changes and “catastrophic” conformational jumps, conditioned on the amino acid changes. The model has interpretable parameters and is comparatively more realistic than previous stochastic models, providing new insights into the relationship between sequence and structure evolution. For example, using the trained model we were able to identify an apparent sequence–structure evolutionary motif present in a large number of homologous protein pairs. The generative nature of our model enables us to evaluate its validity and its ability to simulate aspects of protein evolution conditioned on an amino acid sequence, a related amino acid sequence, a related structure or any combination thereof. PMID:28453724

Decentralized operating procedures for orchestrating data and behavior across distributed military systems and assets

NASA Astrophysics Data System (ADS)

Peach, Nicholas

2011-06-01

In this paper, we present a method for a highly decentralized yet structured and flexible approach to achieve systems interoperability by orchestrating data and behavior across distributed military systems and assets with security considerations addressed from the beginning. We describe an architecture of a tool-based design of business processes called Decentralized Operating Procedures (DOP) and the deployment of DOPs onto run time nodes, supporting the parallel execution of each DOP at multiple implementation nodes (fixed locations, vehicles, sensors and soldiers) throughout a battlefield to achieve flexible and reliable interoperability. The described method allows the architecture to; a) provide fine grain control of the collection and delivery of data between systems; b) allow the definition of a DOP at a strategic (or doctrine) level by defining required system behavior through process syntax at an abstract level, agnostic of implementation details; c) deploy a DOP into heterogeneous environments by the nomination of actual system interfaces and roles at a tactical level; d) rapidly deploy new DOPs in support of new tactics and systems; e) support multiple instances of a DOP in support of multiple missions; f) dynamically add or remove run-time nodes from a specific DOP instance as missions requirements change; g) model the passage of, and business reasons for the transmission of each data message to a specific DOP instance to support accreditation; h) run on low powered computers with lightweight tactical messaging. This approach is designed to extend the capabilities of existing standards, such as the Generic Vehicle Architecture (GVA).

Feeling Present in Arousing Virtual Reality Worlds: Prefrontal Brain Regions Differentially Orchestrate Presence Experience in Adults and Children

PubMed Central

Baumgartner, Thomas; Speck, Dominique; Wettstein, Denise; Masnari, Ornella; Beeli, Gian; Jäncke, Lutz

2008-01-01

Virtual reality (VR) is a powerful tool for simulating aspects of the real world. The success of VR is thought to depend on its ability to evoke a sense of “being there”, that is, the feeling of “Presence”. In view of the rapid progress in the development of increasingly more sophisticated virtual environments (VE), the importance of understanding the neural underpinnings of presence is growing. To date however, the neural correlates of this phenomenon have received very scant attention. An fMRI-based study with 52 adults and 25 children was therefore conducted using a highly immersive VE. The experience of presence in adult subjects was found to be modulated by two major strategies involving two homologous prefrontal brain structures. Whereas the right DLPFC controlled the sense of presence by down-regulating the activation in the egocentric dorsal visual processing stream, the left DLPFC up-regulated widespread areas of the medial prefrontal cortex known to be involved in self-reflective and stimulus-independent thoughts. In contrast, there was no evidence of these two strategies in children. In fact, anatomical analyses showed that these two prefrontal areas have not yet reached full maturity in children. Taken together, this study presents the first findings that show activation of a highly specific neural network orchestrating the experience of presence in adult subjects, and that the absence of activity in this neural network might contribute to the generally increased susceptibility of children for the experience of presence in VEs. PMID:18958209

The effect of time-variant acoustical properties on orchestral instrument timbres

NASA Astrophysics Data System (ADS)

Hajda, John Michael

1999-06-01

The goal of this study was to investigate the timbre of orchestral instrument tones. Kendall (1986) showed that time-variant features are important to instrument categorization. But the relative salience of specific time-variant features to each other and to other acoustical parameters is not known. As part of a convergence strategy, a battery of experiments was conducted to assess the importance of global amplitude envelope, spectral frequencies, and spectral amplitudes. An omnibus identification experiment investigated the salience of global envelope partitions (attack, steady state, and decay). Valid partitioning models should identify important boundary conditions in the evolution of a signal; therefore, these models should be based on signal characteristics. With the use of such a model for sustained continuant tones, the steady-state segment was more salient than the attack. These findings contradicted previous research, which used questionable operational definitions for signal partitioning. For the next set of experiments, instrument tones were analyzed by phase vocoder, and stimuli were created by additive synthesis. Edits and combinations of edits controlled global amplitude envelope, spectral frequencies, and relative spectral amplitudes. Perceptual measurements were made with distance estimation, Verbal Attribute Magnitude Estimation, and similarity scaling. Results indicated that the primary acoustical attribute was the long-time-average spectral centroid. Spectral centroid is a measure of the center of energy distribution for spectral frequency components. Instruments with high values of spectral centroid (bowed strings) sound nasal while instruments with low spectral centroid (flute, clarinet) sound not nasal. The secondary acoustical attribute was spectral amplitude time variance. Predictably, time variance correlated highly with subject ratings of vibrato. The control of relative spectral amplitudes was more salient than the control of global envelope and spectral frequencies. Both amplitude phase relationships and time- variant spectral centroid were affected by the control of relative spectral amplitudes. Further experimentation is required to determine the salience of these features. The finding that instrumental vibrato is a manifestation of spectral amplitude time variance contradicts the common belief that vibrato is due to frequency (pitch) and intensity (loudness) modulation. This study suggests that vibrato is due to a periodic modulation in timbre. Future research should employ musical contexts.

Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation.

PubMed

Aguirre, Jacob D; Dunkerley, Karen M; Mercier, Pascal; Shaw, Gary S

2017-01-10

Mutations in PARK2 and PARK6 genes are responsible for the majority of hereditary Parkinson's disease cases. These genes encode the E3 ubiquitin ligase parkin and the protein kinase PTEN-induced kinase 1 (PINK1), respectively. Together, parkin and PINK1 regulate the mitophagy pathway, which recycles damaged mitochondria following oxidative stress. Native parkin is inactive and exists in an autoinhibited state mediated by its ubiquitin-like (UBL) domain. PINK1 phosphorylation of serine 65 in parkin's UBL and serine 65 of ubiquitin fully activate ubiquitin ligase activity; however, a structural rationale for these observations is not clear. Here, we report the structure of the phosphorylated UBL domain from parkin. We find that destabilization of the UBL results from rearrangements to hydrophobic core packing that modify its structure. Altered surface electrostatics from the phosphoserine group disrupt its intramolecular association, resulting in poorer autoinhibition in phosphorylated parkin. Further, we show that phosphorylation of both the UBL domain and ubiquitin are required to activate parkin by releasing the UBL domain, forming an extended structure needed to facilitate E2-ubiquitin binding. Together, the results underscore the importance of parkin activation by the PINK1 phosphorylation signal and provide a structural picture of the unraveling of parkin's ubiquitin ligase potential.

Interplay between Clinical Guidelines and Organizational Workflow Systems. Experience from the MobiGuide Project.

PubMed

Shabo, Amnon; Peleg, Mor; Parimbelli, Enea; Quaglini, Silvana; Napolitano, Carlo

2016-12-07

Implementing a decision-support system within a healthcare organization requires integration of clinical domain knowledge with resource constraints. Computer-interpretable guidelines (CIG) are excellent instruments for addressing clinical aspects while business process management (BPM) languages and Workflow (Wf) engines manage the logistic organizational constraints. Our objective is the orchestration of all the relevant factors needed for a successful execution of patient's care pathways, especially when spanning the continuum of care, from acute to community or home care. We considered three strategies for integrating CIGs with organizational workflows: extending the CIG or BPM languages and their engines, or creating an interplay between them. We used the interplay approach to implement a set of use cases arising from a CIG implementation in the domain of Atrial Fibrillation. To provide a more scalable and standards-based solution, we explored the use of Cross-Enterprise Document Workflow Integration Profile. We describe our proof-of-concept implementation of five use cases. We utilized the Personal Health Record of the MobiGuide project to implement a loosely-coupled approach between the Activiti BPM engine and the Picard CIG engine. Changes in the PHR were detected by polling. IHE profiles were used to develop workflow documents that orchestrate cross-enterprise execution of cardioversion. Interplay between CIG and BPM engines can support orchestration of care flows within organizational settings.

Underutilization of worker's compensation insurance among professional orchestral musicians.

PubMed

Chimenti, Ruth L; Van Dillen, Linda R; Prather, Heidi; Hunt, Devyani; Chimenti, Peter C; Khoo-Summers, Lynnette

2013-03-01

Orchestral musicians commonly have playing-related symptoms (PRS) but few use worker's compensation (WC) insurance for assessment and treatment. The purpose of this study was to examine the frequency of, and factors related to, filing a WC claim among musicians. An online questionnaire was completed by 261 members of the International Conference of Symphony and Opera Musicians (ICSOM). The responses were analyzed to describe the frequency and type of injuries, perceived cause of PRS, and severity of injury in musicians who did and did not file a WC claim. Of the musicians, 93% reported PRS in the 12 months prior to the study. Only 9 musicians filed WC claims during their careers, and all claims were for upper extremity injuries. The most frequent reason for not filing a WC claim was insufficient severity. Yet among musicians describing their PRS as not severe enough for a WC claim, 47% had symptoms for >15 minutes after playing and 16% had symptoms that interfered with daily activities. These data suggest there is frequent under-reporting of injuries to WC among professional orchestral musicians. Although most musicians reported PRS that persisted after playing, the most common reason for not filing a WC claim was insufficient severity of symptoms perceived by the musicians. Future research should focus on clearly defining severity for PRS-related injuries and determining when treatment for overuse syndromes should be paid for through the WC system.

Demonstration of application-driven network slicing and orchestration in optical/packet domains: on-demand vDC expansion for Hadoop MapReduce optimization.

PubMed

Kong, Bingxin; Liu, Siqi; Yin, Jie; Li, Shengru; Zhu, Zuqing

2018-05-28

Nowadays, it is common for service providers (SPs) to leverage hybrid clouds to improve the quality-of-service (QoS) of their Big Data applications. However, for achieving guaranteed latency and/or bandwidth in its hybrid cloud, an SP might desire to have a virtual datacenter (vDC) network, in which it can manage and manipulate the network connections freely. To address this requirement, we design and implement a network slicing and orchestration (NSO) system that can create and expand vDCs across optical/packet domains on-demand. Considering Hadoop MapReduce (M/R) as the use-case, we describe the proposed architectures of the system's data, control and management planes, and present the operation procedures for creating, expanding, monitoring and managing a vDC for M/R optimization. The proposed NSO system is then realized in a small-scale network testbed that includes four optical/packet domains, and we conduct experiments in it to demonstrate the whole operations of the data, control and management planes. Our experimental results verify that application-driven on-demand vDC expansion across optical/packet domains can be achieved for M/R optimization, and after being provisioned with a vDC, the SP using the NSO system can fully control the vDC network and further optimize the M/R jobs in it with network orchestration.

Structural basis of death domain signaling in the p75 neurotrophin receptor

PubMed Central

Lin, Zhi; Tann, Jason Y; Goh, Eddy TH; Kelly, Claire; Lim, Kim Buay; Gao, Jian Fang; Ibanez, Carlos F

2015-01-01

Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75NTR) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. RIP2 CARD and RhoGDI bind to p75NTR DD at partially overlapping epitopes with over 100-fold difference in affinity, revealing the mechanism by which RIP2 recruitment displaces RhoGDI upon ligand binding. The p75NTR DD forms non-covalent, low-affinity symmetric dimers in solution. The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors. DOI: http://dx.doi.org/10.7554/eLife.11692.001 PMID:26646181

Heterogeneity in iota-carrageenan molecular structure: insights for polymorph II→III transition in the presence of calcium ions

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

Janaswamy, Srinivas; Chandrasekaran, Rengaswami

2008-06-24

Iota-carrageenan is used in pharmaceutical and food applications due to its ability to complex with other hydrocolloids and proteins. Six distinct cation dependent allomorphs, consistent with its versatile functionality, have so far been observed in the solid state. In this contribution, X-ray structural details of calcium iota-carrageenan (form III) are reported. The polysaccharide retains the half-staggered, parallel, 3-fold, right-handed double helix stabilized by interchain hydrogen bonds from O-2H and O-6H in the Galp units. Results show that there are four helices, rather than one in I or three in II, organized in a larger pseudo-trigonal unit cell of dimensions a=27.44,more » c=13.01 A, and gamma=120 degrees . The four helices have similar core structures, but their sulfate group orientations are quite different. Fifteen calcium ions and 64 water molecules hold the helices together and promote helix-helix interactions. The results portray how the helices would shuffle around in an orchestrated manner to yield calcium iota-carrageenan III from II.« less

Biofabrication strategies for 3D in vitro models and regenerative medicine

NASA Astrophysics Data System (ADS)

Moroni, Lorenzo; Burdick, Jason A.; Highley, Christopher; Lee, Sang Jin; Morimoto, Yuya; Takeuchi, Shoji; Yoo, James J.

2018-05-01

Organs are complex systems composed of different cells, proteins and signalling molecules that are arranged in a highly ordered structure to orchestrate a myriad of functions in our body. Biofabrication strategies can be applied to engineer 3D tissue models in vitro by mimicking the structure and function of native tissue through the precise deposition and assembly of materials and cells. This approach allows the spatiotemporal control over cell-cell and cell-extracellular matrix communication and thus the recreation of tissue-like structures. In this Review, we examine biofabrication strategies for the construction of functional tissue replacements and organ models, focusing on the development of biomaterials, such as supramolecular and photosensitive materials, that can be processed using biofabrication techniques. We highlight bioprinted and bioassembled tissue models and survey biofabrication techniques for their potential to recreate complex tissue properties, such as shape, vasculature and specific functionalities. Finally, we discuss challenges, such as scalability and the foreign body response, and opportunities in the field and provide an outlook to the future of biofabrication in regenerative medicine.

Initiation of viral RNA-dependent RNA polymerization.

PubMed

van Dijk, Alberdina A; Makeyev, Eugene V; Bamford, Dennis H

2004-05-01

This review summarizes the combined insights from recent structural and functional studies of viral RNA-dependent RNA polymerases (RdRPs) with the primary focus on the mechanisms of initiation of RNA synthesis. Replication of RNA viruses has traditionally been approached using a combination of biochemical and genetic methods. Recently, high-resolution structures of six viral RdRPs have been determined. For three RdRPs, enzyme complexes with metal ions, single-stranded RNA and/or nucleoside triphosphates have also been solved. These advances have expanded our understanding of the molecular mechanisms of viral RNA synthesis and facilitated further RdRP studies by informed site-directed mutagenesis. What transpires is that the basic polymerase right hand shape provides the correct geometrical arrangement of substrate molecules and metal ions at the active site for the nucleotidyl transfer catalysis, while distinct structural elements have evolved in the different systems to ensure efficient initiation of RNA synthesis. These elements feed the template, NTPs and ions into the catalytic cavity, correctly position the template 3' terminus, transfer the products out of the catalytic site and orchestrate the transition from initiation to elongation.

Revealing the distinct folding phases of an RNA three-helix junction.

PubMed

Plumridge, Alex; Katz, Andrea M; Calvey, George D; Elber, Ron; Kirmizialtin, Serdal; Pollack, Lois

2018-05-14

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.

Structural Basis of Interaction between Urokinase-Type Plasminogen Activator and Its Receptor

PubMed Central

Barinka, Cyril; Parry, Graham; Callahan, Jennifer; Shaw, David E.; Kuo, Alice; Bdeir, Khalil; Cines, Douglas B.; Mazar, Andrew; Lubkowski, Jacek

2009-01-01

Summary Recent studies indicate that binding of urokinase-type plasminogen activator (uPA) to its high affinity receptor (uPAR), orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes including wound healing, angiogenesis, inflammation, and cancer metastasis. However, notwithstanding the wealth of biochemical data available describing the activities of uPAR, little is known as to the exact mode of uPAR-uPA interactions and the presumed conformational changes that accompanying uPA-uPAR engagement. Here we report the crystal structure of soluble urokinase plasminogen activator receptor (suPAR), which contains the three domains of the wild-type receptor but lacks the cell surface anchoring sequence, in complex with the amino terminal fragment of urokinase-type plasminogen activator (ATF), at the resolution of 2.8 Å. We also report the 1.9 Å crystal structure of the free ATF. Our results provide a structural basis, represented by conformational changes induced in uPAR, for several published biochemical observations describing the nature of uPAR-uPA interactions and provide insight into mechanisms that may be responsible for the cellular responses induced by uPA binding. PMID:16979660

Self-assembly programming of DNA polyominoes.

PubMed

Ong, Hui San; Syafiq-Rahim, Mohd; Kasim, Noor Hayaty Abu; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

2016-10-20

Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously. Copyright © 2016 Elsevier B.V. All rights reserved.

The dynamics and tuning of orchestral crotales

NASA Astrophysics Data System (ADS)

Deutsch, Bradley M.; Ramirez, Cherie L.; Moore, Thomas R.

2004-10-01

An experimental and theoretical investigation of the acoustic and vibrational properties of orchestral crotales within the range C6 to C8 is reported. Interferograms of the acoustically important modes of vibration are presented and the frequencies are reported. It is shown that the acoustic spectra of crotales are not predicted by assuming that they are either thin circular plates or annular plates clamped at the center, despite the physical resemblance to these objects. Results from finite element analysis are presented that demonstrate how changing the size of the central mass affects the tuning of the instruments, and it is concluded that crotales are not currently designed to ensure optimal tuning. The possibility of using annular plates as crotales is also investigated and the physical parameters for such a set of instruments are presented. .

Adolescent Development of Value-Guided Goal Pursuit.

PubMed

Davidow, Juliet Y; Insel, Catherine; Somerville, Leah H

2018-06-04

Adolescents are challenged to orchestrate goal-directed actions in increasingly independent and consequential ways. In doing so, it is advantageous to use information about value to select which goals to pursue and how much effort to devote to them. Here, we examine age-related changes in how individuals use value signals to orchestrate goal-directed behavior. Drawing on emerging literature on value-guided cognitive control and reinforcement learning, we demonstrate how value and task difficulty modulate the execution of goal-directed action in complex ways across development from childhood to adulthood. We propose that the scope of value-guided goal pursuit expands with age to include increasingly challenging cognitive demands, and scaffolds on the emergence of functional integration within brain networks supporting valuation, cognition, and action. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanical regulation of cardiac development

PubMed Central

Lindsey, Stephanie E.; Butcher, Jonathan T.; Yalcin, Huseyin C.

2014-01-01

Mechanical forces are essential contributors to and unavoidable components of cardiac formation, both inducing and orchestrating local and global molecular and cellular changes. Experimental animal studies have contributed substantially to understanding the mechanobiology of heart development. More recent integration of high-resolution imaging modalities with computational modeling has greatly improved our quantitative understanding of hemodynamic flow in heart development. Merging these latest experimental technologies with molecular and genetic signaling analysis will accelerate our understanding of the relationships integrating mechanical and biological signaling for proper cardiac formation. These advances will likely be essential for clinically translatable guidance for targeted interventions to rescue malforming hearts and/or reconfigure malformed circulations for optimal performance. This review summarizes our current understanding on the levels of mechanical signaling in the heart and their roles in orchestrating cardiac development. PMID:25191277

A Symphony of Software.

ERIC Educational Resources Information Center

Currents, 2002

2002-01-01

Offers a descriptive table of databases that help higher education institutions orchestrate advancement operations. Information includes vendor, contact, software, price, database engine/server platform, recommended reporting tools, record capacity, and client type. (EV)

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

Xu, Ren; Boudreau, Aaron; Bissell, Mina J

Mammary gland development, functional differentiation, and homeostasis are orchestrated and sustained by a balance of biochemical and biophysical cues from the organ's microenvironment. The three-dimensional microenvironment of the mammary gland, predominantly 'encoded' by a collaboration between the extracellular matrix (ECM), hormones, and growth factors, sends signals from ECM receptors through the cytoskeletal intracellular matrix to nuclear and chromatin structures resulting in gene expression; the ECM in turn is regulated and remodeled by signals from the nucleus. In this chapter, we discuss how coordinated ECM deposition and remodeling is necessary for mammary gland development, how the ECM provides structural and biochemicalmore » cues necessary for tissue-specific function, and the role of the cytoskeleton in mediating the extra - to intracellular dialogue occurring between the nucleus and the microenvironment. When operating normally, the cytoskeletal-mediated dynamic and reciprocal integration of tissue architecture and function directs mammary gland development, tissue polarity, and ultimately, tissue-specific gene expression. Cancer occurs when these dynamic interactions go awry for an extended time.« less

Brushes, cables, and anchors: recent insights into multiscale assembly and mechanics of cellular structural networks.

PubMed

Lele, Tanmay P; Kumar, Sanjay

2007-01-01

The remarkable ability of living cells to sense, process, and respond to mechanical stimuli in their environment depends on the rapid and efficient interconversion of mechanical and chemical energy at specific times and places within the cell. For example, application of force to cells leads to conformational changes in specific mechanosensitive molecules which then trigger cellular signaling cascades that may alter cellular structure, mechanics, and migration and profoundly influence gene expression. Similarly, the sensitivity of cells to mechanical stresses is governed by the composition, architecture, and mechanics of the cellular cytoskeleton and extracellular matrix (ECM), which are in turn driven by molecular-scale forces between the constituent biopolymers. Understanding how these mechanochemical systems coordinate over multiple length and time scales to produce orchestrated cell behaviors represents a fundamental challenge in cell biology. Here, we review recent advances in our understanding of these complex processes in three experimental systems: the assembly of axonal neurofilaments, generation of tensile forces by actomyosin stress fiber bundles, and mechanical control of adhesion assembly.

Maltose conjugation to PCL: Advanced structural characterization and preliminary biological properties

NASA Astrophysics Data System (ADS)

Secchi, Valeria; Guizzardi, Roberto; Russo, Laura; Pastori, Valentina; Lecchi, Marzia; Franchi, Stefano; Iucci, Giovanna; Battocchio, Chiara; Cipolla, Laura

2018-05-01

The emerging trends in regenerative medicine rely among others on biomaterial-based therapies, with the use of biomaterials as a central delivery system for biochemical and physical cues to manipulate transplanted or ingrowth cells and to orchestrate tissue regeneration. Cell adhesion properties of a biomaterial strongly depend on its surface characteristics. Among others poly(ε-caprolactone) (PCL) is a biocompatible and biodegradable material with low cytotoxicity that is widely adopted as synthetic polymer in several applications. However, it is hydrophobic, which limits its use in tissue engineering. In order to improve its hydrophilicity and cellular compatibility, PCL surface was grafted with maltose through a two-step procedure in which controlled aminolysis of PCL ester bonds by hexanediamine was followed by reductive amination with the carbohydrate reducing end. The modified PCL surface was then characterized in detail by x-ray Photoelectron Spectroscopy (XPS) and Near Edge x-ray Absorption Fine Structure (NEXAFS) spectroscopies. In addition, the biocompatibility of the proposed biomaterial was investigated in preliminary biological assays.

Speech research: Studies on the nature of speech, instrumentation for its investigation, and practical applications

NASA Astrophysics Data System (ADS)

Liberman, A. M.

1982-03-01

This report is one of a regular series on the status and progress of studies on the nature of speech, instrumentation for its investigation and practical applications. Manuscripts cover the following topics: Speech perception and memory coding in relation to reading ability; The use of orthographic structure by deaf adults: Recognition of finger-spelled letters; Exploring the information support for speech; The stream of speech; Using the acoustic signal to make inferences about place and duration of tongue-palate contact. Patterns of human interlimb coordination emerge from the the properties of nonlinear limit cycle oscillatory processes: Theory and data; Motor control: Which themes do we orchestrate? Exploring the nature of motor control in Down's syndrome; Periodicity and auditory memory: A pilot study; Reading skill and language skill: On the role of sign order and morphological structure in memory for American Sign Language sentences; Perception of nasal consonants with special reference to Catalan; and Speech production Characteristics of the hearing impaired.

Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains.

PubMed

Gronnier, Julien; Crowet, Jean-Marc; Habenstein, Birgit; Nasir, Mehmet Nail; Bayle, Vincent; Hosy, Eric; Platre, Matthieu Pierre; Gouguet, Paul; Raffaele, Sylvain; Martinez, Denis; Grelard, Axelle; Loquet, Antoine; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia; Der, Christophe; Bayer, Emmanuelle M; Jaillais, Yvon; Deleu, Magali; Germain, Véronique; Lins, Laurence; Mongrand, Sébastien

2017-07-31

Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function.

Ubiquitin Utilizes an Acidic Surface Patch to Alter Chromatin Structure

PubMed Central

Debelouchina, Galia T.; Gerecht, Karola; Muir, Tom W.

2016-01-01

Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features. PMID:27870837

The Lepidoptera Odorant Binding Protein gene family: Gene gain and loss within the GOBP/PBP complex of moths and butterflies.

PubMed

Vogt, Richard G; Große-Wilde, Ewald; Zhou, Jing-Jiang

2015-07-01

Butterflies and moths differ significantly in their daily activities: butterflies are diurnal while moths are largely nocturnal or crepuscular. This life history difference is presumably reflected in their sensory biology, and especially the balance between the use of chemical versus visual signals. Odorant Binding Proteins (OBP) are a class of insect proteins, at least some of which are thought to orchestrate the transfer of odor molecules within an olfactory sensillum (olfactory organ), between the air and odor receptor proteins (ORs) on the olfactory neurons. A Lepidoptera specific subclass of OBPs are the GOBPs and PBPs; these were the first OBPs studied and have well documented associations with olfactory sensilla. We have used the available genomes of two moths, Manduca sexta and Bombyx mori, and two butterflies, Danaus plexippus and Heliconius melpomene, to characterize the GOBP/PBP genes, attempting to identify gene orthologs and document specific gene gain and loss. First, we identified the full repertoire of OBPs in the M. sexta genome, and compared these with the full repertoire of OBPs from the other three lepidopteran genomes, the OBPs of Drosophila melanogaster and select OBPs from other Lepidoptera. We also evaluated the tissue specific expression of the M. sexta OBPs using an available RNAseq databases. In the four lepidopteran species, GOBP2 and all PBPs reside in single gene clusters; in two species GOBP1 is documented to be nearby, about 100 kb from the cluster; all GOBP/PBP genes share a common gene structure indicating a common origin. As such, the GOBP/PBP genes form a gene complex. Our findings suggest that (1) the lepidopteran GOBP/PBP complex is a monophyletic lineage with origins deep within Lepidoptera phylogeny, (2) within this lineage PBP gene evolution is much more dynamic than GOBP gene evolution, and (3) butterflies may have lost a PBP gene that plays an important role in moth pheromone detection, correlating with a shift from olfactory (moth) to visual (butterfly) communication, at least regarding long distance mate recognition. These findings will be clarified by additional lepidopteran genomic data, but the observation that moths and butterflies share most of the PBP/GOBP genes suggests that they also share common chemosensory-based behavioral pathways. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predictive Modeling and Computational Toxicology

EPA Science Inventory

Embryonic development is orchestrated via a complex series of cellular interactions controlling behaviors such as mitosis, migration, differentiation, adhesion, contractility, apoptosis, and extracellular matrix remodeling. Any chemical exposure that perturbs these cellular proce...

Music Careers

ERIC Educational Resources Information Center

Alfaro, Daniel

1977-01-01

Careers in the music field for Hispanos are available for the industrious, competitive, and talented person. Among the careers are: composer, orchestrator-arranger, church musician, conductor, teacher, music librarian, tuner-technician, copyist, and instrument repairer. (NQ)

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection

PubMed Central

Valkov, Eugene; Stamp, Anna; DiMaio, Frank; Baker, David; Verstak, Brett; Roversi, Pietro; Kellie, Stuart; Sweet, Matthew J.; Mansell, Ashley; Gay, Nicholas J.; Martin, Jennifer L.; Kobe, Bostjan

2011-01-01

Initiation of the innate immune response requires agonist recognition by pathogen-recognition receptors such as the Toll-like receptors (TLRs). Toll/interleukin-1 receptor (TIR) domain-containing adaptors are critical in orchestrating the signal transduction pathways after TLR and interleukin-1 receptor activation. Myeloid differentiation primary response gene 88 (MyD88) adaptor-like (MAL)/TIR domain-containing adaptor protein (TIRAP) is involved in bridging MyD88 to TLR2 and TLR4 in response to bacterial infection. Genetic studies have associated a number of unique single-nucleotide polymorphisms in MAL with protection against invasive microbial infection, but a molecular understanding has been hampered by a lack of structural information. The present study describes the crystal structure of MAL TIR domain. Significant structural differences exist in the overall fold of MAL compared with other TIR domain structures: A sequence motif comprising a β-strand in other TIR domains instead corresponds to a long loop, placing the functionally important “BB loop” proline motif in a unique surface position in MAL. The structure suggests possible dimerization and MyD88-interacting interfaces, and we confirm the key interface residues by coimmunoprecipitation using site-directed mutants. Jointly, our results provide a molecular and structural basis for the role of MAL in TLR signaling and disease protection. PMID:21873236

Courtship Pheromone Use in a Model Urodele, the Mexican Axolotl (Ambystoma mexicanum)

PubMed Central

Maex, Margo; Van Bocxlaer, Ines; Mortier, Anneleen; Proost, Paul; Bossuyt, Franky

2016-01-01

Sex pheromones have been shown to constitute a crucial aspect of salamander reproduction. Until now, courtship pheromones of Salamandridae and Plethodontidae have been intensively studied, but information on chemical communication in other urodelan families is essentially lacking. The axolotl (Ambystoma mexicanum, Ambystomatidae) has a courtship display that suggests a key role for chemical communication in the orchestration of its sexual behavior, but no sex pheromones have yet been characterized from this species. Here we combined whole transcriptome analyses of the male cloaca with proteomic analyses of water in which axolotls were allowed to court to show that male axolotls secrete multiple ca. 20 kDa glycosylated sodefrin precursor-like factor (SPF) proteins during courtship. In combination with phylogenetic analyses, our data show that the male cloaca essentially secretes a courtship-specific clade of SPF proteins that is orthologous to salamandrid courtship pheromones. In addition, we identified an SPF protein for which no orthologs have been described from other salamanders so far. Overall, our study advocates a central role for SPF proteins during the courtship display of axolotls and adds knowledge on pheromone use in a previously unexplored deep evolutionary branch of salamander evolution. PMID:26842386

Courtship Pheromone Use in a Model Urodele, the Mexican Axolotl (Ambystoma mexicanum).

PubMed

Maex, Margo; Van Bocxlaer, Ines; Mortier, Anneleen; Proost, Paul; Bossuyt, Franky

2016-02-04

Sex pheromones have been shown to constitute a crucial aspect of salamander reproduction. Until now, courtship pheromones of Salamandridae and Plethodontidae have been intensively studied, but information on chemical communication in other urodelan families is essentially lacking. The axolotl (Ambystoma mexicanum, Ambystomatidae) has a courtship display that suggests a key role for chemical communication in the orchestration of its sexual behavior, but no sex pheromones have yet been characterized from this species. Here we combined whole transcriptome analyses of the male cloaca with proteomic analyses of water in which axolotls were allowed to court to show that male axolotls secrete multiple ca. 20 kDa glycosylated sodefrin precursor-like factor (SPF) proteins during courtship. In combination with phylogenetic analyses, our data show that the male cloaca essentially secretes a courtship-specific clade of SPF proteins that is orthologous to salamandrid courtship pheromones. In addition, we identified an SPF protein for which no orthologs have been described from other salamanders so far. Overall, our study advocates a central role for SPF proteins during the courtship display of axolotls and adds knowledge on pheromone use in a previously unexplored deep evolutionary branch of salamander evolution.

Predictive assimilation framework to support contaminated site understanding and remediation

NASA Astrophysics Data System (ADS)

Versteeg, R. J.; Bianchi, M.; Hubbard, S. S.

2014-12-01

Subsurface system behavior at contaminated sites is driven and controlled by the interplay of physical, chemical, and biological processes occurring at multiple temporal and spatial scales. Effective remediation and monitoring planning requires an understanding of this complexity that is current, predictive (with some level of confidence) and actionable. We present and demonstrate a predictive assimilation framework (PAF). This framework automatically ingests, quality controls and stores near real-time environmental data and processes these data using different inversion and modeling codes to provide information on the current state and evolution of the subsurface system. PAF is implemented as a cloud based software application which has five components: (1) data acquisition, (2) data management, (3) data assimilation and processing, (4) visualization and result deliver and (5) orchestration. Access to and interaction with PAF is done through a standard browser. PAF is designed to be modular so that it can ingest and process different data streams dependent on the site. We will present an implementation of PAF which uses data from a highly instrumented site (the DOE Rifle Subsurface Biogeochemistry Field Observatory in Rifle, Colorado) for which PAF automatically ingests hydrological data and forward models groundwater flow in the saturated zone.

The mucosal immune system of fish: the evolution of tolerating commensals while fighting pathogens

PubMed Central

Gomez, Daniela; Sunyer, J Oriol; Salinas, Irene

2013-01-01

The field of mucosal immunology research has grown fast over the past few years, and our understanding on how mucosal surfaces respond to complex antigenic cocktails is expanding tremendously. With the advent of new molecular sequencing techniques, it is easier to understand how the immune system of vertebrates is, to a great extent, orchestrated by the complex microbial communities that live in symbiosis with their hosts. The commensal microbiota is now seen as the “extended self” by many scientists. Similarly, fish immunologist are devoting important research efforts to the field of mucosal immunity and commensals. Recent breakthroughs on our understanding of mucosal immune responses in teleost fish open up the potential of teleosts as animal research models for the study of human mucosal diseases. Additionally, this new knowledge places immunologists in a better position to specifically target the fish mucosal immune system while rationally designing mucosal vaccines and other immunotherapies. In this review, an updated view on how teleost skin, gills and gut immune cells and molecules, function in response to pathogens and commensals is provided. Finally, some of the future avenues that the field of fish mucosal immunity may follow in the next years are highlighted. PMID:24099804

Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.

PubMed

Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

2015-08-25

Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.

Disgust as an adaptive system for disease avoidance behaviour

PubMed Central

Curtis, Valerie; de Barra, Mícheál; Aunger, Robert

2011-01-01

Disgust is an evolved psychological system for protecting organisms from infection through disease avoidant behaviour. This ‘behavioural immune system’, present in a diverse array of species, exhibits universal features that orchestrate hygienic behaviour in response to cues of risk of contact with pathogens. However, disgust is also a dynamic adaptive system. Individuals show variation in pathogen avoidance associated with psychological traits like having a neurotic personality, as well as a consequence of being in certain physiological states such as pregnancy or infancy. Three specialized learning mechanisms modify the disgust response: the Garcia effect, evaluative conditioning and the law of contagion. Hygiene behaviour is influenced at the group level through social learning heuristics such as ‘copy the frequent’. Finally, group hygiene is extended symbolically to cultural rules about purity and pollution, which create social separations and are enforced as manners. Cooperative hygiene endeavours such as sanitation also reduce pathogen prevalence. Our model allows us to integrate perspectives from psychology, ecology and cultural evolution with those of epidemiology and anthropology. Understanding the nature of disease avoidance psychology at all levels of human organization can inform the design of programmes to improve public health. PMID:21199843

Fatal autoimmunity results from the conditional deletion of Snai2 and Snai3

PubMed Central

Pioli, Peter D.; Chen, Xinjian; Weis, Janis J.; Weis, John H.

2015-01-01

Transcriptional regulation of gene expression is a key component of orchestrating proper immune cell development and function. One strategy for maintaining these transcriptional programs has been the evolution of transcription factor families with members possessing overlapping functions. Using the germ line deletion of Snai2 combined with the hematopoietic specific deletion of Snai3, we report that these factors function redundantly to preserve the development of B and T cells. Such animals display severe lymphopenia, alopecia and dermatitis as well as profound autoimmunity manifested by the production of high levels of autoantibodies as early as 3 weeks of age and die by 30 days after birth. Autoantibodies included both IgM and IgG isotypes and were reactive against cytoplasmic and membranous components. A regulatory T cell defect contributed to the autoimmune response in that adoptive transfer of wild type regulatory T cells alleviated symptoms of autoimmunity. Additionally, transplantation of Snai2/Snai3 double deficient bone marrow into Snai2 sufficient Rag2−/− recipients resulted in autoantibody generation. The results demonstrated that appropriate expression of Snai2 and Snai3 in cells of hematopoietic derivation plays an important role in development and maintenance of immune tolerance. PMID:25732600

Herpesvirus gB: A Finely Tuned Fusion Machine

PubMed Central

Cooper, Rebecca S.; Heldwein, Ekaterina E.

2015-01-01

Enveloped viruses employ a class of proteins known as fusogens to orchestrate the merger of their surrounding envelope and a target cell membrane. Most fusogens accomplish this task alone, by binding cellular receptors and subsequently catalyzing the membrane fusion process. Surprisingly, in herpesviruses, these functions are distributed among multiple proteins: the conserved fusogen gB, the conserved gH/gL heterodimer of poorly defined function, and various non-conserved receptor-binding proteins. We summarize what is currently known about gB from two closely related herpesviruses, HSV-1 and HSV-2, with emphasis on the structure of the largely uncharted membrane interacting regions of this fusogen. We propose that the unusual mechanism of herpesvirus fusion could be linked to the unique architecture of gB. PMID:26690469

The solid state environment orchestrates embryonic development and tissue remodeling

NASA Technical Reports Server (NTRS)

Damsky, C. H.; Moursi, A.; Zhou, Y.; Fisher, S. J.; Globus, R. K.

1997-01-01

Cell interactions with extracellular matrix and with other cells play critical roles in morphogenesis during development and in tissue homeostasis and remodeling throughout life. Extracellular matrix is information-rich, not only because it is comprised of multifunctional structural ligands for cell surface adhesion receptors, but also because it contains peptide signaling factors, and proteinases and their inhibitors. The functions of these groups of molecules are extensively interrelated. In this review, three primary cell culture models are described that focus on adhesion receptors and their roles in complex aspects of morphogenesis and remodeling: the regulation of proteinase expression by fibronectin and integrins in synovial fibroblasts; the regulation of osteoblast differentiation and survival by fibronectin, and the regulation of trophoblast differentiation and invasion by integrins, cadherins and immunoglobulin family adhesion receptors.

Targeting oncogenic Myc as a strategy for cancer treatment.

PubMed

Chen, Hui; Liu, Hudan; Qing, Guoliang

2018-01-01

The MYC family oncogene is deregulated in >50% of human cancers, and this deregulation is frequently associated with poor prognosis and unfavorable patient survival. Myc has a central role in almost every aspect of the oncogenic process, orchestrating proliferation, apoptosis, differentiation, and metabolism. Although Myc inhibition would be a powerful approach for the treatment of many types of cancers, direct targeting of Myc has been a challenge for decades owing to its "undruggable" protein structure. Hence, alternatives to Myc blockade have been widely explored to achieve desirable anti-tumor effects, including Myc/Max complex disruption, MYC transcription and/or translation inhibition, and Myc destabilization as well as the synthetic lethality associated with Myc overexpression. In this review, we summarize the latest advances in targeting oncogenic Myc, particularly for cancer therapeutic purposes.

Multifunctional Nature of the Arenavirus RING Finger Protein Z

PubMed Central

Fehling, Sarah Katharina; Lennartz, Frank; Strecker, Thomas

2012-01-01

Arenaviruses are a family of enveloped negative-stranded RNA viruses that can cause severe human disease ranging from encephalitis symptoms to fulminant hemorrhagic fever. The bi‑segmented RNA genome encodes four polypeptides: the nucleoprotein NP, the surface glycoprotein GP, the polymerase L, and the RING finger protein Z. Although it is the smallest arenavirus protein with a length of 90 to 99 amino acids and a molecular weight of approx. 11 kDa, the Z protein has multiple functions in the viral life cycle including (i) regulation of viral RNA synthesis, (ii) orchestration of viral assembly and budding, (iii) interaction with host cell proteins, and (iv) interferon antagonism. In this review, we summarize our current understanding of the structural and functional role of the Z protein in the arenavirus replication cycle. PMID:23202512

Implementing High-Performance Geometric Multigrid Solver with Naturally Grained Messages

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

Shan, Hongzhang; Williams, Samuel; Zheng, Yili

2015-10-26

Structured-grid linear solvers often require manually packing and unpacking of communication data to achieve high performance.Orchestrating this process efficiently is challenging, labor-intensive, and potentially error-prone.In this paper, we explore an alternative approach that communicates the data with naturally grained messagesizes without manual packing and unpacking. This approach is the distributed analogue of shared-memory programming, taking advantage of the global addressspace in PGAS languages to provide substantial programming ease. However, its performance may suffer from the large number of small messages. We investigate theruntime support required in the UPC ++ library for this naturally grained version to close the performance gapmore » between the two approaches and attain comparable performance at scale using the High-Performance Geometric Multgrid (HPGMG-FV) benchmark as a driver.« less

Chemical chronobiology: Toward drugs manipulating time.

PubMed

Wallach, Thomas; Kramer, Achim

2015-06-22

Circadian clocks are endogenous timing systems orchestrating the daily regulation of a huge variety of physiological, metabolic and behavioral processes. These clocks are important for health - in mammals, their disruption leads to a diverse number of pathologies. While genetic and biochemical approaches largely uncovered the molecular bases of circadian rhythm generation, chemical biology strategies targeting the circadian oscillator by small chemical compounds are increasingly developed. Here, we review the recent progress in the identification of small molecules modulating circadian rhythms. We focus on high-throughput screening approaches using circadian bioluminescence reporter cell lines as well as describe alternative mechanistic screens. Furthermore, we discuss the potential for chemical optimization of small molecule ligands with regard to the recent progress in structural chronobiology. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Comparative Structural Models of Similarities and Differences between "Vehicle" and "Target" in Order to Teach Darwinian "Evolution"

ERIC Educational Resources Information Center

Marcelos, Maria Fatima; Nagem, Ronaldo L.

2010-01-01

Our objective is to contribute to the teaching of Classical Darwinian "Evolution" by means of a study of analogies and metaphors. Throughout the history of knowledge about "Evolution" and in Science teaching, tree structures have been used an analogs to refer to "Evolution," such as by Darwin in the "Tree of Life" passage contained in "On The…

Evolution processes of the corrosion behavior and structural characteristics of plasma electrolytic oxidation coatings on AZ31 magnesium alloy

NASA Astrophysics Data System (ADS)

Chen, Dong; Wang, Ruiqiang; Huang, Zhiquan; Wu, Yekang; Zhang, Yi; Wu, Guorui; Li, Dalong; Guo, Changhong; Jiang, Guirong; Yu, Shengxue; Shen, Dejiu; Nash, Philip

2018-03-01

Evolution processes of the corrosion behavior and structural characteristics of the plasma electrolytic oxidation (PEO) coated AZ31 magnesium alloy were investigated by using scanning electron microscope (SEM) equipped with energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), potentio-dynamic polarization curves and electrochemical impedance spectroscopy (EIS) measurements. Detached coating samples were fabricated by an electrochemical method and more details of the internal micro-structure of coatings were clearly observed on the fractured cross-section morphologies of the samples compared to general polished cross-section morphologies. Evolution mechanisms of the coating corrosion behavior in relation to the evolution of micro-structural characteristics were discussed in detail.

Metaphors, models and organisational ethics in health care

PubMed Central

McCrickerd, J.

2000-01-01

Crucial to discussions in organisational ethics is an evaluation of the metaphors and models we use to understand the organisations we are discussing. I briefly defend this contention and evaluate three possible models: the current corporate model, an orchestrator model which puts hospitals in the same class as malls and airports, and a community model. I argue that the corporate and orchestrator model push to the background some important organisational ethics issues and bias us inappropriately towards certain solutions. Furthermore, I argue that the community model allows these to be more easily brought up. I also respond to the likely challenge that hospitals really are corporations by arguing that this is not relevant to evaluations of the appropriateness of the corporate model. Key Words: Metaphor • model • organisational ethics • health care ethics PMID:11055036

A UV-B-specific signaling component orchestrates plant UV protection

PubMed Central

Brown, Bobby A.; Cloix, Catherine; Jiang, Guang Huai; Kaiserli, Eirini; Herzyk, Pawel; Kliebenstein, Daniel J.; Jenkins, Gareth I.

2005-01-01

UV-B radiation in sunlight has diverse effects on humans, animals, plants, and microorganisms. UV-B can cause damage to molecules and cells, and consequently organisms need to protect against and repair UV damage to survive in sunlight. In plants, low nondamaging levels of UV-B stimulate transcription of genes involved in UV-protective responses. However, remarkably little is known about the underlying mechanisms of UV-B perception and signal transduction. Here we report that Arabidopsis UV RESISTANCE LOCUS 8 (UVR8) is a UV-B-specific signaling component that orchestrates expression of a range of genes with vital UV-protective functions. Moreover, we show that UVR8 regulates expression of the transcription factor HY5 specifically when the plant is exposed to UV-B. We demonstrate that HY5 is a key effector of the UVR8 pathway, and that it is required for survival under UV-B radiation. UVR8 has sequence similarity to the eukaryotic guanine nucleotide exchange factor RCC1, but we found that it has little exchange activity. However, UVR8, like RCC1, is located principally in the nucleus and associates with chromatin via histones. Chromatin immunoprecipitation showed that UVR8 associates with chromatin in the HY5 promoter region, providing a mechanistic basis for its involvement in regulating transcription. We conclude that UVR8 defines a UV-B-specific signaling pathway in plants that orchestrates the protective gene expression responses to UV-B required for plant survival in sunlight. PMID:16330762

Orchestrating the Selection and Packaging of Genomic RNA by Retroviruses: An Ensemble of Viral and Host Factors

PubMed Central

Kaddis Maldonado, Rebecca J.; Parent, Leslie J.

2016-01-01

Infectious retrovirus particles contain two copies of unspliced viral RNA that serve as the viral genome. Unspliced retroviral RNA is transcribed in the nucleus by the host RNA polymerase II and has three potential fates: (1) it can be spliced into subgenomic messenger RNAs (mRNAs) for the translation of viral proteins; or it can remain unspliced to serve as either (2) the mRNA for the translation of Gag and Gag–Pol; or (3) the genomic RNA (gRNA) that is packaged into virions. The Gag structural protein recognizes and binds the unspliced viral RNA to select it as a genome, which is selected in preference to spliced viral RNAs and cellular RNAs. In this review, we summarize the current state of understanding about how retroviral packaging is orchestrated within the cell and explore potential new mechanisms based on recent discoveries in the field. We discuss the cis-acting elements in the unspliced viral RNA and the properties of the Gag protein that are required for their interaction. In addition, we discuss the role of host factors in influencing the fate of the newly transcribed viral RNA, current models for how retroviruses distinguish unspliced viral mRNA from viral genomic RNA, and the possible subcellular sites of genomic RNA dimerization and selection by Gag. Although this review centers primarily on the wealth of data available for the alpharetrovirus Rous sarcoma virus, in which a discrete RNA packaging sequence has been identified, we have also summarized the cis- and trans-acting factors as well as the mechanisms governing gRNA packaging of other retroviruses for comparison. PMID:27657110

Structure and Evolution of the Lunar Interior

NASA Technical Reports Server (NTRS)

Andrews-Hanna, J. C.; Weber, R. C.; Ishihara, Y.; Kamata, S.; Keane, J.; Kiefer, W. S.; Matsuyama, I.; Siegler, M.; Warren, P.

2017-01-01

Early in its evolution, the Moon underwent a magma ocean phase leading to its differentiation into a feldspathic crust, cumulate mantle, and iron core. However, far from the simplest view of a uniform plagioclase flotation crust, the present-day crust of the Moon varies greatly in thickness, composition, and physical properties. Recent significant improvements in both data and analysis techniques have yielded fundamental advances in our understanding of the structure and evolution of the lunar interior. The structure of the crust is revealed by gravity, topography, magnetics, seismic, radar, electromagnetic, and VNIR remote sensing data. The mantle structure of the Moon is revealed primarily by seismic and laser ranging data. Together, this data paints a picture of a Moon that is heterogeneous in all directions and across all scales, whose structure is a result of its unique formation, differentiation, and subsequent evolution. This brief review highlights a small number of recent advances in our understanding of lunar structure.

Structural evolution and properties of small-size thiol-protected gold nanoclusters

NASA Astrophysics Data System (ADS)

Ma, Miaomiao; Liu, Liren; Zhu, Hengjiang; Lu, Junzhe; Tan, Guiping

2018-07-01

Ligand-protected gold clusters are widely used in biosensors and catalysis. Understanding the structural evolution of these kinds of nanoclusters is important for experimental synthesis. Herein, based on the particle swarm optimisation algorithm and density functional theory method, we use [Au1(SH)2]n, [Au2(SH)3]n, [Au3(SH)4]n (n = 1-3) as basic units to research the structural evolution relationships from building blocks to the final whole structures. Results show that there is a 'line-ring-core' structural evolution pattern in the growth process of the nanoclusters. The core structures of the ligand-protected gold clusters consist of Au3, Au4, Au6 and Au7 atoms. The electronics and optics analysis reflects that stability and optical properties gradually enhance with increase in size. These results can be used to understand the initial growth stage and design new ligand-protected nanoclusters.

PIECE 2.0: an update for the plant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparision and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in ...

Orchestrating the Soundscape.

ERIC Educational Resources Information Center

Neill, William G.

1982-01-01

Suggests discussion questions, demonstrations, and activities related to a Public Broadcasting Service documentary ("To Hear"). The basic theme of the program is that people don't realize the dangers of excessive noise because it is pervasive and invisible. (Author/JN)

The Academic Structure in Japan: Institutional Hierarchy and Academic Mobility.

ERIC Educational Resources Information Center

Arimoto, Akira

The characteristics of the Japanese academic structure are examined with attention to the evolution of institutional hierarchy, the closed academic structure, and the effects of the academic structure upon academic research. The evolution of Japan's institutional hierarchy in academics has been tightly related to factors of nationalism,…

Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

PubMed

Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

2016-06-01

Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

Monogamy, strongly bonded groups, and the evolution of human social structure.

PubMed

Chapais, Bernard

2013-01-01

Human social evolution has most often been treated in a piecemeal fashion, with studies focusing on the evolution of specific components of human society such as pair-bonding, cooperative hunting, male provisioning, grandmothering, cooperative breeding, food sharing, male competition, male violence, sexual coercion, territoriality, and between-group conflicts. Evolutionary models about any one of those components are usually concerned with two categories of questions, one relating to the origins of the component and the other to its impact on the evolution of human cognition and social life. Remarkably few studies have been concerned with the evolution of the entity that integrates all components, the human social system itself. That social system has as its core feature human social structure, which I define here as the common denominator of all human societies in terms of group composition, mating system, residence patterns, and kinship structures. The paucity of information on the evolution of human social structure poses substantial problems because that information is useful, if not essential, to assess both the origins and impact of any particular aspect of human society. Copyright © 2013 Wiley Periodicals, Inc.

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

PubMed Central

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

2014-01-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

Transitions in Sexuality: Recapitulation of an Ancestral Tri- and Tetrapolar Mating System in Cryptococcus neoformans▿ †

PubMed Central

Hsueh, Yen-Ping; Fraser, James A.; Heitman, Joseph

2008-01-01

Sex is orchestrated by the mating-type locus (MAT) in fungi and by sex chromosomes in plants and animals. In fungi, two patterns of sexuality occur: bipolar with a single, typically biallelic sex determinant that promotes inbreeding, and tetrapolar with two unlinked, often multiallelic sex determinants that restrict inbreeding. Multiallelism in either bipolar or tetrapolar mating systems promotes outcrossing. Cryptococcus neoformans is a pathogenic bipolar yeast with two unusually large MAT alleles (a/α) spanning >100 kb, ∼100-fold larger than many other fungal MAT loci. Based on comparative genomic analysis, this unusual MAT locus is hypothesized to have evolved from an ancestral tetrapolar system. In this model, the unlinked homeodomain (HD) transcription factor and pheromone/receptor tetrapolar loci acquired additional sex-related genes and then fused via chromosomal translocation, forming an intermediate transitional mating system (which we term tripolar), which then underwent recombination and gene conversion to fashion the extant bipolar MAT alleles. To experimentally validate this model, C. neoformans was engineered to have a tetrapolar mating system by relocating the MAT SXI1α and SXI2a HD genes to an unlinked genomic locale. Genetic and molecular analyses revealed that this modified organism could complete a tetrapolar sexual cycle. Analysis of progeny generated from bipolar, tripolar, and tetrapolar crosses provides direct experimental evidence that the tripolar state confers decreased fertility and therefore may represent an unstable evolutionary intermediate. These findings illustrate how transitions between outcrossing and inbreeding preference occur by involving sex determinant linkage and collapse from multiallelic to biallelic sex determination, providing insights into both fungal sex evolution and early steps in sex chromosome evolution. PMID:18723606

Biology of bone and how it orchestrates the form and function of the skeleton

NASA Technical Reports Server (NTRS)

Sommerfeldt, D. W.; Rubin, C. T.

2001-01-01

The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

Acoustic structure of the five perceptual dimensions of timbre in orchestral instrument tones

PubMed Central

Elliott, Taffeta M.; Hamilton, Liberty S.; Theunissen, Frédéric E.

2013-01-01

Attempts to relate the perceptual dimensions of timbre to quantitative acoustical dimensions have been tenuous, leading to claims that timbre is an emergent property, if measurable at all. Here, a three-pronged analysis shows that the timbre space of sustained instrument tones occupies 5 dimensions and that a specific combination of acoustic properties uniquely determines gestalt perception of timbre. Firstly, multidimensional scaling (MDS) of dissimilarity judgments generated a perceptual timbre space in which 5 dimensions were cross-validated and selected by traditional model comparisons. Secondly, subjects rated tones on semantic scales. A discriminant function analysis (DFA) accounting for variance of these semantic ratings across instruments and between subjects also yielded 5 significant dimensions with similar stimulus ordination. The dimensions of timbre space were then interpreted semantically by rotational and reflectional projection of the MDS solution into two DFA dimensions. Thirdly, to relate this final space to acoustical structure, the perceptual MDS coordinates of each sound were regressed with its joint spectrotemporal modulation power spectrum. Sound structures correlated significantly with distances in perceptual timbre space. Contrary to previous studies, most perceptual timbre dimensions are not the result of purely temporal or spectral features but instead depend on signature spectrotemporal patterns. PMID:23297911

Biology of Bone Tissue: Structure, Function, and Factors That Influence Bone Cells

PubMed Central

Florencio-Silva, Rinaldo; Sasso-Cerri, Estela; Simões, Manuel Jesus; Cerri, Paulo Sérgio

2015-01-01

Bone tissue is continuously remodeled through the concerted actions of bone cells, which include bone resorption by osteoclasts and bone formation by osteoblasts, whereas osteocytes act as mechanosensors and orchestrators of the bone remodeling process. This process is under the control of local (e.g., growth factors and cytokines) and systemic (e.g., calcitonin and estrogens) factors that all together contribute for bone homeostasis. An imbalance between bone resorption and formation can result in bone diseases including osteoporosis. Recently, it has been recognized that, during bone remodeling, there are an intricate communication among bone cells. For instance, the coupling from bone resorption to bone formation is achieved by interaction between osteoclasts and osteoblasts. Moreover, osteocytes produce factors that influence osteoblast and osteoclast activities, whereas osteocyte apoptosis is followed by osteoclastic bone resorption. The increasing knowledge about the structure and functions of bone cells contributed to a better understanding of bone biology. It has been suggested that there is a complex communication between bone cells and other organs, indicating the dynamic nature of bone tissue. In this review, we discuss the current data about the structure and functions of bone cells and the factors that influence bone remodeling. PMID:26247020

Cleft Lip and Palate Surgery

MedlinePlus

... The experts in face, mouth and jaw surgery. Cleft Lip / Palate and Craniofacial Surgery This type of surgery is ... the carefully orchestrated, multiple-stage correctional program for cleft lip and palate patients. The goal is to help restore the ...

Teaching Children How to Discuss What They Read.

ERIC Educational Resources Information Center

Perez, Samuel A.; Strickland, Eric V.

1986-01-01

Explains that teachers must understand that discussion is not a simple collection of listening and speaking skills but a dynamic event that requires children to orchestrate a number of language skills. Offers suggestions for improving discussions. (FL)

Constituency Input into Budget Management.

ERIC Educational Resources Information Center

Miller, Norman E.

1995-01-01

Presents techniques for ensuring constituency involvement in district- and site-level budget management. Outlines four models for securing constituent input and focuses on strategies to orchestrate the more complex model for staff and community participation. Two figures are included. (LMI)

Retrograde Signals: Integrators of Interorganellar Communication and Orchestrators of Plant Development.

PubMed

de Souza, Amancio; Wang, Jin-Zheng; Dehesh, Katayoon

2017-04-28

Interorganellar cooperation maintained via exquisitely controlled retrograde-signaling pathways is an evolutionary necessity for maintenance of cellular homeostasis. This signaling feature has therefore attracted much research attention aimed at improving understanding of the nature of these communication signals, how the signals are sensed, and ultimately the mechanism by which they integrate targeted processes that collectively culminate in organellar cooperativity. The answers to these questions will provide insight into how retrograde-signal-mediated regulatory mechanisms are recruited and which biological processes are targeted, and will advance our understanding of how organisms balance metabolic investments in growth against adaptation to environmental stress. This review summarizes the present understanding of the nature and the functional complexity of retrograde signals as integrators of interorganellar communication and orchestrators of plant development, and offers a perspective on the future of this critical and dynamic area of research.

Orchestration of carbohydrate processing for crassulacean acid metabolism

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

Borland, Anne M.; Guo, Hao-Bo; Yang, Xiaohan

The production of phosphoenolpyruvate as a substrate for nocturnal CO 2 uptake represents a significant sink for carbohydrate in CAM plants which has to be balanced with the provisioning of carbohydrate for growth and maintenance. In starch-storing CAM species, diversification in chloroplast metabolite transporters, and the deployment of both phosphorolytic and hydrolytic routes of starch degradation accommodate a division of labour in directing C-skeletons towards nocturnal carboxylation or production of sucrose for growth. In soluble-sugar storing CAM plants, the vacuole plays a central role in managing carbon homeostasis. The molecular identities of various types of vacuolar sugar transporters have onlymore » been identified for C 3 species within the last 10 years. In conclusion, the recent availability of CAM genomes enables the identification of putative orthologues of vacuolar sugar transporters which represent strategic targets for orchestrating the diel provisioning of substrate for nocturnal carboxylation and growth.« less

Cascade of neural processing orchestrates cognitive control in human frontal cortex

PubMed Central

Tang, Hanlin; Yu, Hsiang-Yu; Chou, Chien-Chen; Crone, Nathan E; Madsen, Joseph R; Anderson, William S; Kreiman, Gabriel

2016-01-01

Rapid and flexible interpretation of conflicting sensory inputs in the context of current goals is a critical component of cognitive control that is orchestrated by frontal cortex. The relative roles of distinct subregions within frontal cortex are poorly understood. To examine the dynamics underlying cognitive control across frontal regions, we took advantage of the spatiotemporal resolution of intracranial recordings in epilepsy patients while subjects resolved color-word conflict. We observed differential activity preceding the behavioral responses to conflict trials throughout frontal cortex; this activity was correlated with behavioral reaction times. These signals emerged first in anterior cingulate cortex (ACC) before dorsolateral prefrontal cortex (dlPFC), followed by medial frontal cortex (mFC) and then by orbitofrontal cortex (OFC). These results disassociate the frontal subregions based on their dynamics, and suggest a temporal hierarchy for cognitive control in human cortex. DOI: http://dx.doi.org/10.7554/eLife.12352.001 PMID:26888070

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut.

PubMed

Howitt, Michael R; Lavoie, Sydney; Michaud, Monia; Blum, Arthur M; Tran, Sara V; Weinstock, Joel V; Gallini, Carey Ann; Redding, Kevin; Margolskee, Robert F; Osborne, Lisa C; Artis, David; Garrett, Wendy S

2016-03-18

The intestinal epithelium forms an essential barrier between a host and its microbiota. Protozoa and helminths are members of the gut microbiota of mammals, including humans, yet the many ways that gut epithelial cells orchestrate responses to these eukaryotes remain unclear. Here we show that tuft cells, which are taste-chemosensory epithelial cells, accumulate during parasite colonization and infection. Disruption of chemosensory signaling through the loss of TRMP5 abrogates the expansion of tuft cells, goblet cells, eosinophils, and type 2 innate lymphoid cells during parasite colonization. Tuft cells are the primary source of the parasite-induced cytokine interleukin-25, which indirectly induces tuft cell expansion by promoting interleukin-13 production by innate lymphoid cells. Our results identify intestinal tuft cells as critical sentinels in the gut epithelium that promote type 2 immunity in response to intestinal parasites. Copyright © 2016, American Association for the Advancement of Science.

Roles of Teachers in Orchestrating Learning in Elementary Science Classrooms

NASA Astrophysics Data System (ADS)

Zhai, Junqing; Tan, Aik-Ling

2015-12-01

This study delves into the different roles that elementary science teachers play in the classroom to orchestrate science learning opportunities for students. Examining the classroom practices of three elementary science teachers in Singapore, we found that teachers shuttle between four key roles in enabling student learning in science. Teachers can play the role of (1) dispenser of knowledge (giver), (2) mentor of learning (advisor), (3) monitor of students' activities (police), and (4) partner in inquiry (colearner). These roles are dynamic, and while teachers show a preference for one of the four roles, factors such as the nature of the task, the types of students, as well as the availability of time and resources affect the role that teachers adopt. The roles that teachers play in the classroom have implications for the practice of science as inquiry in the classroom as well as the identities that teachers and students form in the science learning process.

Agile battle management efficiency for command, control, communications, computers and intelligence (C4I)

NASA Astrophysics Data System (ADS)

Blasch, Erik; Bélanger, Micheline

2016-05-01

Various operations such as civil-military co-operation (CIMIC) affairs require orchestration of communications, assets, and actors. A key component includes technology advancements to enable coordination among people and machines the ability to know where things are, who to coordinate with, and open and consistent lines of communication. In this paper, we explore concepts of battle management (BM) to support high-tempo emergency response scenarios such as a disaster action response team (DART). Three concepts highlighted of agile battle management (ABM) include source orchestration (e.g., sensors and domains), battle management language (BML) development (e.g., software and ontologies), and command and control (C2) coordination (e.g., people and visualization); which require correlation and de-confliction. These concepts of ABM support the physical, information, and cognitive domains for efficient command, control, communications, and information (C3I) to synchronize data and people for efficient and effective operations.

Design and implementation of a non-linear symphonic soundtrack of a video game

NASA Astrophysics Data System (ADS)

Sporka, Adam J.; Valta, Jan

2017-10-01

The music in the contemporary video games is often interactive. The music playback is based on transitions between pieces of available music material. These transitions happen in response to evolving gameplay. This paradigm is referred to as the adaptive music. Our challenge was to design, create, and implement the soundtrack of the upcoming video game Kingdom Come: Deliverance. Our soundtrack is a collection of compositions with symphonic orchestration. Per our design decision, our intention was to implement the adaptive music in a way which respected the nature of the orchestral film score. We created our own adaptive music middleware, called Sequence Music Engine, implementing a high-level music logic as well as the low-level playback infrastructure. Our system can handle hours of video game music, helps maintain the relevance of the music throughout the video game, and minimises the repetitiveness of the individual pieces.

Orchestration of carbohydrate processing for crassulacean acid metabolism

DOE PAGES

Borland, Anne M.; Guo, Hao-Bo; Yang, Xiaohan; ...

2016-04-19

The production of phosphoenolpyruvate as a substrate for nocturnal CO 2 uptake represents a significant sink for carbohydrate in CAM plants which has to be balanced with the provisioning of carbohydrate for growth and maintenance. In starch-storing CAM species, diversification in chloroplast metabolite transporters, and the deployment of both phosphorolytic and hydrolytic routes of starch degradation accommodate a division of labour in directing C-skeletons towards nocturnal carboxylation or production of sucrose for growth. In soluble-sugar storing CAM plants, the vacuole plays a central role in managing carbon homeostasis. The molecular identities of various types of vacuolar sugar transporters have onlymore » been identified for C 3 species within the last 10 years. In conclusion, the recent availability of CAM genomes enables the identification of putative orthologues of vacuolar sugar transporters which represent strategic targets for orchestrating the diel provisioning of substrate for nocturnal carboxylation and growth.« less

Multimodal Teaching Analytics: Automated Extraction of Orchestration Graphs from Wearable Sensor Data.

PubMed

Prieto, Luis P; Sharma, Kshitij; Kidzinski, Łukasz; Rodríguez-Triana, María Jesús; Dillenbourg, Pierre

2018-04-01

The pedagogical modelling of everyday classroom practice is an interesting kind of evidence, both for educational research and teachers' own professional development. This paper explores the usage of wearable sensors and machine learning techniques to automatically extract orchestration graphs (teaching activities and their social plane over time), on a dataset of 12 classroom sessions enacted by two different teachers in different classroom settings. The dataset included mobile eye-tracking as well as audiovisual and accelerometry data from sensors worn by the teacher. We evaluated both time-independent and time-aware models, achieving median F1 scores of about 0.7-0.8 on leave-one-session-out k-fold cross-validation. Although these results show the feasibility of this approach, they also highlight the need for larger datasets, recorded in a wider variety of classroom settings, to provide automated tagging of classroom practice that can be used in everyday practice across multiple teachers.

Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years

PubMed Central

Nicosia, Aldo; Maggio, Teresa; Costa, Salvatore; Salamone, Monica; Tagliavia, Marcello; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela

2016-01-01

Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations. PMID:26957029

Spontaneous oscillation and fluid-structure interaction of cilia.

PubMed

Han, Jihun; Peskin, Charles S

2018-04-24

The exact mechanism to orchestrate the action of hundreds of dynein motor proteins to generate wave-like ciliary beating remains puzzling and has fascinated many scientists. We present a 3D model of a cilium and the simulation of its beating in a fluid environment. The model cilium obeys a simple geometric constraint that arises naturally from the microscopic structure of a real cilium. This constraint allows us to determine the whole 3D structure at any instant in terms of the configuration of a single space curve. The tensions of active links, which model the dynein motor proteins, follow a postulated dynamical law, and together with the passive elasticity of microtubules, this dynamical law is responsible for the ciliary motions. In particular, our postulated tension dynamics lead to the instability of a symmetrical steady state, in which the cilium is straight and its active links are under equal tensions. The result of this instability is a stable, wave-like, limit cycle oscillation. We have also investigated the fluid-structure interaction of cilia using the immersed boundary (IB) method. In this setting, we see not only coordination within a single cilium but also, coordinated motion, in which multiple cilia in an array organize their beating to pump fluid, in particular by breaking phase synchronization.

Culture and biology in the origins of linguistic structure.

PubMed

Kirby, Simon

2017-02-01

Language is systematically structured at all levels of description, arguably setting it apart from all other instances of communication in nature. In this article, I survey work over the last 20 years that emphasises the contributions of individual learning, cultural transmission, and biological evolution to explaining the structural design features of language. These 3 complex adaptive systems exist in a network of interactions: individual learning biases shape the dynamics of cultural evolution; universal features of linguistic structure arise from this cultural process and form the ultimate linguistic phenotype; the nature of this phenotype affects the fitness landscape for the biological evolution of the language faculty; and in turn this determines individuals' learning bias. Using a combination of computational simulation, laboratory experiments, and comparison with real-world cases of language emergence, I show that linguistic structure emerges as a natural outcome of cultural evolution once certain minimal biological requirements are in place.

Tidal dissipation in rotating low-mass stars and implications for the orbital evolution of close-in planets. I. From the PMS to the RGB at solar metallicity

NASA Astrophysics Data System (ADS)

Gallet, F.; Bolmont, E.; Mathis, S.; Charbonnel, C.; Amard, L.

2017-08-01

Context. Star-planet interactions must be taken into account in stellar models to understand the dynamical evolution of close-in planets. The dependence of the tidal interactions on the structural and rotational evolution of the star is of particular importance and should be correctly treated. Aims: We quantify how tidal dissipation in the convective envelope of rotating low-mass stars evolves from the pre-main sequence up to the red-giant branch depending on the initial stellar mass. We investigate the consequences of this evolution on planetary orbital evolution. Methods: We couple the tidal dissipation formalism previously described to the stellar evolution code STAREVOL and apply this coupling to rotating stars with masses between 0.3 and 1.4 M⊙. As a first step, this formalism assumes a simplified bi-layer stellar structure with corresponding averaged densities for the radiative core and the convective envelope. We use a frequency-averaged treatment of the dissipation of tidal inertial waves in the convection zone (but neglect the dissipation of tidal gravity waves in the radiation zone). In addition, we generalize a recent work by following the orbital evolution of close-in planets using the new tidal dissipation predictions for advanced phases of stellar evolution. Results: On the pre-main sequence the evolution of tidal dissipation is controlled by the evolution of the internal structure of the contracting star. On the main sequence it is strongly driven by the variation of surface rotation that is impacted by magnetized stellar winds braking. The main effect of taking into account the rotational evolution of the stars is to lower the tidal dissipation strength by about four orders of magnitude on the main sequence, compared to a normalized dissipation rate that only takes into account structural changes. Conclusions: The evolution of the dissipation strongly depends on the evolution of the internal structure and rotation of the star. From the pre-main sequence up to the tip of the red-giant branch, it varies by several orders of magnitude, with strong consequences for the orbital evolution of close-in massive planets. These effects are the strongest during the pre-main sequence, implying that the planets are mainly sensitive to the star's early history.

Responds of Bone Cells to Microgravity: Ground-Based Research

NASA Astrophysics Data System (ADS)

Zhang, Jian; Li, Jingbao; Xu, Huiyun; Yang, Pengfei; Xie, Li; Qian, Airong; Zhao, Yong; Shang, Peng

2015-11-01

Severe loss of bone occurs due to long-duration spaceflight. Mechanical loading stimulates bone formation, while bone degradation happens under mechanical unloading. Bone remodeling is a dynamic process in which bone formation and bone resorption are tightly coupled. Increased bone resorption and decreased bone formation caused by reduced mechanical loading, generally result in disrupted bone remodeling. Bone remodeling is orchestrated by multiple bone cells including osteoblast, osteocyte, osteoclast and mesenchymal stem cell. It is yet not clear that how these bone cells sense altered gravity, translate physical stimulus into biochemical signals, and then regulate themselves structurally and functionally. In this paper, studies elucidating the bioeffects of microgravity on bone cells (osteoblast, osteocyte, osteoclast, mesenchymal stem cell) using various platforms including spaceflight and ground-based simulated microgravity were summarized. Promising gravity-sensitive signaling pathways and protein molecules were proposed.

How to Crack the Sugar Code.

PubMed

Gabius, H-J

2017-01-01

The known ubiquitous presence of glycans fulfils an essential prerequisite for fundamental roles in cell sociology. Since carbohydrates are chemically predestined to form biochemical messages of a maximum of structural diversity in a minimum of space, coding of biological information by sugars is the reason for the broad occurrence of cellular glycoconjugates. Their glycans originate from sophisticated enzymatic assembly and dynamically adaptable remodelling. These signals are read and translated into effects by receptors (lectins). The functional pairing between lectins and their counterreceptor(s) is highly specific, often orchestrated by intimate co-regulation of the receptor, the cognate glycan and the bioactive scaffold (e.g., an integrin). Bottom-up approaches, teaming up synthetic and supramolecular chemistry to prepare fully programmable nanoparticles as binding partners with systematic network analysis of lectins and rational design of variants, enable us to delineate the rules of the sugar code.

From data to the decision: A software architecture to integrate predictive modelling in clinical settings.

PubMed

Martinez-Millana, A; Fernandez-Llatas, C; Sacchi, L; Segagni, D; Guillen, S; Bellazzi, R; Traver, V

2015-08-01

The application of statistics and mathematics over large amounts of data is providing healthcare systems with new tools for screening and managing multiple diseases. Nonetheless, these tools have many technical and clinical limitations as they are based on datasets with concrete characteristics. This proposition paper describes a novel architecture focused on providing a validation framework for discrimination and prediction models in the screening of Type 2 diabetes. For that, the architecture has been designed to gather different data sources under a common data structure and, furthermore, to be controlled by a centralized component (Orchestrator) in charge of directing the interaction flows among data sources, models and graphical user interfaces. This innovative approach aims to overcome the data-dependency of the models by providing a validation framework for the models as they are used within clinical settings.

Models of chromatin spatial organisation in the cell nucleus

NASA Astrophysics Data System (ADS)

Nicodemi, Mario

2014-03-01

In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Recent experiments have started unveiling the interaction map of DNA sites genome-wide, revealing different levels of organisation at different scales. The principles, though, which orchestrate such a complex 3D structure remain still mysterious. I will overview the scenario emerging from some classical polymer physics models of the general aspect of chromatin spatial organisation. The available experimental data, which can be rationalised in a single framework, support a picture where chromatin is a complex mixture of differently folded regions, self-organised across spatial scales according to basic physical mechanisms. I will also discuss applications to specific DNA loci, e.g. the HoxB locus, where models informed with biological details, and tested against targeted experiments, can help identifying the determinants of folding.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

PubMed Central

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-01-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions. PMID:26355955

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co(2+) Solution: Interactional Performance and Mechanism.

PubMed

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-10

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co(2+) solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co(2+) reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the "structural influence" crucial for the full and dynamical understanding of nZVI reactions.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions.

A study of an adaptive replication framework for orchestrated composite web services.

PubMed

Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

2013-01-01

Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

Evidence-informed physical therapy management of performance-related musculoskeletal disorders in musicians

PubMed Central

Chan, Cliffton; Ackermann, Bronwen

2014-01-01

Playing a musical instrument at an elite level is a highly complex motor skill. The regular daily training loads resulting from practice, rehearsals and performances place great demands on the neuromusculoskeletal systems of the body. As a consequence, performance-related musculoskeletal disorders (PRMDs) are globally recognized as common phenomena amongst professional orchestral musicians. These disorders create a significant financial burden to individuals and orchestras as well as lead to serious consequences to the musicians’ performance and ultimately their career. Physical therapists are experts in treating musculoskeletal injuries and are ideally placed to apply their skills to manage PRMDs in this hyper-functioning population, but there is little available evidence to guide specific injury management approaches. An Australia-wide survey of professional orchestral musicians revealed that the musicians attributed excessively high or sudden increase in playing-load as major contributors to their PRMDs. Therefore, facilitating musicians to better manage these loads should be a cornerstone of physical therapy management. The Sound Practice orchestral musicians work health and safety project used formative and process evaluation approaches to develop evidence-informed and clinically applicable physical therapy interventions, ultimately resulting in favorable outcomes. After these methodologies were employed, the intervention studies were conducted with a national cohort of professional musicians including: health education, onsite injury management, cross-training exercise regimes, performance postural analysis, and music performance biomechanics feedback. The outcomes of all these interventions will be discussed alongside a focussed review on the existing literature of these management strategies. Finally, a framework for best-practice physical therapy management of PRMDs in musicians will be provided. PMID:25071671

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

Expanding protein universe and its origin from the biological Big Bang.

PubMed

Dokholyan, Nikolay V; Shakhnovich, Boris; Shakhnovich, Eugene I

2002-10-29

The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. By understanding the cause of these patterns, we attempt to glance at the very origin of life.

32 CFR 159.6 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... as country information and cultural training, and guidance on working with host country nationals and... geographic Combatant Commander shall develop and publish guidance and procedures for PSCs and PSC personnel....49, “Orchestrating, Synchronizing, and Integrating Program Management of Contingency Acquisition...

32 CFR 159.6 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... as country information and cultural training, and guidance on working with host country nationals and... geographic Combatant Commander shall develop and publish guidance and procedures for PSCs and PSC personnel....49, “Orchestrating, Synchronizing, and Integrating Program Management of Contingency Acquisition...

32 CFR 159.6 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... as country information and cultural training, and guidance on working with host country nationals and... geographic Combatant Commander shall develop and publish guidance and procedures for PSCs and PSC personnel....49, “Orchestrating, Synchronizing, and Integrating Program Management of Contingency Acquisition...

32 CFR 159.6 - Procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

....49, “Orchestrating, Synchronizing, and Integrating Program Management of Contingency Acquisition... increased risk or planned or ongoing military operations, including how PSC personnel will be rapidly... 13 shall provide the framework for the development of guidance and procedures without regard to the...

Understanding the evolution of Mammalian brain structures; the need for a (new) cerebrotype approach.

PubMed

Willemet, Romain

2012-05-18

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular ("mosaic evolution") to coordinated changes in brain structure size ("concerted evolution") or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a "taxon cerebrotype". In other taxa, no clear pattern is found, reflecting heterogeneity of the species' lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex "space" of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution.

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Microstructural properties and evolution of nanoclusters in liquid Si during a rapid cooling process

NASA Astrophysics Data System (ADS)

Gao, T.; Hu, X.; Li, Y.; Tian, Z.; Xie, Q.; Chen, Q.; Liang, Y.; Luo, X.; Ren, L.; Luo, J.

2017-11-01

The formation of amorphous structures in Si during the rapid quenching process was studied based on molecular dynamics simulation by using the Stillinger-Weber potential. The evolution characteristics of nanoclusters during the solidification were analyzed by several structural analysis methods. The amorphous Si has been formed with many tetrahedral clusters and few nanoclusters. During the solidification, tetrahedral polyhedrons affect the local structures by their different positions and connection modes. The main kinds of polyhedrons randomly linked with one another to form an amorphous network structures in the system. The structural evolution of crystal nanocluster demonstrates that the nanocluster has difficulty to growth because of the high cooling rate of 1012 K/s.

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.

PubMed

Havird, Justin C; Whitehill, Nicholas S; Snow, Christopher D; Sloan, Daniel B

2015-12-01

Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Flow Modulation and Force Control of Flapping Wings

DTIC Science & Technology

2014-10-29

evolution of which reflect the wing morphology and kinematics. While the near-wake vortex system directly reflects the action of the wing on the...at 8 different stroke positions, which demonstrate the evolution of the vortex wake structure. The contour plot of Z vorticity at X-Y plane (Z...20 Figure 14. Smoke patterns showing the evolution of the flow structure in an

Ion transport across the biological membrane by computational protein design

NASA Astrophysics Data System (ADS)

Grigoryan, Gevorg

The cellular membrane is impermeable to most of the chemicals the cell needs to take in or discard to survive. Therefore, transporters-a class of transmembrane proteins tasked with shuttling cargo chemicals in and out of the cell-are essential to all cellular life. From existing crystal structures, we know transporters to be complex machines, exquisitely tuned for specificity and controllability. But how could membrane-bound life have evolved if it needed such complex machines to exist first? To shed light onto this question, we considered the task of designing a transporter de novo. As our guiding principle, we took the ``alternating-access model''-a conceptual mechanism stating that transporters work by rocking between two conformations, each exposing the cargo-binding site to either the intra- or the extra-cellular environment. A computational design framework was developed to encode an anti-parallel four-helix bundle that rocked between two alternative states to orchestrate the movement of Zn(II) ions across the membrane. The ensemble nature of both states was accounted for using a free energy-based approach, and sequences were chosen based on predicted formation of the targeted topology in the membrane and bi-stability. A single sequence was prepared experimentally and shown to function as a Zn(II) transporter in lipid vesicles. Further, transport was specific to Zn(II) ions and several control peptides supported the underlying design principles. This included a mutant designed to retain all properties but with reduced rocking, which showed greatly depressed transport ability. These results suggest that early transporters could have evolved in the context of simple topologies, to be later tuned by evolution for improved properties and controllability. Our study also serves as an important advance in computational protein design, showing the feasibility of designing functional membrane proteins and of tuning conformational landscapes for desired function. Alfred P. Sloan Foundation Research Fellowship.

Workshop on the Tectonic Evolution of Greenstone Belts (supplement containing abstracts of invited talks and late abstracts)

NASA Technical Reports Server (NTRS)

1986-01-01

Topics addressed include: greenstone belt tectonics, thermal constaints, geological structure, rock components, crustal accretion model, geological evolution, synsedimentary deformation, Archean structures and geological faults.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+Soultion : Interactional Performance and Mechanism

NASA Astrophysics Data System (ADS)

Dai, C.; Zhang, Y.

2015-12-01

The nanoscale particle and low oxidation reduction potential make nano zero-valent iron (nZVI) an efficient sorbent and reductant for treating many kinds of organic contaminants and heavy metals.The structures of nanoscale zero-valent iron (nZVI) particles are evolving in reactions, and the reactions are influenced by the evolved structures. In order to understand the detail removal process, it is important to investigate the interactions between reactions and structural evolution. In this work, reactions between nZVI and Co2+ at different initial concentrations in anoxic aqueous solutions (to eliminate the effects of O2) were tracked for 10 days using a variety of methods including inductively coupled plasma optical emission spectrometry (ICP-OES), high resolution-transmission electron microscopy (HR-TEM), energy dispersive spectrometer (EDS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM). Continuous removal and reduction of Co2+ by nZVI caused by structural evolution were revealed in reaction processes. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the corrosion rate of nZVI, was deemed as the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results showed that the formation and dissolution of sheet structure impacts on the ratio of Fe (0) on nZVI's surface and the surface reduction of Co2+. The cavity structure provides the possibility of Co migrating from surface to inside of nZVI leading a continuous removal. A subacidity condition could accelerate the evolution to improve the removal of Co2+ and the results of structural controlled reactions further indicated that the removal was suspended by sheet structure and enhanced by cavity structure. The results in this study revealed "structural influence" for fully and dynamically understanding nZVI's reactions.

The effect of large-scale model time step and multiscale coupling frequency on cloud climatology, vertical structure, and rainfall extremes in a superparameterized GCM

DOE PAGES

Yu, Sungduk; Pritchard, Michael S.

2015-12-17

The effect of global climate model (GCM) time step—which also controls how frequently global and embedded cloud resolving scales are coupled—is examined in the Superparameterized Community Atmosphere Model ver 3.0. Systematic bias reductions of time-mean shortwave cloud forcing (~10 W/m 2) and longwave cloud forcing (~5 W/m 2) occur as scale coupling frequency increases, but with systematically increasing rainfall variance and extremes throughout the tropics. An overarching change in the vertical structure of deep tropical convection, favoring more bottom-heavy deep convection as a global model time step is reduced may help orchestrate these responses. The weak temperature gradient approximation ismore » more faithfully satisfied when a high scale coupling frequency (a short global model time step) is used. These findings are distinct from the global model time step sensitivities of conventionally parameterized GCMs and have implications for understanding emergent behaviors of multiscale deep convective organization in superparameterized GCMs. Lastly, the results may also be useful for helping to tune them.« less

The effect of large-scale model time step and multiscale coupling frequency on cloud climatology, vertical structure, and rainfall extremes in a superparameterized GCM

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

Yu, Sungduk; Pritchard, Michael S.

The effect of global climate model (GCM) time step—which also controls how frequently global and embedded cloud resolving scales are coupled—is examined in the Superparameterized Community Atmosphere Model ver 3.0. Systematic bias reductions of time-mean shortwave cloud forcing (~10 W/m 2) and longwave cloud forcing (~5 W/m 2) occur as scale coupling frequency increases, but with systematically increasing rainfall variance and extremes throughout the tropics. An overarching change in the vertical structure of deep tropical convection, favoring more bottom-heavy deep convection as a global model time step is reduced may help orchestrate these responses. The weak temperature gradient approximation ismore » more faithfully satisfied when a high scale coupling frequency (a short global model time step) is used. These findings are distinct from the global model time step sensitivities of conventionally parameterized GCMs and have implications for understanding emergent behaviors of multiscale deep convective organization in superparameterized GCMs. Lastly, the results may also be useful for helping to tune them.« less

How Configuration Management (CM) Can Help Project Teams To Innovate and Communicate

NASA Technical Reports Server (NTRS)

Cioletti, Louis

2009-01-01

Traditionally, CM is relegated to a support role in project management activities. CM s traditional functions of identification, change control, status accounting, and audits/verification are still necessary and play a vital role. However, this presentation proposes CM s role in a new and innovative manner that will significantly improve communication throughout the organization and, in turn, augment the project s success. CM s new role is elevated to the project management level, above the engineering or sub-project level in the Work Breakdown Structure (WBS), where it can more effectively accommodate changes, reduce corrective actions, and ensure that requirements are clear, concise, and valid, and that results conform to the requirements. By elevating CM s role in project management and orchestrating new measures, a new communication will emerge that will improve information integrity, structured baselines, interchangeability/traceability, metrics, conformance to standards, and standardize the best practices in the organization. Overall project performance (schedule, quality, and cost) can be no better than the ability to communicate requirements which, in turn, is no better than the CM process to communicate project decisions and the correct requirements.

PBX/extradenticle is required to re-establish axial structures and polarity during planarian regeneration

PubMed Central

Blassberg, Robert A.; Felix, Daniel A.; Tejada-Romero, Belen; Aboobaker, A. Aziz

2013-01-01

Recent advances in a number of systems suggest many genes involved in orchestrating regeneration are redeployed from similar processes in development, with others being novel to the regeneration process in particular lineages. Of particular importance will be understanding the architecture of regenerative genetic regulatory networks and whether they are conserved across broad phylogenetic distances. Here, we describe the role of the conserved TALE class protein PBX/Extradenticle in planarians, a representative member of the Lophotrocozoa. PBX/Extradenticle proteins play central roles in both embryonic and post-embryonic developmental patterning in both vertebrates and insects, and we demonstrate a broad requirement during planarian regeneration. We observe that Smed-pbx has pleiotropic functions during regeneration, with a primary role in patterning the anterior-posterior (AP) axis and AP polarity. Smed-pbx is required for expression of polarity determinants notum and wnt1 and for correct patterning of the structures polarized along the AP axis, such as the brain, pharynx and gut. Overall, our data suggest that Smed-pbx functions as a central integrator of positional information to drive patterning of regeneration along the body axis. PMID:23318635

PBX/extradenticle is required to re-establish axial structures and polarity during planarian regeneration.

PubMed

Blassberg, Robert A; Felix, Daniel A; Tejada-Romero, Belen; Aboobaker, A Aziz

2013-02-01

Recent advances in a number of systems suggest many genes involved in orchestrating regeneration are redeployed from similar processes in development, with others being novel to the regeneration process in particular lineages. Of particular importance will be understanding the architecture of regenerative genetic regulatory networks and whether they are conserved across broad phylogenetic distances. Here, we describe the role of the conserved TALE class protein PBX/Extradenticle in planarians, a representative member of the Lophotrocozoa. PBX/Extradenticle proteins play central roles in both embryonic and post-embryonic developmental patterning in both vertebrates and insects, and we demonstrate a broad requirement during planarian regeneration. We observe that Smed-pbx has pleiotropic functions during regeneration, with a primary role in patterning the anterior-posterior (AP) axis and AP polarity. Smed-pbx is required for expression of polarity determinants notum and wnt1 and for correct patterning of the structures polarized along the AP axis, such as the brain, pharynx and gut. Overall, our data suggest that Smed-pbx functions as a central integrator of positional information to drive patterning of regeneration along the body axis.

Cellular commitment in the developing cerebellum

PubMed Central

Marzban, Hassan; Del Bigio, Marc R.; Alizadeh, Javad; Ghavami, Saeid; Zachariah, Robby M.; Rastegar, Mojgan

2014-01-01

The mammalian cerebellum is located in the posterior cranial fossa and is critical for motor coordination and non-motor functions including cognitive and emotional processes. The anatomical structure of cerebellum is distinct with a three-layered cortex. During development, neurogenesis and fate decisions of cerebellar primordium cells are orchestrated through tightly controlled molecular events involving multiple genetic pathways. In this review, we will highlight the anatomical structure of human and mouse cerebellum, the cellular composition of developing cerebellum, and the underlying gene expression programs involved in cell fate commitments in the cerebellum. A critical evaluation of the cell death literature suggests that apoptosis occurs in ~5% of cerebellar cells, most shortly after mitosis. Apoptosis and cellular autophagy likely play significant roles in cerebellar development, we provide a comprehensive discussion of their role in cerebellar development and organization. We also address the possible function of unfolded protein response in regulation of cerebellar neurogenesis. We discuss recent advancements in understanding the epigenetic signature of cerebellar compartments and possible connections between DNA methylation, microRNAs and cerebellar neurodegeneration. Finally, we discuss genetic diseases associated with cerebellar dysfunction and their role in the aging cerebellum. PMID:25628535

Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs.

PubMed

Zhu, Jinwei; Zhou, Qingqing; Shang, Yuan; Li, Hao; Peng, Mengjuan; Ke, Xiao; Weng, Zhuangfeng; Zhang, Rongguang; Huang, Xuhui; Li, Shawn S C; Feng, Guoping; Lu, Youming; Zhang, Mingjie

2017-12-26

The PSD-95/SAPAP/Shank complex functions as the major scaffold in orchestrating the formation and plasticity of the post-synaptic densities (PSDs). We previously demonstrated that the exquisitely specific SAPAP/Shank interaction is critical for Shank synaptic targeting and Shank-mediated synaptogenesis. Here, we show that the PSD-95/SAPAP interaction, SAPAP synaptic targeting, and SAPAP-mediated synaptogenesis require phosphorylation of the N-terminal repeat sequences of SAPAPs. The atomic structure of the PSD-95 guanylate kinase (GK) in complex with a phosphor-SAPAP repeat peptide, together with biochemical studies, reveals the molecular mechanism underlying the phosphorylation-dependent PSD-95/SAPAP interaction, and it also provides an explanation of a PSD-95 mutation found in patients with intellectual disabilities. Guided by the structural data, we developed potent non-phosphorylated GK inhibitory peptides capable of blocking the PSD-95/SAPAP interaction and interfering with PSD-95/SAPAP-mediated synaptic maturation and strength. These peptides are genetically encodable for investigating the functions of the PSD-95/SAPAP interaction in vivo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Review paper: DNA delivery strategies to promote periodontal regeneration.

PubMed

Elangovan, Satheesh; Karimbux, Nadeem

2010-07-01

Periodontal diseases are caused by bacteria with an inflammatory component that result in the loss of bone and soft tissue around the neck of the teeth. Recent therapies allow clinicians to regenerate some of the lost structures of the periodontium. Regeneration of these lost supporting structures is a highly orchestrated process, involving various cellular and molecular players, leading to the complete restoration of the periodontium (the tooth-supporting apparatus). The introduction of growth factors has positively influenced the clinical outcome of the existing regenerative procedures but the supra-physiological doses and the high cost associated with these growth factors can be drawbacks. Gene therapy may offer some interesting advantages to current therapies. In the field of periodontology, several studies have been conducted to explore the efficacy of delivering the DNA of key growth factors using viral vectors in both periodontal and peri-implant bone regeneration. Relatively few studies have explored the application of nonviral gene therapy in periodontal regeneration. This article is aimed at reviewing the studies conducted so far using viral and nonviral gene delivery approaches to achieve periodontal and peri-implant bone regeneration.

Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains

PubMed Central

Gronnier, Julien; Crowet, Jean-Marc; Habenstein, Birgit; Nasir, Mehmet Nail; Bayle, Vincent; Hosy, Eric; Platre, Matthieu Pierre; Gouguet, Paul; Raffaele, Sylvain; Martinez, Denis; Grelard, Axelle; Loquet, Antoine; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia; Der, Christophe; Bayer, Emmanuelle M; Jaillais, Yvon; Deleu, Magali; Germain, Véronique; Lins, Laurence; Mongrand, Sébastien

2017-01-01

Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function. DOI: http://dx.doi.org/10.7554/eLife.26404.001 PMID:28758890

Moving and Learning in Every Way. Profiles/Elizabeth O'Brien.

ERIC Educational Resources Information Center

Rife, Frank

1982-01-01

A physical education teacher's approach to orchestrating individual and group learning is described. Cognitive and affective learning are stressed in addition to physical skill development. Creative use of learning resources--milk cartons, "direction boxes," and newspapers--is illustrated. (PP)

Quantification of bovine oxylipids during intramammary Streptococcus uberis infection

USDA-ARS?s Scientific Manuscript database

Streptococcus uberis mastitis results in severe mammary tissue damage in dairy cows due to uncontrolled inflammation. Oxylipids are potent lipid mediators that orchestrate pathogen-induced inflammatory responses, however, changes in oxylipid biosynthesis during S. uberis mastitis are unknown. Thus, ...

Implementation Recommendations for MOSAIC: A Workflow Architecture for Analytic Enrichment. Analysis and Recommendations for the Implementation of a Cohesive Method for Orchestrating Analytics in a Distributed Model

DTIC Science & Technology

2011-02-01

Process Architecture Technology Analysis: Executive .............................................. 15 UIMA as Executive...44 A.4: Flow Code in UIMA ......................................................................................................... 46... UIMA ................................................................................................................................ 57 E.2

Demonstrating Distributed Resource Communications at NREL - Video Text

Science.gov Websites

video. Kevin Lynn, DOE Director of Grid Modernization: This is a whole new way of thinking about the way orchestration and coordination is more of what's coming and utilities are thinking more and more about what

Taking Care of Your Voice

MedlinePlus

... open so that you can breathe. When it's time to speak, however, the brain orchestrates a series of events. The vocal folds snap together while ... Communication Disorders (NIDCD) supports research that includes laboratory ... other scientists design better treatments for conditions such as vocal fold ...

Understanding Business Analytics

DTIC Science & Technology

2015-01-05

analytics have been used in organizations for a variety of reasons for quite some time; ranging from the simple (generating and understanding business analytics...process. understanding business analytics 3 How well these two components are orchestrated will determine the level of success an organization has in

The structure of common-envelope remnants

NASA Astrophysics Data System (ADS)

Hall, Philip D.

2015-05-01

We investigate the structure and evolution of the remnants of common-envelope evolution in binary star systems. In a common-envelope phase, two stars become engulfed in a gaseous envelope and, under the influence of drag forces, spiral to smaller separations. They may merge to form a single star or the envelope may be ejected to leave the stars in a shorter period orbit. This process explains the short orbital periods of many observed binary systems, such as cataclysmic variables and low-mass X-ray binary systems. Despite the importance of these systems, and of common-envelope evolution to their formation, it remains poorly understood. Specifically, we are unable to confidently predict the outcome of a common-envelope phase from the properties at its onset. After presenting a review of work on stellar evolution, binary systems, common-envelope evolution and the computer programs used, we describe the results of three computational projects on common-envelope evolution. Our work specifically relates to the methods and prescriptions which are used for predicting the outcome. We use the Cambridge stellar-evolution code STARS to produce detailed models of the structure and evolution of remnants of common-envelope evolution. We compare different assumptions about the uncertain end-of-common envelope structure and envelope mass of remnants which successfully eject their common envelopes. In the first project, we use detailed remnant models to investigate whether planetary nebulae are predicted after common-envelope phases initiated by low-mass red giants. We focus on the requirement that a remnant evolves rapidly enough to photoionize the nebula and compare the predictions for different ideas about the structure at the end of a common-envelope phase. We find that planetary nebulae are possible for some prescriptions for the end-of-common envelope structure. In our second contribution, we compute a large set of single-star models and fit new formulae to the core radii of evolved stars. These formulae can be used to better compute the outcome of common-envelope evolution with rapid evolution codes. We find that the new formulae are necessary for accurate predictions of the properties of post-common envelope systems. Finally, we use detailed remnant models of massive stars to investigate whether hydrogen may be retained after a common-envelope phase to the point of core-collapse and so be observable in supernovae. We find that this is possible and thus common-envelope evolution may contribute to the formation of Type IIb supernovae.

In situ visualization of domain structure evolution during field cooling in 0.67PMN-0.33PT single crystal

NASA Astrophysics Data System (ADS)

Ushakov, A. D.; Esin, A. A.; Chezganov, D. S.; Turygin, A. P.; Akhmatkhanov, A. R.; Hu, Q.; Sun, L.; Wei, X.; Shur, V. Ya

2017-10-01

The evolution of the domain structure during in-field cooling was in situ studied in [001]-cut single crystals of relaxor ferroelectric (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 (PMN-PT) with x = 0.33 with maximum of dielectric permittivity at 150°C. The main stages of domain evolution have been separated. The visualization of the static as-grown and polarized domain structures with high spatial resolution by piezoresponse force microscopy and scanning electron microscopy allowed measuring the characteristic features of maze and needle-like domain structures.

Classification of proteins: available structural space for molecular modeling.

PubMed

Andreeva, Antonina

2012-01-01

The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

Exploring social structure effect on language evolution based on a computational model

NASA Astrophysics Data System (ADS)

Gong, Tao; Minett, James; Wang, William

2008-06-01

A compositionality-regularity coevolution model is adopted to explore the effect of social structure on language emergence and maintenance. Based on this model, we explore language evolution in three experiments, and discuss the role of a popular agent in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of inter-community communications and that of simple linguistic features on convergence of communal languages in two communities. This work embodies several important interactions during social learning, and introduces a new approach that manipulates individuals' probabilities to participate in social interactions to study the effect of social structure. We hope it will stimulate further theoretical and empirical explorations on language evolution in a social environment.

Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach

PubMed Central

Westermark, Stefanie; Steuer, Ralf

2016-01-01

Oxygenic photosynthesis dominates global primary productivity ever since its evolution more than three billion years ago. While many aspects of phototrophic growth are well understood, it remains a considerable challenge to elucidate the manifold dependencies and interconnections between the diverse cellular processes that together facilitate the synthesis of new cells. Phototrophic growth involves the coordinated action of several layers of cellular functioning, ranging from the photosynthetic light reactions and the electron transport chain, to carbon-concentrating mechanisms and the assimilation of inorganic carbon. It requires the synthesis of new building blocks by cellular metabolism, protection against excessive light, as well as diurnal regulation by a circadian clock and the orchestration of gene expression and cell division. Computational modeling allows us to quantitatively describe these cellular functions and processes relevant for phototrophic growth. As yet, however, computational models are mostly confined to the inner workings of individual cellular processes, rather than describing the manifold interactions between them in the context of a living cell. Using cyanobacteria as model organisms, this contribution seeks to summarize existing computational models that are relevant to describe phototrophic growth and seeks to outline their interactions and dependencies. Our ultimate aim is to understand cellular functioning and growth as the outcome of a coordinated operation of diverse yet interconnected cellular processes. PMID:28083530

Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements

PubMed Central

Gowda, Malali

2016-01-01

Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck), finger millet (leaf and neck), foxtail millet (leaf) and buffel grass (leaf). Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors. PMID:27658241

Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness

NASA Astrophysics Data System (ADS)

Kamimura, Atsushi; Kaneko, Kunihiko

2018-03-01

Explanation of exponential growth in self-reproduction is an important step toward elucidation of the origins of life because optimization of the growth potential across rounds of selection is necessary for Darwinian evolution. To produce another copy with approximately the same composition, the exponential growth rates for all components have to be equal. How such balanced growth is achieved, however, is not a trivial question, because this kind of growth requires orchestrated replication of the components in stochastic and nonlinear catalytic reactions. By considering a mutually catalyzing reaction in two- and three-dimensional lattices, as represented by a cellular automaton model, we show that self-reproduction with exponential growth is possible only when the replication and degradation of one molecular species is much slower than those of the others, i.e., when there is a minority molecule. Here, the synergetic effect of molecular discreteness and crowding is necessary to produce the exponential growth. Otherwise, the growth curves show superexponential growth because of nonlinearity of the catalytic reactions or subexponential growth due to replication inhibition by overcrowding of molecules. Our study emphasizes that the minority molecular species in a catalytic reaction network is necessary for exponential growth at the primitive stage of life.

Command and Compensation in a Neuromodulatory Decision Network

PubMed Central

Luan, Haojiang; Diao, Fengqiu; Peabody, Nathan C.; White, Benjamin H.

2012-01-01

The neural circuits that mediate behavioral choices must not only weigh internal demands and environmental circumstances, but also select and implement specific actions, including associated visceral or neuroendocrine functions. Coordinating these multiple processes suggests considerable complexity. As a consequence, even circuits that support simple behavioral decisions remain poorly understood. Here we show that the environmentally-sensitive wing expansion decision of adult fruit flies is coordinated by a single pair of neuromodulatory neurons with command-like function. Targeted suppression of these neurons using the Split Gal4 system abrogates the fly's ability to expand its wings in the face of environmental challenges, while stimulating them forces expansion by coordinately activating both motor and neuroendocrine outputs. The arbitration and implementation of the wing expansion decision by this neuronal pair may illustrate a general strategy by which neuromodulatory neurons orchestrate behavior. Interestingly, the decision network shows a behavioral plasticity that is unmasked under conducive environmental conditions in flies lacking the function of the command-like neuromodulatory neurons. Such flies can often expand their wings using a motor program distinct from that of wildtype animals and controls. This compensatory program may be the vestige of an ancestral, environmentally-insensitive program used for wing expansion that existed prior to the evolution of the environmentally-adaptive program currently used by Drosophila and other cyclorrhaphan flies. PMID:22262886

Cell-size distribution in epithelial tissue formation and homeostasis

PubMed Central

Primo, Luca; Celani, Antonio

2017-01-01

How cell growth and proliferation are orchestrated in living tissues to achieve a given biological function is a central problem in biology. During development, tissue regeneration and homeostasis, cell proliferation must be coordinated by spatial cues in order for cells to attain the correct size and shape. Biological tissues also feature a notable homogeneity of cell size, which, in specific cases, represents a physiological need. Here, we study the temporal evolution of the cell-size distribution by applying the theory of kinetic fragmentation to tissue development and homeostasis. Our theory predicts self-similar probability density function (PDF) of cell size and explains how division times and redistribution ensure cell size homogeneity across the tissue. Theoretical predictions and numerical simulations of confluent non-homeostatic tissue cultures show that cell size distribution is self-similar. Our experimental data confirm predictions and reveal that, as assumed in the theory, cell division times scale like a power-law of the cell size. We find that in homeostatic conditions there is a stationary distribution with lognormal tails, consistently with our experimental data. Our theoretical predictions and numerical simulations show that the shape of the PDF depends on how the space inherited by apoptotic cells is redistributed and that apoptotic cell rates might also depend on size. PMID:28330988

Cell-size distribution in epithelial tissue formation and homeostasis.

PubMed

Puliafito, Alberto; Primo, Luca; Celani, Antonio

2017-03-01

How cell growth and proliferation are orchestrated in living tissues to achieve a given biological function is a central problem in biology. During development, tissue regeneration and homeostasis, cell proliferation must be coordinated by spatial cues in order for cells to attain the correct size and shape. Biological tissues also feature a notable homogeneity of cell size, which, in specific cases, represents a physiological need. Here, we study the temporal evolution of the cell-size distribution by applying the theory of kinetic fragmentation to tissue development and homeostasis. Our theory predicts self-similar probability density function (PDF) of cell size and explains how division times and redistribution ensure cell size homogeneity across the tissue. Theoretical predictions and numerical simulations of confluent non-homeostatic tissue cultures show that cell size distribution is self-similar. Our experimental data confirm predictions and reveal that, as assumed in the theory, cell division times scale like a power-law of the cell size. We find that in homeostatic conditions there is a stationary distribution with lognormal tails, consistently with our experimental data. Our theoretical predictions and numerical simulations show that the shape of the PDF depends on how the space inherited by apoptotic cells is redistributed and that apoptotic cell rates might also depend on size. © 2017 The Author(s).

Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots.

PubMed

de Vries, Jan; Fischer, Angela Melanie; Roettger, Mayo; Rommel, Sophie; Schluepmann, Henriette; Bräutigam, Andrea; Carlsbecker, Annelie; Gould, Sven Bernhard

2016-01-01

The phytohormones cytokinin and auxin orchestrate the root meristem development in angiosperms by determining embryonic bipolarity. Ferns, having the most basal euphyllophyte root, form neither bipolar embryos nor permanent embryonic primary roots but rather an adventitious root system. This raises the questions of how auxin and cytokinin govern fern root system architecture and whether this can tell us something about the origin of that root. Using Azolla filiculoides, we characterized the influence of IAA and zeatin on adventitious fern root meristems and vasculature by Nomarski microscopy. Simultaneously, RNAseq analyses, yielding 36,091 contigs, were used to uncover how the phytohormones affect root tip gene expression. We show that auxin restricts Azolla root meristem development, while cytokinin promotes it; it is the opposite effect of what is observed in Arabidopsis. Global gene expression profiling uncovered 145 genes significantly regulated by cytokinin or auxin, including cell wall modulators, cell division regulators and lateral root formation coordinators. Our data illuminate both evolution and development of fern roots. Promotion of meristem size through cytokinin supports the idea that root meristems of euphyllophytes evolved from shoot meristems. The foundation of these roots was laid in a postembryonically branching shoot system. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes

PubMed Central

Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

2016-01-01

Abstract Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. PMID:27112572

Structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kanzyuba, Vasily; Dong, Sining; Liu, Xinyu; Li, Xiang; Rouvimov, Sergei; Okuno, Hanako; Mariette, Henri; Zhang, Xueqiang; Ptasinska, Sylwia; Tracy, Brian D.; Smith, David J.; Dobrowolska, Margaret; Furdyna, Jacek K.

2017-02-01

We describe the structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy on GaAs (111) substrates, as revealed by transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. When the Mn concentration is increased, the lattice of the ternary (Sn,Mn)Se films evolves quasi-coherently from a SnSe2 two-dimensional (2D) crystal structure into a more complex quasi-2D lattice rearrangement, ultimately transforming into the magnetically concentrated antiferromagnetic MnSe 3D rock-salt structure as Mn approaches 50 at. % of this material. These structural transformations are expected to underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.

Alterations in Skeletal Muscle Indicators of Mitochondrial Structure and Biogenesis in Patients with Type 2 Diabetes and Heart Failure: Effects of Epicatechin Rich Cocoa

PubMed Central

Taub, Pam R.; Ramirez‐Sanchez, Israel; Ciaraldi, Theodore P.; Perkins, Guy; Murphy, Anne N.; Naviaux, Robert; Hogan, Michael; Maisel, Alan S.; Henry, Robert R.; Ceballos, Guillermo

2012-01-01

Abstract (‐)‐Epicatechin (Epi), a flavanol in cacao stimulates mitochondrial volume and cristae density and protein markers of skeletal muscle (SkM) mitochondrial biogenesis in mice. Type 2 diabetes mellitus (DM2) and heart failure (HF) are diseases associated with defects in SkM mitochondrial structure/function. A study was implemented to assess perturbations and to determine the effects of Epi‐rich cocoa in SkM mitochondrial structure and mediators of biogenesis. Five patients with DM2 and stage II/III HF consumed dark chocolate and a beverage containing approximately 100 mg of Epi per day for 3 months. We assessed changes in protein and/or activity levels of oxidative phosphorylation proteins, porin, mitofilin, nNOS, nitric oxide, cGMP, SIRT1, PGC1α, Tfam, and mitochondria volume and cristae abundance by electron microscopy from SkM. Apparent major losses in normal mitochondria structure were observed before treatment. Epi‐rich cocoa increased protein and/or activity of mediators of biogenesis and cristae abundance while not changing mitochondrial volume density. Epi‐rich cocoa treatment improves SkM mitochondrial structure and in an orchestrated manner, increases molecular markers of mitochondrial biogenesis resulting in enhanced cristae density. Future controlled studies are warranted using Epi‐rich cocoa (or pure Epi) to translate improved mitochondrial structure into enhanced cardiac and/or SkM muscle function. Clin Trans Sci 2012; Volume 5: 43–47 PMID:22376256

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

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

Nakamachi, Eiji; Yoshida, Takashi; Yamaguchi, Toshihiko

2014-10-06

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture andmore » hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.« less

Synergy and Self-organization in Tribosystem’s evolution. Energy Model of Friction

NASA Astrophysics Data System (ADS)

Fedorov, S. V.; Assenova, E.

2018-01-01

Different approaches are known to treat self-organization in tribosystems, related to the structural adaptation in the formation of dissipative surface structures and of frictional or tribo-films, using of synergistic modifying of layers and coatings, e.g. of the selective material transfer during friction, etc. Regarding tribological processes in contact systems, self-organization is observed as spontaneous creation of higher ordered structures during the contact interaction. The proposed paper considers friction as process of transformation and dissipation of energy and process of elasto-plastic deformation localized in thin surface layers of the interacting bodies. Еnergetic interpretation of friction is proposed. Based on the energy balance equations of friction, the evolution of tribosystems is followed in its adaptive-dissipative character. It reflects the variable friction surfaces compatibility and the nonlinear dynamics of friction evolution. Structural-energy relationships in the contacting surfaces evolution are obtained. Maximum of tribosystem’s efficiency during the evolution is the stage of self-organzation of the friction surface layers, which is a state of abnormal low friction and wear.

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

NASA Astrophysics Data System (ADS)

Nakamachi, Eiji; Yoshida, Takashi; Kuramae, Hiroyuki; Morimoto, Hideo; Yamaguchi, Toshihiko; Morita, Yusuke

2014-10-01

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture and hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.

Lost in Translation

ERIC Educational Resources Information Center

Thompson, Jane

2004-01-01

A conference event is mediated through keynote speeches, power point presentations, professional role-playing and the turgid language of policy agendas, initiatives, benchmarks and outputs. Serious human concerns rarely surface in the orchestrated and anodyne arena of professional conference-going. The ready recourse to ritual and procedure means…

Enrollment Management: A Market-Centered Perspective

ERIC Educational Resources Information Center

Kalsbeek, David H.; Hossler, Donald

2009-01-01

Enrollment management, the authors suggested in earlier essays, is a deliberate process of achieving an institution's preferred enrollment profile, starting by identifying the strategic purposes and mission of the institution, and then orchestrating the marketing, recruitment, admissions, pricing and aid, retention programs, academic support…

Authoring and Enactment of Mobile Pyramid-Based Collaborative Learning Activities

ERIC Educational Resources Information Center

Manathunga, Kalpani; Hernández-Leo, Davinia

2018-01-01

Collaborative learning flow patterns (CLFPs) formulate best practices for the orchestration of activity sequences and collaboration mechanisms that can elicit fruitful social interactions. Mobile technology features offer opportunities to support interaction mediation and content accessibility. However, existing mobile collaborative learning…

Aligning the PRME: How Study Abroad Nurtures Responsible Leadership

ERIC Educational Resources Information Center

Sroufe, Robert; Sivasubramaniam, Nagaraj; Ramos, Diane; Saiia, David

2015-01-01

Productive relationships between business schools and corporate organizations provide fertile ground for bringing business leaders, faculty, students, and community partners face-to-face with contemporaries abroad to foster development of responsible global leadership competencies. While well-orchestrated multicountry collaboration offers unique…

Wargame Pathologies

DTIC Science & Technology

2004-09-01

excluded) do not apply a rigorous and disciplined process of game development , especially in the area of objective definition. Without clear...prior to the game, in controlled circumstances. The actual “game” becomes a discussion of the very orchestrated results of the pre- game “ development ” efforts

Crystal Clear Assessment

ERIC Educational Resources Information Center

Stone, Jody H.; Lockhart, Amy

2013-01-01

Great science activities don't just happen; they are orchestrated by highly skilled teachers who are creative, caring, and innovative. Effective classroom teachers possess a deep understanding of the developmental characteristics of their students and are adept at translating this understanding into opportunities for individual students to…

Theoretical Frameworks to Guide School Improvement

ERIC Educational Resources Information Center

Evans, Lisa; Thornton, Bill; Usinger, Janet

2012-01-01

A firm grounding in change theory can provide educational leaders with an opportunity to orchestrate meaningful organizational improvements. This article provides an opportunity for practicing leaders to review four major theories of organizational change--continuous improvement, two approaches to organizational learning, and appreciative inquiry.…

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

PubMed

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T

2014-11-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Evolutionary dynamics of general group interactions in structured populations

NASA Astrophysics Data System (ADS)

Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

2016-02-01

The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.

Friction-induced nano-structural evolution of graphene as a lubrication additive

NASA Astrophysics Data System (ADS)

Zhao, Jun; Mao, Junyuan; Li, Yingru; He, Yongyong; Luo, Jianbin

2018-03-01

Graphene has attracted enormous attention in the field of lubrication based on its excellent physical and chemical properties. Although many studies have obtained thermally or chemically- exfoliated graphene and investigated their wide and important application, few studies have reported their physical nano-structural evolution under friction. In this study, we investigated the lubrication properties of graphene additives with different layer numbers and interlayer spacing by exfoliating. The additives with a higher degrees of exfoliation changed to ordering under friction, and had better lubrication properties, while that with a lower degrees exhibited obvious structural defects and high friction. Therefore, the original degrees of exfoliation plays a key role in the structural evolution of graphene and superior lubrication can be achieved through the physical nano-structure changing to ordering, even graphitization. Furthermore, the ordered tribofilm on the frictional interfaces was parallel to the sliding direction, meaning the highly exfoliated graphene indeed reaching slippage between its layers, which wasn't experimentally discovered in previous studies. This work provides a new understanding of the relationship between friction-induced nano-structural evolution and lubrication properties of graphene as a lubrication additive, and has great potential for the structural design of graphene as a lubrication additive.

The Clostridium sporulation programs: diversity and preservation of endospore differentiation.

PubMed

Al-Hinai, Mohab A; Jones, Shawn W; Papoutsakis, Eleftherios T

2015-03-01

Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σ(F), σ(E), σ(G), and σ(K)) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σ(K), the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation

PubMed Central

Al-Hinai, Mohab A.; Jones, Shawn W.

2015-01-01

SUMMARY Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σF, σE, σG, and σK) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σK, the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level. PMID:25631287

The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation

DOE PAGES

Al-Hinai, Mohab A.; Jones, Shawn W.; Papoutsakis, Eleftherios T.

2015-01-28

Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of amore » Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σF, σE, σG, and σK) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σK, the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.« less

The dynamics and evolution of clusters of galaxies

NASA Technical Reports Server (NTRS)

Geller, Margaret; Huchra, John P.

1987-01-01

Research was undertaken to produce a coherent picture of the formation and evolution of large-scale structures in the universe. The program is divided into projects which examine four areas: the relationship between individual galaxies and their environment; the structure and evolution of individual rich clusters of galaxies; the nature of superclusters; and the large-scale distribution of individual galaxies. A brief review of results in each area is provided.

The Further Evolution of Cooperation

NASA Astrophysics Data System (ADS)

Axelrod, Robert; Dion, Douglas

1988-12-01

Axelrod's model of the evolution of cooperation was based on the iterated Prisoner's Dilemma. Empirical work following this approach has helped establish the prevalence of cooperation based on reciprocity. Theoretical work has led to a deeper understanding of the role of other factors in the evolution of cooperation: the number of players, the range of possible choices, variation in the payoff structure, noise, the shadow of the future, population dynamics, and population structure.

Diagnostics in the Extendable Integrated Support Environment (EISE)

NASA Technical Reports Server (NTRS)

Brink, James R.; Storey, Paul

1988-01-01

Extendable Integrated Support Environment (EISE) is a real-time computer network consisting of commercially available hardware and software components to support systems level integration, modifications, and enhancement to weapons systems. The EISE approach offers substantial potential savings by eliminating unique support environments in favor of sharing common modules for the support of operational weapon systems. An expert system is being developed that will help support diagnosing faults in this network. This is a multi-level, multi-expert diagnostic system that uses experiential knowledge relating symptoms to faults and also reasons from structural and functional models of the underlying physical model when experiential reasoning is inadequate. The individual expert systems are orchestrated by a supervisory reasoning controller, a meta-level reasoner which plans the sequence of reasoning steps to solve the given specific problem. The overall system, termed the Diagnostic Executive, accesses systems level performance checks and error reports, and issues remote test procedures to formulate and confirm fault hypotheses.

Ethnographic model of acoustic use of space in the southern Andes for an archaeo-musicological investigation

NASA Astrophysics Data System (ADS)

Perez de Arce, Jose

2002-11-01

Studies of ritual celebrations in central Chile conducted in the past 15 years show that the spatial component of sound is a crucial component of the whole. The sonic compositions of these rituals generate complex musical structures that the author has termed ''multi-orchestral polyphonies.'' Their origins have been documented from archaeological remains in a vast region of southern Andes (southern Peru, Bolivia, northern Argentina, north-central Chile). It consists of a combination of dance, space walk-through, spatial extension, multiple movements between listener and orchestra, and multiple relations between ritual and ambient sounds. The characteristics of these observables reveal a complex schematic relation between space and sound. This schema can be used as a valid hypothesis for the study of pre-Hispanic uses of acoustic ritual space. The acoustic features observed in this study are common in Andean ritual and, to some extent are seen in Mesoamerica as well.

Neural correlates of cognitive processing in monolinguals and bilinguals

PubMed Central

Grundy, John G.; Anderson, John A.E.; Bialystok, Ellen

2017-01-01

Here we review the neural correlates of cognitive control associated with bilingualism. We demonstrate that lifelong practice managing two languages orchestrates global changes to both the structure and function of the brain. Compared with monolinguals, bilinguals generally show greater gray matter volume, especially in perceptual/motor regions, greater white matter integrity, and greater functional connectivity between gray matter regions. These changes complement electroencephalography findings showing that bilinguals devote neural resources earlier than monolinguals. Parallel functional findings emerge from the functional magnetic resonance imaging literature: bilinguals show reduced frontal activity, suggesting that they do not need to rely on top-down mechanisms to the same extent as monolinguals. This shift for bilinguals to rely more on subcortical/posterior regions, which we term the bilingual anterior-to-posterior and subcortical shift (BAPSS), fits with results from cognitive aging studies and helps to explain why bilinguals experience cognitive decline at later stages of development than monolinguals. PMID:28415142

Marrying Excitons and Plasmons in Monolayer Transition-Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Van Tuan, Dinh; Scharf, Benedikt; Žutić, Igor; Dery, Hanan

2017-10-01

Just as photons are the quanta of light, plasmons are the quanta of orchestrated charge-density oscillations in conducting media. Plasmon phenomena in normal metals, superconductors, and doped semiconductors are often driven by long-wavelength Coulomb interactions. However, in crystals whose Fermi surface is comprised of disconnected pockets in the Brillouin zone, collective electron excitations can also attain a shortwave component when electrons transition between these pockets. In this work, we show that the band structure of monolayer transition-metal dichalcogenides gives rise to an intriguing mechanism through which shortwave plasmons are paired up with excitons. The coupling elucidates the origin for the optical sideband that is observed repeatedly in monolayers of WSe2 and WS2 but not understood. The theory makes it clear why exciton-plasmon coupling has the right conditions to manifest itself distinctly only in the optical spectra of electron-doped tungsten-based monolayers.

Timing is everything: Fine-tuned molecular machines orchestrate paramyxovirus entry

PubMed Central

Bose, Sayantan; Jardetzky, Theodore S.; Lamb, Robert A.

2015-01-01

The Paramyxoviridae include some of the great and ubiquitous disease-causing viruses of humans and animals. In most paramyxoviruses, two viral membrane glycoproteins, fusion protein (F) and receptor binding protein (HN, H or G) mediate a concerted process of recognition of host cell surface molecules followed by fusion of viral and cellular membranes, resulting in viral nucleocapsid entry into the cytoplasm. The interactions between the F and HN, H or G viral glycoproteins and host molecules are critical in determining host range, virulence and spread of these viruses. Recently, atomic structures, together with biochemical and biophysical studies, have provided major insights into how these two viral glycoproteins successfully interact with host receptors on cellular membranes and initiate the membrane fusion process to gain entry into cells. These studies highlight the conserved core mechanisms of paramyxovirus entry that provide the fundamental basis for rational anti-viral drug design and vaccine development. PMID:25771804

A Content Markup Language for Data Services

NASA Astrophysics Data System (ADS)

Noviello, C.; Acampa, P.; Mango Furnari, M.

Network content delivery and documents sharing is possible using a variety of technologies, such as distributed databases, service-oriented applications, and so forth. The development of such systems is a complex job, because document life cycle involves a strong cooperation between domain experts and software developers. Furthermore, the emerging software methodologies, such as the service-oriented architecture and knowledge organization (e.g., semantic web) did not really solve the problems faced in a real distributed and cooperating settlement. In this chapter the authors' efforts to design and deploy a distribute and cooperating content management system are described. The main features of the system are a user configurable document type definition and a management middleware layer. It allows CMS developers to orchestrate the composition of specialized software components around the structure of a document. In this chapter are also reported some of the experiences gained on deploying the developed framework in a cultural heritage dissemination settlement.

Optimizing the structure and function of the 50-plus radiology organizations, part 2: a unified strategic plan-a summary of the 2011 Intersociety Conference.

PubMed

Dodd, Gerald D

2012-05-01

The member organizations of the Intersociety Conference have agreed that radiology would benefit from consolidation and collaboration of the 50-plus radiology organizations. At this year's annual meeting, the participants concluded that the educational and research missions of the organizations would benefit from the creation of a unified strategic plan that addressed the coordination of annual meetings, online educational materials, research infrastructure, and the creation of a direct relationship between the research initiatives of the organizations and the patient advocacy groups of the Academy of Radiology Research. The socioeconomic mission of the organizations would be enhanced through the creation of a formal communication network with the ACR, and certification could be enhanced by the orchestration of the creation of educational materials related to the maintenance of certification. Copyright © 2012 American College of Radiology. Published by Elsevier Inc. All rights reserved.

The endomembrane sheath: a key structure for understanding the plant cell?

NASA Technical Reports Server (NTRS)

Reuzeau, C.; McNally, J. G.; Pickard, B. G.

1997-01-01

Recent evidence suggests that integrin is abundant in endomembranes of plant cells, and the endomembranes are clad by a sheath of cytoskeleton including F-actin. A role for endomembrane integrin and the endomembrane sheath is proposed: this system might orchestrate metabolic regulation by providing and modulating loci for channelling, and might accelerate channeling as needed by dragging the endoplasmic reticulum (ER) and organelles through the cytoplasm. To accomplish this "streaming", F-actin might lever against the rest of the endomembrane sheath and the ER might also lever against adhesion sites (i.e., plasmodesmata and plasmalemmal control centers). As an important agent in the control of cellular activities, according to this model, the endomembrane sheath would play a major part in responses to diverse signals and stresses, and under extreme stress cell survival would depend on the ability of the system to maintain enough integrity to direct critical syntheses and degradations.

Sec63p and Kar2p are required for the translocation of SRP-dependent precursors into the yeast endoplasmic reticulum in vivo

PubMed Central

Young, Barry P.; Craven, Rachel A.; Reid, Peter J.; Willer, Martin; Stirling, Colin J.

2001-01-01

The translocation of secretory polypeptides into the endoplasmic reticulum (ER) occurs at the translocon, a pore-forming structure that orchestrates the transport and maturation of polypeptides at the ER membrane. In yeast, targeting of secretory precursors to the translocon can occur by two distinct pathways that are distinguished by their dependence upon the signal recognition particle (SRP). The SRP-dependent pathway requires SRP and its membrane-bound receptor, whereas the SRP-independent pathway requires a separate receptor complex consisting of Sec62p, Sec63p, Sec71p, Sec72p plus lumenal Kar2p/BiP. Here we demonstrate that Sec63p and Kar2p are also required for the SRP-dependent targeting pathway in vivo. Furthermore, we demonstrate multiple roles for Sec63p, at least one of which is exclusive to the SRP-independent pathway. PMID:11226176

Large-scale recording of neuronal ensembles.

PubMed

Buzsáki, György

2004-05-01

How does the brain orchestrate perceptions, thoughts and actions from the spiking activity of its neurons? Early single-neuron recording research treated spike pattern variability as noise that needed to be averaged out to reveal the brain's representation of invariant input. Another view is that variability of spikes is centrally coordinated and that this brain-generated ensemble pattern in cortical structures is itself a potential source of cognition. Large-scale recordings from neuronal ensembles now offer the opportunity to test these competing theoretical frameworks. Currently, wire and micro-machined silicon electrode arrays can record from large numbers of neurons and monitor local neural circuits at work. Achieving the full potential of massively parallel neuronal recordings, however, will require further development of the neuron-electrode interface, automated and efficient spike-sorting algorithms for effective isolation and identification of single neurons, and new mathematical insights for the analysis of network properties.

Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro.

PubMed

Harrison, Sarah Ellys; Sozen, Berna; Christodoulou, Neophytos; Kyprianou, Christos; Zernicka-Goetz, Magdalena

2017-04-14

Mammalian embryogenesis requires intricate interactions between embryonic and extraembryonic tissues to orchestrate and coordinate morphogenesis with changes in developmental potential. Here, we combined mouse embryonic stem cells (ESCs) and extraembryonic trophoblast stem cells (TSCs) in a three-dimensional scaffold to generate structures whose morphogenesis is markedly similar to that of natural embryos. By using genetically modified stem cells and specific inhibitors, we show that embryogenesis of ESC- and TSC-derived embryos-ETS-embryos-depends on cross-talk involving Nodal signaling. When ETS-embryos develop, they spontaneously initiate expression of mesoderm and primordial germ cell markers asymmetrically on the embryonic and extraembryonic border, in response to Wnt and BMP signaling. Our study demonstrates the ability of distinct stem cell types to self-assemble in vitro to generate embryos whose morphogenesis, architecture, and constituent cell types resemble those of natural embryos. Copyright © 2017, American Association for the Advancement of Science.

The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans

PubMed Central

Michelmann, Sebastian; Bowman, Howard; Hanslmayr, Simon

2016-01-01

Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception. However, little is known about the mechanisms that guide such a temporally structured replay in humans, because previous studies used either unsuitable methods or paradigms to address this question. Here, we overcome these limitations by developing a new analysis method to detect the replay of temporal patterns in a paradigm that requires participants to mentally replay short sound or video clips. We show that memory reinstatement is accompanied by a decrease of low-frequency (8 Hz) power, which carries a temporal phase signature of the replayed stimulus. These replay effects were evident in the visual as well as in the auditory domain and were localized to sensory-specific regions. These results suggest low-frequency phase to be a domain-general mechanism that orchestrates dynamic memory replay in humans. PMID:27494601

Threshold responses to interacting global changes in a California grassland ecosystem

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

Field, Christopher; Mooney, Harold; Vitousek, Peter

2015-02-02

Building on the history and infrastructure of the Jasper Ridge Global Change Experiment, we conducted experiments to explore the potential for single and combined global changes to stimulate fundamental type changes in ecosystems that start the experiment as California annual grassland. Using a carefully orchestrated set of seedling introductions, followed by careful study and later removal, the grassland was poised to enable two major kinds of transitions that occur in real life and that have major implications for ecosystem structure, function, and services. These are transitions from grassland to shrubland/forest and grassland to thistle patch. The experiment took place inmore » the context of 4 global change factors – warming, elevated CO 2, N deposition, and increased precipitation – in a full-factorial array, present as all possible 1, 2, 3, and 4-factor combinations, with each combination replicated 8 times.« less

Professional Orchestral Conductors' Use of Selected Teaching Behaviors in Rehearsal

ERIC Educational Resources Information Center

Whitaker, Jennifer A.

2017-01-01

This descriptive study examined professional conductors' use of rehearsal time in sequential pattern components, discussing task presentation targets, and using verbal imagery and modeling techniques. Commercially available videos of 15 professional conductors rehearsing prominent orchestras were scripted, coded, and timed for selected teaching…

Handbook for Teaching Korean-American Students.

ERIC Educational Resources Information Center

California State Dept. of Education, Sacramento. Bilingual Education Office.

This handbook is designed for teachers, administrators, and other school personnel. It provides an explanation of the sociocultural and linguistic characteristics of Korean-Americans so educators can address their needs more effectively and orchestrate a better teaching environment by understanding and supporting the Korean-American cultural…

Orchestrating Multiple Intelligences

ERIC Educational Resources Information Center

Moran, Seana; Kornhaber, Mindy; Gardner, Howard

2006-01-01

Education policymakers often go astray when they attempt to integrate multiple intelligences theory into schools, according to the originator of the theory, Howard Gardner, and his colleagues. The greatest potential of a multiple intelligences approach to education grows from the concept of a profile of intelligences. Each learner's intelligence…

The Mediation of Acculturation: Orchestrating School Leadership Development in England

ERIC Educational Resources Information Center

Wallace, Mike; Tomlinson, Michael; O'Reilly, Dermot

2011-01-01

Among western governments large-scale leadership development initiatives represent an increasingly deployed means of promoting the acculturation of school leaders to support educational reforms and ongoing improvement. England's sophisticated initiative centres on the National College for Leadership in Schools and Children's Services, a…

Epithelial cells from smokers modify dendritic cell responses in the context of influenza infection

EPA Science Inventory

Epidemiologic evidence suggests that cigarette smoking is a risk factor for infection with influenza, but the mechanisms underlying this susceptibility remain unknown. To ascertain if airway epithelial cells from smokers demonstrate a decreased ability to orchestrate an influenza...

Orchestrating Semiotic Resources in Explicit Strategy Instruction

ERIC Educational Resources Information Center

Shanahan, Lynn E.; Flury-Kashmanian, Caroline

2014-01-01

Research and pedagogical information provided to teachers on implementing explicit strategy instruction has primarily focused on teachers' speech, with limited attention to other modes of communication, such as gesture and artefacts. This interpretive case study investigates two teachers' use of different semiotic resources when introducing…

Orchestrating Inquiry Learning

ERIC Educational Resources Information Center

Littleton, Karen, Ed.; Scanlon, Eileen, Ed.; Sharples, Mike, Ed.

2011-01-01

There is currently a rapidly growing interest in inquiry learning and an emerging consensus among researchers that, particularly when supported by technology, it can be a significant vehicle for developing higher order thinking skills. Inquiry learning methods also offer learners meaningful and productive approaches to the development of their…

Research in Corporate Communication: An Overview of an Emerging Field.

ERIC Educational Resources Information Center

van Riel, Cees B. M.

1997-01-01

Provides an overview of research in corporate communication, focusing on achievements found in the international academic literature in both communication and business school disciplines. Gives three key concepts in such research: corporate identity, corporate reputation, and orchestration of communication. Advocates an interdisciplinary approach…

Programming for Adolescents with Behavioral Disorders, Vol. 5.

ERIC Educational Resources Information Center

Braaten, Sheldon L., Ed.; Wild, Estelle, Ed.

This collection of 13 author-contributed papers addresses various aspects of programming for students with behavioral disorders. Papers have the following titles and authors: (1) "System Support and Transition to Adulthood for Adolescents with Seriously Disordered Behaviors: Orchestrating Successful Transitions" (Eugene Edgar); (2) "Targets for…

Tackling Misconceptions about Linear Associations

ERIC Educational Resources Information Center

Huey, Maryann E.; Baker, Deidra L.

2015-01-01

Many teachers of required secondary school mathematics classes are introducing statistics and probability topics traditionally relegated to college or AP Statistics courses. As a result, they need guidance in preparing lesson plans and orchestrating effective classroom discussions. In this article, the authors will describe the students' learning…

DISTINGUISHING BETWEEN FERTILIZATION FAILURE AND EARLY PREGNANCY LOSS WHEN IDENTIFYING MALE-MEDIATED ADVERSE PREGNANCY OUTCOMES

EPA Science Inventory

Successful reproduction depends upon the precise orchestration of many physiological processes. With respect to male reproductive performance, normal copulatory behavior and ejaculatory function are required to insure that semen is deposited in the female tract. Then, a suffici...

Religion as dialogical resource: a socio-cultural approach.

PubMed

Baucal, Aleksandar; Zittoun, Tania

2013-06-01

William James proposed a psychological study of religion examining people's religious experiences, and to see in what sense these were good for them. The recent developments of psychology of religion moved far from that initial proposition. In this paper, we propose a sociocultural perspective to religion that renews with that initial stance. After recalling Vygtotsky's core ideas, we suggest that religion, as cultural and symbolic system, participates to the orchestration of human activities and sense-making. Such orchestration works both from within the person, through internalized values and ideas, and from without, through the person's interactions with others, discourses, cultural objects etc. This leads us to consider religions as supporting various forms of dialogical dynamics-intra-psychological dialogues, interpersonal with present, absent or imaginary others, as well as inter-group dialogues-which we illustrate with empirical vignettes. The example of religious tensions in the Balkans in the 90's highlights how much the historical-cultural embeddedness of these dynamics can also lead to the end of dialogicality, and therefore, sense-making.

Orchestrating cytoskeleton and intracellular vesicle traffic to build functional immunological synapses.

PubMed

Soares, Helena; Lasserre, Rémi; Alcover, Andrés

2013-11-01

Immunological synapses are specialized cell-cell contacts formed between T lymphocytes and antigen-presenting cells. They are induced upon antigen recognition and are crucial for T-cell activation and effector functions. The generation and function of immunological synapses depend on an active T-cell polarization process, which results from a finely orchestrated crosstalk between the antigen receptor signal transduction machinery, the actin and microtubule cytoskeletons, and controlled vesicle traffic. Although we understand how some of these particular events are regulated, we still lack knowledge on how these multiple cellular elements are harmonized to ensure appropriate T-cell responses. We discuss here our view on how T-cell receptor signal transduction initially commands cytoskeletal and vesicle traffic polarization, which in turn sets the immunological synapse molecular design that regulates T-cell activation. We also discuss how the human immunodeficiency virus (HIV-1) hijacks some of these processes impairing immunological synapse generation and function. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The interferon-dependent orchestration of innate and adaptive immunity after transplantation.

PubMed

Robb, Renee J; Hill, Geoffrey R

2012-06-07

The therapeutic GVL effect after allogeneic stem cell transplantation is limited by the development of GVHD. The ultimate aim of current research is to separate the 2 processes in a meaningful fashion. The IFNs are a pleiotropic group of cytokines that were originally recognized because of their ability to interfere with viral replication. However, it is now established that these cytokines play an important role in orchestrating both innate and adaptive immunity. Multiple studies have investigated the effects of both types I and II IFN on GVHD and GVL in preclinical transplant models. The results indicate variable effects that are dependent on the period of activity within the developing immune response, the presence and type of pretransplant conditioning and the differential mechanisms, and IFN sensitivity of immune pathology within individual target organs during GVHD. This Perspective discusses the current literature on the IFNs and their potential modulation within clinical transplantation, focusing particularly on enhancing the therapeutic GVL effects.

Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin.

PubMed

Bitschar, Katharina; Wolz, Christiane; Krismer, Bernhard; Peschel, Andreas; Schittek, Birgit

2017-09-01

Healthy human skin provides an effective mechanical as well as immunologic barrier against pathogenic microorganisms with keratinocytes as the main cell type in the epidermis actively participating and orchestrating the innate immune response of the skin. As constituent of the outermost layer encountering potential pathogens they have to sense signals from the environment and must be able to initiate a differential immune response to harmless commensals and harmful pathogens. Staphylococci are among the most abundant colonizers of the skin: Whereas Staphylococcus epidermidis is part of the skin microbiota and ubiquitously colonizes human skin, Staphylococcus aureus is only rarely found on healthy human skin, but frequently colonizes the skin of atopic dermatitis (AD) patients. This review highlights recent advances in understanding how keratinocytes as sessile innate immune cells orchestrate an effective defense against S. aureus in healthy skin and the mechanisms leading to an impaired keratinocyte function in AD patients. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling

PubMed Central

Sciammas, Roger; Li, Ying; Warmflash, Aryeh; Song, Yiqiang; Dinner, Aaron R; Singh, Harinder

2011-01-01

The B-lymphocyte lineage is a leading system for analyzing gene regulatory networks (GRNs) that orchestrate distinct cell fate transitions. Upon antigen recognition, B cells can diversify their immunoglobulin (Ig) repertoire via somatic hypermutation (SHM) and/or class switch DNA recombination (CSR) before differentiating into antibody-secreting plasma cells. We construct a mathematical model for a GRN underlying this developmental dynamic. The intensity of signaling through the Ig receptor is shown to control the bimodal expression of a pivotal transcription factor, IRF-4, which dictates B cell fate outcomes. Computational modeling coupled with experimental analysis supports a model of ‘kinetic control', in which B cell developmental trajectories pass through an obligate transient state of variable duration that promotes diversification of the antibody repertoire by SHM/CSR in direct response to antigens. More generally, this network motif could be used to translate a morphogen gradient into developmental inductive events of varying time, thereby enabling the specification of distinct cell fates. PMID:21613984

De-optical-line-terminal hybrid access-aggregation optical network for time-sensitive services based on software-defined networking orchestration

NASA Astrophysics Data System (ADS)

Bai, Wei; Yang, Hui; Xiao, Hongyun; Yu, Ao; He, Linkuan; Zhang, Jie; Li, Zhen; Du, Yi

2017-11-01

With the increase in varieties of services in network, time-sensitive services (TSSs) appear and bring forward an impending need for delay performance. Ultralow-latency communication has become one of the important development goals for many scenarios in the coming 5G era (e.g., robotics and driverless cars). However, the conventional methods, which decrease delay by promoting the available resources and the network transmission speed, have limited effect; a new breakthrough for ultralow-latency communication is necessary. We propose a de-optical-line-terminal (De-OLT) hybrid access-aggregation optical network (DAON) for TSS based on software-defined networking (SDN) orchestration. In this network, low-latency all-optical communication based on optical burst switching can be achieved by removing OLT. For supporting this network and guaranteeing the quality of service for TSSs, we design SDN-driven control method and service provision method. Numerical results demonstrate the proposed DAON promotes network service efficiency and avoids traffic congestion.

Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks

PubMed Central

Luccioli, Stefano; Ben-Jacob, Eshel; Barzilai, Ari; Bonifazi, Paolo; Torcini, Alessandro

2014-01-01

It has recently been discovered that single neuron stimulation can impact network dynamics in immature and adult neuronal circuits. Here we report a novel mechanism which can explain in neuronal circuits, at an early stage of development, the peculiar role played by a few specific neurons in promoting/arresting the population activity. For this purpose, we consider a standard neuronal network model, with short-term synaptic plasticity, whose population activity is characterized by bursting behavior. The addition of developmentally inspired constraints and correlations in the distribution of the neuronal connectivities and excitabilities leads to the emergence of functional hub neurons, whose stimulation/deletion is critical for the network activity. Functional hubs form a clique, where a precise sequential activation of the neurons is essential to ignite collective events without any need for a specific topological architecture. Unsupervised time-lagged firings of supra-threshold cells, in connection with coordinated entrainments of near-threshold neurons, are the key ingredients to orchestrate population activity. PMID:25255443

Dust evolution, a global view: II. Top-down branching, nanoparticle fragmentation and the mystery of the diffuse interstellar band carriers

PubMed Central

2016-01-01

The origin of the diffuse interstellar bands (DIBs), one of the longest-standing mysteries of the interstellar medium (ISM), is explored within the framework of The Heterogeneous dust Evolution Model for Interstellar Solids (THEMIS). The likely nature of the DIB carriers and their evolution is here explored within the framework of the structures and sub-structures inherent to doped hydrogenated amorphous carbon grains in the ISM. Based on the natural aromatic-rich moieties (asphaltenes) recovered from coal and oil, the likely structure of their interstellar analogues is investigated within the context of the diffuse band problem. It is here proposed that the top-down evolution of interstellar carbonaceous grains, and, in particular, a-C(:H) nanoparticles, is at the heart of the formation and evolution of the DIB carriers and their associations with small molecules and radicals, such as C2, C3, CH and CN. It is most probable that the DIBs are carried by dehydrogenated, ionized, hetero-cyclic, olefinic and aromatic-rich moieties that form an integral part of the contiguous structure of hetero-atom-doped hydrogenated amorphous carbon nanoparticles and their daughter fragmentation products. Within this framework, it is proposed that polyene structures in all their variants could be viable DIB carrier candidates. PMID:28083089

Dust evolution, a global view: II. Top-down branching, nanoparticle fragmentation and the mystery of the diffuse interstellar band carriers

NASA Astrophysics Data System (ADS)

Jones, A. P.

2016-12-01

The origin of the diffuse interstellar bands (DIBs), one of the longest-standing mysteries of the interstellar medium (ISM), is explored within the framework of The Heterogeneous dust Evolution Model for Interstellar Solids (THEMIS). The likely nature of the DIB carriers and their evolution is here explored within the framework of the structures and sub-structures inherent to doped hydrogenated amorphous carbon grains in the ISM. Based on the natural aromatic-rich moieties (asphaltenes) recovered from coal and oil, the likely structure of their interstellar analogues is investigated within the context of the diffuse band problem. It is here proposed that the top-down evolution of interstellar carbonaceous grains, and, in particular, a-C(:H) nanoparticles, is at the heart of the formation and evolution of the DIB carriers and their associations with small molecules and radicals, such as C2, C3, CH and CN. It is most probable that the DIBs are carried by dehydrogenated, ionized, hetero-cyclic, olefinic and aromatic-rich moieties that form an integral part of the contiguous structure of hetero-atom-doped hydrogenated amorphous carbon nanoparticles and their daughter fragmentation products. Within this framework, it is proposed that polyene structures in all their variants could be viable DIB carrier candidates.

Synchronization in dynamical networks with unconstrained structure switching

NASA Astrophysics Data System (ADS)

del Genio, Charo I.; Romance, Miguel; Criado, Regino; Boccaletti, Stefano

2015-12-01

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows one to extend the master stability function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the dynamics of the units.

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

Pham, Grace H.; Rana, Ambar S. J. B.; Korkmaz, E. Nihal

Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we comparemore » the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.« less

Proton structure functions at small x

DOE PAGES

Hentschinski, Martin

2015-11-03

Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recentmore » result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F 2 and F L, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F 2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F 2 in the small x region, as measured at HERA. As a result, predictions for the structure function F L are found to be in agreement with the existing HERA data.« less

FERMT2 links cortical actin structures, plasma membrane tension and focal adhesion function to stabilize podocyte morphology.

PubMed

Yasuda-Yamahara, M; Rogg, M; Frimmel, J; Trachte, P; Helmstaedter, M; Schroder, P; Schiffer, M; Schell, C; Huber, T B

2018-01-11

Simplification and retraction of podocyte protrusions, generally termed as foot process effacement, is a uniform pathological pattern observed in the majority of glomerular disease, including focal segmental glomerulosclerosis. However, it is still incompletely understood how the interaction of cortical actin structures, actomyosin contractility and focal adhesions, is being orchestrated to control foot process morphology in health and disease. By uncovering the functional role of fermitin family member 2 (FERMT2 or kindlin-2) in podocytes, we provide now evidence, how cell-extracellular matrix (ECM) interactions modulate membrane tension and actomyosin contractility. A genetic modeling approach was applied by deleting FERMT2 in a set of in vivo systems as well as in CRISPR/Cas9 modified human podocytes. Loss of FERMT2 results in altered cortical actin composition, cell cortex destabilization associated with plasma membrane blebbing and a remodeling of focal adhesions. We further show that FERMT2 knockout podocytes have high levels of RhoA activation and concomitantly increased actomyosin contractility. Inhibition of actomyosin tension reverses the membrane blebbing phenotype. Thus, our findings establish a direct link between cell-matrix adhesions, cortical actin structures and plasma membrane tension allowing to better explain cell morphological changes in foot process effacement. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

The structural basis of arrestin-mediated regulation of G-protein-coupled receptors

PubMed Central

Gurevich, Vsevolod V.; Gurevich, Eugenia V.

2008-01-01

The 4 mammalian arrestins serve as almost universal regulators of the largest known family of signaling proteins, G-protein-coupled receptors (GPCRs). Arrestins terminate receptor interactions with G proteins, redirect the signaling to a variety of alternative pathways, and orchestrate receptor internalization and subsequent intracellular trafficking. The elucidation of the structural basis and fine molecular mechanisms of the arrestin–receptor interaction paved the way to the targeted manipulation of this interaction from both sides to produce very stable or extremely transient complexes that helped to understand the regulation of many biologically important processes initiated by active GPCRs. The elucidation of the structural basis of arrestin interactions with numerous non-receptor-binding partners is long overdue. It will allow the construction of fully functional arrestins in which the ability to interact with individual partners is specifically disrupted or enhanced by targeted mutagenesis. These “custom-designed” arrestin mutants will be valuable tools in defining the role of various interactions in the intricate interplay of multiple signaling pathways in the living cell. The identification of arrestin-binding sites for various signaling molecules will also set the stage for designing molecular tools for therapeutic intervention that may prove useful in numerous disorders associated with congenital or acquired disregulation of GPCR signaling. PMID:16460808

Structural signatures of DRD4 mutants revealed using molecular dynamics simulations: Implications for drug targeting.

PubMed

Jatana, Nidhi; Thukral, Lipi; Latha, N

2016-01-01

Human Dopamine Receptor D4 (DRD4) orchestrates several neurological functions and represents a target for many psychological disorders. Here, we examined two rare variants in DRD4; V194G and R237L, which elicit functional alterations leading to disruption of ligand binding and G protein coupling, respectively. Using atomistic molecular dynamics (MD) simulations, we provide in-depth analysis to reveal structural signatures of wild and mutant complexes with their bound agonist and antagonist ligands. We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. The data suggest that the mutation in transmembrane V (V194G) drastically disrupts the organization of ligand binding site and causes disorder in the native helical arrangement. Interestingly, the R237L mutation leads to significant rewiring of side-chain contacts in the intracellular loop 3 (site of mutation) and also affects the distant transmembrane topology. Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. Our findings thus reveal unreported structural determinants of the mutated DRD4 receptor and provide a robust framework for design of effective novel drugs.

The Cosmic Century

NASA Astrophysics Data System (ADS)

Longair, Malcolm S.

2013-04-01

Part I. Stars and Stellar Evolution up to the Second World War: 1. The legacy of the nineteenth century; 2. The classification of stellar spectra; 3. Stellar structure and evolution; 4. The end points of stellar evolution; Part II. The Large-Scale Structure of the Universe, 1900-1939: 5. The Galaxy and the nature of spiral nebulae; 6. The origins of astrophysical cosmology; Part III. The Opening up of the Electromagnetic Spectrum: 7. The opening up of the electromagnetic spectrum and the new astronomies; Part IV. The Astrophysics of Stars and Galaxies since 1945: 8. Stars and stellar evolution; 9. The physics of the interstellar medium; 10. The physics of galaxies and clusters of galaxies; 11. High-energy astrophysics; Part V. Astrophysical Cosmology since 1945: 12. Astrophysical cosmology; 13. The determination of cosmological parameters; 14. The evolution of galaxies and active galaxies with cosmic epoch; 15. The origin of galaxies and the large-scale structure of the Universe; 16. The very early Universe; References; Name index; Object index; Subject index.

Thermally Induced Structural Evolution and Performance of Mesoporous Block Copolymer-Directed Alumina Perovskite Solar Cells

PubMed Central

2015-01-01

Structure control in solution-processed hybrid perovskites is crucial to design and fabricate highly efficient solar cells. Here, we utilize in situ grazing incidence wide-angle X-ray scattering and scanning electron microscopy to investigate the structural evolution and film morphologies of methylammonium lead tri-iodide/chloride (CH3NH3PbI3–xClx) in mesoporous block copolymer derived alumina superstructures during thermal annealing. We show the CH3NH3PbI3–xClx material evolution to be characterized by three distinct structures: a crystalline precursor structure not described previously, a 3D perovskite structure, and a mixture of compounds resulting from degradation. Finally, we demonstrate how understanding the processing parameters provides the foundation needed for optimal perovskite film morphology and coverage, leading to enhanced block copolymer-directed perovskite solar cell performance. PMID:24684494

Launching Complex Tasks

ERIC Educational Resources Information Center

Jackson, Kara J.; Shahan, Emily C.; Gibbons, Lynsey K.; Cobb, Paul A.

2012-01-01

Mathematics lessons can take a variety of formats. In this article, the authors discuss lessons organized around complex mathematical tasks. These lessons usually unfold in three phases. First, the task is introduced to students. Second, students work on solving the task. Third, the teacher "orchestrates" a concluding whole-class discussion in…

Orchestrating Mathematical Discourse: Affordances and Hindrances for Novice Elementary Teachers

ERIC Educational Resources Information Center

Lee, Carrie Wilkerson

2016-01-01

The purpose of this study was to examine the mathematical discourse within novice elementary teachers' classrooms. More specifically, this study employed a sequential, explanatory mixed methods design to first quantitatively analyze the relationship between teachers' discourse practices and teacher attributes and school context. Next, a…

Strengthening Discussions

ERIC Educational Resources Information Center

Hintz, Allison B.

2013-01-01

"Strategy sharing" is a certain type of discussion that centers on students' ideas and occurs when children present different approaches to problems and provide information about how they solved the problem (Wood, Williams, and McNeal 2004). A teacher may orchestrate a strategy-sharing discussion to achieve one or more of the…

The role of mitochondria in plant development and stress tolerance

USDA-ARS?s Scientific Manuscript database

Proper cellular function requires orchestrated communication among cellular compartments and the ability of the cell to sense and respond to its environment. Plant cells contain three distinct compartments that house DNA. The nucleus contains the nuclear genome, which provides a majority of a cell's...

View from 30,000 Feet

ERIC Educational Resources Information Center

Freifeld, Lorri

2012-01-01

Orchestrating a smooth training transition during a merger or acquisition is never easy. When Delta Air Lines absorbed Northwest Airlines Corp. in 2008, the Training function realized it was in for a bumpy ride. This article looks at the strategies used and progress made since the takeover was announced.

Supporting Secondary Novices' Efforts to Implement Student- and Discourse-Centred Pedagogical Practices

ERIC Educational Resources Information Center

Lewis, Gary

2012-01-01

Novice secondary mathematics teachers attempting teaching consonant with NCTM (1991) Professional Standards for Teaching Mathematics experience stresses related to those attempts. Foremost among those stresses are challenges while orchestrating student-centred, whole-class discussions. Such discussions can create uncertainty and stress as novices…

Genome organization during the cell cycle: unity in division.

PubMed

Golloshi, Rosela; Sanders, Jacob T; McCord, Rachel Patton

2017-09-01

During the cell cycle, the genome must undergo dramatic changes in structure, from a decondensed, yet highly organized interphase structure to a condensed, generic mitotic chromosome and then back again. For faithful cell division, the genome must be replicated and chromosomes and sister chromatids physically segregated from one another. Throughout these processes, there is feedback and tension between the information-storing role and the physical properties of chromosomes. With a combination of recent techniques in fluorescence microscopy, chromosome conformation capture (Hi-C), biophysical experiments, and computational modeling, we can now attribute mechanisms to many long-observed features of chromosome structure changes during cell division. Apparent conflicts that arise when integrating the concepts from these different proposed mechanisms emphasize that orchestrating chromosome organization during cell division requires a complex system of factors rather than a simple pathway. Cell division is both essential for and threatening to proper genome organization. As interphase three-dimensional (3D) genome structure is quite static at a global level, cell division provides an important window of opportunity to make substantial changes in 3D genome organization in daughter cells, allowing for proper differentiation and development. Mistakes in the process of chromosome condensation or rebuilding the structure after mitosis can lead to diseases such as cancer, premature aging, and neurodegeneration. WIREs Syst Biol Med 2017, 9:e1389. doi: 10.1002/wsbm.1389 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

Structural Control of Metabolic Flux

PubMed Central

Sajitz-Hermstein, Max; Nikoloski, Zoran

2013-01-01

Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions. PMID:24367246

Cannibals in space: the coevolution of cannibalism and dispersal in spatially structured populations.

PubMed

Rudolf, Volker H W; Kamo, Masashi; Boots, Mike

2010-05-01

The propensity for cannibalism varies considerably both within and between species. Currently we have little understanding of both the causes of this variation and its evolutionary consequences for other life-history traits. We examine how different levels of spatial structure affect the evolution of cannibalism and how cannibalism in turn drives the evolution of dispersal. Using pair approximations and simulations, we show that cannibalism can easily evolve in spatially structured populations as long as some dispersal exists. Furthermore, for a wide range of intermediate levels of spatial structure, we find the possibility of evolutionary branching leading to polymorphism in cannibalism. We also show that cannibalism itself can have important evolutionary consequences and select for increased dispersal rates, thus helping to determine the spatial structure of populations. The coevolution of cannibalism and dispersal results in the evolution of various alternative life-history strategies with different dispersal and cannibalism regimes. Which strategy evolves depends on the environmental conditions that determine initial cannibalism rates. Our results therefore suggest that differences in spatial structure could explain variation in the propensity for cannibalism and cannibalistic polyphenism. Furthermore, results emphasize that cannibalism can drive the evolution of other life-history traits and determine the spatial structure of natural populations.

Evolution and development of gas exchange structures in Mammalia: the placenta and the lung.

PubMed

Mess, Andrea M; Ferner, Kirsten J

2010-08-31

Appropriate oxygen supply is crucial for organisms. Here we examine the evolution of structures associated with the delivery of oxygen in the pre- and postnatal phases in mammals. There is an enormous structural and functional variability in the placenta that has facilitated the evolution of specialized reproductive strategies, such as precociality. In particular the cell layers separating fetal and maternal blood differ markedly: a non-invasive epitheliochorial placenta, which increases the diffusion distance, represents a derived state in ungulates. Rodents and their relatives have an invasive haemochorial placental type as optimum for the diffusion distance. In contrast, lung development is highly conserved and differences in the lungs of neonates can be explained by different developmental rates. Monotremes and marsupials have altricial stages with lungs at the early saccular phase, whereas newborn eutherians have lungs at the late saccular or alveolar phase. In conclusion, the evolution of exchange structures in the pre- and postnatal periods does not follow similar principles. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

DOE PAGES

Merritt, Elizabeth Catherine; Doss, Forrest William

2016-07-06

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. Lastly, the evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

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

Merritt, E. C., E-mail: emerritt@lanl.gov; Doss, F. W.

2016-07-15

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. The evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

New knowledge-based genetic algorithm for excavator boom structural optimization

NASA Astrophysics Data System (ADS)

Hua, Haiyan; Lin, Shuwen

2014-03-01

Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the configurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, are taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem.

On Line Service Composition in the Integrated Clinical Environment for eHealth and Medical Systems

PubMed Central

García-Valls, Marisol; Touahria, Imad Eddine

2017-01-01

Medical and eHealth systems are progressively realized in the context of standardized architectures that support safety and ease the integration of the heterogeneous (and often proprietary) medical devices and sensors. The Integrated Clinical Environment (ICE) architecture appeared recently with the goal of becoming a common framework for defining the structure of the medical applications as concerns the safe integration of medical devices and sensors. ICE is simply a high level architecture that defines the functional blocks that should be part of a medical system to support interoperability. As a result, the underlying communication backbone is broadly undefined as concerns the enabling software technology (including the middleware) and associated algorithms that meet the ICE requirements of the flexible integration of medical devices and services. Supporting the on line composition of services in a medical system is also not part of ICE; however, supporting this behavior would enable flexible orchestration of functions (e.g., addition and/or removal of services and medical equipment) on the fly. iLandis one of the few software technologies that supports on line service composition and reconfiguration, ensuring time-bounded transitions across different service orchestrations; it supports the design, deployment and on line reconfiguration of applications, which this paper applies to service-based eHealth domains. This paper designs the integration between ICE architecture and iLand middleware to enhance the capabilities of ICE with on line service composition and the time-bounded reconfiguration of medical systems based on distributed services. A prototype implementation of a service-based eHealth system for the remote monitoring of patients is described; it validates the enhanced capacity of ICE to support dynamic reconfiguration of the application services. Results show that the temporal cost of the on line reconfiguration of the eHealth application is bounded, achieving a low overhead resulting from the addition of ICE compliance. PMID:28594371

On Line Service Composition in the Integrated Clinical Environment for eHealth and Medical Systems.

PubMed

García-Valls, Marisol; Touahria, Imad Eddine

2017-06-08

Medical and eHealth systems are progressively realized in the context of standardized architectures that support safety and ease the integration of the heterogeneous (and often proprietary) medical devices and sensors. The Integrated Clinical Environment (ICE) architecture appeared recently with the goal of becoming a common framework for defining the structure of the medical applications as concerns the safe integration of medical devices and sensors. ICE is simply a high level architecture that defines the functional blocks that should be part of a medical system to support interoperability. As a result, the underlying communication backbone is broadly undefined as concerns the enabling software technology (including the middleware) and associated algorithms that meet the ICE requirements of the flexible integration of medical devices and services. Supporting the on line composition of services in a medical system is also not part of ICE; however, supporting this behavior would enable flexible orchestration of functions (e.g., addition and/or removal of services and medical equipment) on the fly. iLandis one of the few software technologies that supports on line service composition and reconfiguration, ensuring time-bounded transitions across different service orchestrations; it supports the design, deployment and on line reconfiguration of applications, which this paper applies to service-based eHealth domains. This paper designs the integration between ICE architecture and iLand middleware to enhance the capabilities of ICE with on line service composition and the time-bounded reconfiguration of medical systems based on distributed services. A prototype implementation of a service-based eHealth system for the remote monitoring of patients is described; it validates the enhanced capacity of ICE to support dynamic reconfiguration of the application services. Results show that the temporal cost of the on line reconfiguration of the eHealth application is bounded, achieving a low overhead resulting from the addition of ICE compliance.

Family routines within the ecological niche: an analysis of the psychological well-being of U.S. caregivers of children with disabilities

PubMed Central

Larson, Elizabeth; Miller-Bishoff, Thomas

2014-01-01

Using mixed methods, this study examined the relationship of caregivers of children with disabilities’ psychological well-being (PWB) and their orchestration of daily routines within their ecological niche. Thirty-nine U.S. caregivers completed in-depth interviews, PWB Scales, and Family Time and Routines Index (FTRI). We used a multi-step analysis. Interview data was coded and vignettes created without knowledge of PWB and FTRI ratings. Next, the relationship of quantitative measures was analyzed. Four groups were created using FTRI-extent and PWB means: (1) low routine-low PWB, (2) low routine-high PWB, (3) high routine-low PWB, and (4) high routine-high PWB. We examined qualitative differences in key features between groups. Findings: Total PWB and FTRI scores were not significantly correlated, PWB Purpose in Life and FTRI-extent scores were moderately positively correlated, and PWB Environmental Mastery and FTRI-extent correlation approached significance. Qualitative findings describe caregivers’ structuring of routines, intensity of oversight, support in routines, management of dinner, paid work, and needs for respite. The four groups differed in paid work, household support, degree the child could self-occupy, Environmental Mastery, and opportunities to recuperate. Caregivers with higher levels of well-being and more regular routines did paid work, had supportive spouses, had children who more often could follow routines, had higher Environmental Mastery, could orchestrate a family meal, and had breaks from care in either work or leisure. All Native American caregivers and Mexican American caregivers with spouses were in the high routine-high PWB group. Insight into this complex negotiation between family members within daily routines may provide practitioners a better understanding of how to work within family circles to foster therapeutic alliances, identify focused intervention targets, and promote positive family wide outcomes. PMID:24910625

North Atlantic climate variability: The role of the North Atlantic Oscillation

NASA Astrophysics Data System (ADS)

Hurrell, James W.; Deser, Clara

2009-08-01

Marine ecosystems are undergoing rapid change at local and global scales. To understand these changes, including the relative roles of natural variability and anthropogenic effects, and to predict the future state of marine ecosystems requires quantitative understanding of the physics, biogeochemistry and ecology of oceanic systems at mechanistic levels. Central to this understanding is the role played by dominant patterns or "modes" of atmospheric and oceanic variability, which orchestrate coherent variations in climate over large regions with profound impacts on ecosystems. We review the spatial structure of extratropical climate variability over the Northern Hemisphere and, specifically, focus on modes of climate variability over the extratropical North Atlantic. A leading pattern of weather and climate variability over the Northern Hemisphere is the North Atlantic Oscillation (NAO). The NAO refers to a redistribution of atmospheric mass between the Arctic and the subtropical Atlantic, and swings from one phase to another producing large changes in surface air temperature, winds, storminess and precipitation over the Atlantic as well as the adjacent continents. The NAO also affects the ocean through changes in heat content, gyre circulations, mixed layer depth, salinity, high latitude deep water formation and sea ice cover. Thus, indices of the NAO have become widely used to document and understand how this mode of variability alters the structure and functioning of marine ecosystems. There is no unique way, however, to define the NAO. Several approaches are discussed including both linear (e.g., principal component analysis) and nonlinear (e.g., cluster analysis) techniques. The former, which have been most widely used, assume preferred atmospheric circulation states come in pairs, in which anomalies of opposite polarity have the same spatial structure. In contrast, nonlinear techniques search for recurrent patterns of a specific amplitude and sign. They reveal, for instance, spatial asymmetries between different phases of the NAO that are likely important for ecological studies. It also follows that there is no universally accepted index to describe the temporal evolution of the NAO. Several of the most common measures are presented and compared. All reveal that there is no preferred time scale of variability for the NAO: large changes occur from one winter to the next and from one decade to the next. There is also a large amount of within-season variability in the patterns of atmospheric circulation of the North Atlantic, so that most winters cannot be characterized solely by a canonical NAO structure. A better understanding of how the NAO responds to external forcing, including sea surface temperature changes in the tropics, stratospheric influences, and increasing greenhouse gas concentrations, is crucial to the current debate on climate variability and change.

North Atlantic climate variability: The role of the North Atlantic Oscillation

NASA Astrophysics Data System (ADS)

Hurrell, James W.; Deser, Clara

2010-02-01

Marine ecosystems are undergoing rapid change at local and global scales. To understand these changes, including the relative roles of natural variability and anthropogenic effects, and to predict the future state of marine ecosystems requires quantitative understanding of the physics, biogeochemistry and ecology of oceanic systems at mechanistic levels. Central to this understanding is the role played by dominant patterns or "modes" of atmospheric and oceanic variability, which orchestrate coherent variations in climate over large regions with profound impacts on ecosystems. We review the spatial structure of extratropical climate variability over the Northern Hemisphere and, specifically, focus on modes of climate variability over the extratropical North Atlantic. A leading pattern of weather and climate variability over the Northern Hemisphere is the North Atlantic Oscillation (NAO). The NAO refers to a redistribution of atmospheric mass between the Arctic and the subtropical Atlantic, and swings from one phase to another producing large changes in surface air temperature, winds, storminess and precipitation over the Atlantic as well as the adjacent continents. The NAO also affects the ocean through changes in heat content, gyre circulations, mixed layer depth, salinity, high latitude deep water formation and sea ice cover. Thus, indices of the NAO have become widely used to document and understand how this mode of variability alters the structure and functioning of marine ecosystems. There is no unique way, however, to define the NAO. Several approaches are discussed including both linear (e.g., principal component analysis) and nonlinear (e.g., cluster analysis) techniques. The former, which have been most widely used, assume preferred atmospheric circulation states come in pairs, in which anomalies of opposite polarity have the same spatial structure. In contrast, nonlinear techniques search for recurrent patterns of a specific amplitude and sign. They reveal, for instance, spatial asymmetries between different phases of the NAO that are likely important for ecological studies. It also follows that there is no universally accepted index to describe the temporal evolution of the NAO. Several of the most common measures are presented and compared. All reveal that there is no preferred time scale of variability for the NAO: large changes occur from one winter to the next and from one decade to the next. There is also a large amount of within-season variability in the patterns of atmospheric circulation of the North Atlantic, so that most winters cannot be characterized solely by a canonical NAO structure. A better understanding of how the NAO responds to external forcing, including sea surface temperature changes in the tropics, stratospheric influences, and increasing greenhouse gas concentrations, is crucial to the current debate on climate variability and change.

Evolution of individual versus social learning on social networks

PubMed Central

Tamura, Kohei; Kobayashi, Yutaka; Ihara, Yasuo

2015-01-01

A number of studies have investigated the roles played by individual and social learning in cultural phenomena and the relative advantages of the two learning strategies in variable environments. Because social learning involves the acquisition of behaviours from others, its utility depends on the availability of ‘cultural models’ exhibiting adaptive behaviours. This indicates that social networks play an essential role in the evolution of learning. However, possible effects of social structure on the evolution of learning have not been fully explored. Here, we develop a mathematical model to explore the evolutionary dynamics of learning strategies on social networks. We first derive the condition under which social learners (SLs) are selectively favoured over individual learners in a broad range of social network. We then obtain an analytical approximation of the long-term average frequency of SLs in homogeneous networks, from which we specify the condition, in terms of three relatedness measures, for social structure to facilitate the long-term evolution of social learning. Finally, we evaluate our approximation by Monte Carlo simulations in complete graphs, regular random graphs and scale-free networks. We formally show that whether social structure favours the evolution of social learning is determined by the relative magnitudes of two effects of social structure: localization in competition, by which competition between learning strategies is evaded, and localization in cultural transmission, which slows down the spread of adaptive traits. In addition, our estimates of the relatedness measures suggest that social structure disfavours the evolution of social learning when selection is weak. PMID:25631568

Evolution of individual versus social learning on social networks.

PubMed

Tamura, Kohei; Kobayashi, Yutaka; Ihara, Yasuo

2015-03-06

A number of studies have investigated the roles played by individual and social learning in cultural phenomena and the relative advantages of the two learning strategies in variable environments. Because social learning involves the acquisition of behaviours from others, its utility depends on the availability of 'cultural models' exhibiting adaptive behaviours. This indicates that social networks play an essential role in the evolution of learning. However, possible effects of social structure on the evolution of learning have not been fully explored. Here, we develop a mathematical model to explore the evolutionary dynamics of learning strategies on social networks. We first derive the condition under which social learners (SLs) are selectively favoured over individual learners in a broad range of social network. We then obtain an analytical approximation of the long-term average frequency of SLs in homogeneous networks, from which we specify the condition, in terms of three relatedness measures, for social structure to facilitate the long-term evolution of social learning. Finally, we evaluate our approximation by Monte Carlo simulations in complete graphs, regular random graphs and scale-free networks. We formally show that whether social structure favours the evolution of social learning is determined by the relative magnitudes of two effects of social structure: localization in competition, by which competition between learning strategies is evaded, and localization in cultural transmission, which slows down the spread of adaptive traits. In addition, our estimates of the relatedness measures suggest that social structure disfavours the evolution of social learning when selection is weak. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants.

PubMed

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-10-24

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

Helicity evolution at small-x

DOE PAGES

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2016-01-13

We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g1 structure function. These evolution equations resum powers of α s ln 2(1/x) in the polarization-dependent evolution along with the powers of α s ln(1/x) in the unpolarized evolution which includes saturation efects. The equations are written in an operator form in terms of polarization-dependent Wilson line-like operators. While the equations do not close in general, they become closed and self-contained systems of non-linear equations in the large-N c and large-N c & N f limits. As a cross-check,more » in the ladder approximation, our equations map onto the same ladder limit of the infrared evolution equations for g 1 structure function derived previously by Bartels, Ermolaev and Ryskin.« less

The isotopic and chemical evolution of planets: Mars as a missing link

NASA Technical Reports Server (NTRS)

Depaolo, D. J.

1988-01-01

The study of planetary bodies has advanced to a stage where it is possible to contemplate general models for the chemical and physical evolution of planetary interiors, which might be referred to as UMPES (Unified Models of Planetary Evolution and Structure). UMPES would be able to predict the internal evolution and structure of a planet given certain input parameters such as mass, distance from the sun, and a time scale for accretion. Such models are highly dependent on natural observations because the basic material properties of planetary interiors, and the processes that take place during the evolution of planets are imperfectly understood. The idea of UMPES was particularly unrealistic when the only information available was from the earth. However, advances have been made in the understanding of the general aspects of planetary evolution now that there is geochemical and petrological data available for the moon and for meteorites.

The Big Picture: An Overview

ERIC Educational Resources Information Center

Hom, Willard C.

2010-01-01

The system office for community college institutional research (SOCCIR) plays a role in the drama of higher education that states must orchestrate to help community college systems operate effectively and efficiently over the long term. But how exactly does the SOCCIR enable a state to accomplish what the separate institutional research (IR)…

Orchestrating Authorship: Teaching Writing across the Psychology Curriculum

ERIC Educational Resources Information Center

Soysa, Champika K.; Dunn, Dana S.; Dottolo, Andrea L.; Burns-Glover, Alyson L.; Gurung, Regan A. R.

2013-01-01

This article describes the kinds of writing that could be introduced at the beginner, intermediate, and advanced course levels in the psychology major. We present exemplars of writing assignments across three institutions, including textual analysis, integrating intratext and intertext writing, and a capstone thesis project, where the skills…

Interactive Whiteboards and All That Jazz: Analysing Classroom Activity with Interactive Technologies

ERIC Educational Resources Information Center

Tanner, Howard; Beauchamp, Gary; Jones, Sonia; Kennewell, Steve

2010-01-01

The term "orchestration", has been used to describe the teacher's role in activity settings incorporating interactive technologies. This musical analogy suggests pre-planned manipulation of events to generate "performance" leading to learning. However, in two recent projects we have observed how effective teaching and learning…

Music: Instrumental Techniques, Strings.

ERIC Educational Resources Information Center

Ryan, Philip

A course in music which emphasizes harmony is presented. The approach used is a laboratory one in which pupils will develop skill in playing orchestral string instruments, sing, listen to, read and compose music with emphasis on elementary concepts of harmony. Course objectives include: (1) The student will select the title of a familiar melody…

Strings in General Music: An Experience with Multiple Sequencing

ERIC Educational Resources Information Center

Martin, Jeffrey

2012-01-01

Instrumental performance that approximates real-world models is one way in which a general music curriculum can encourage high levels of engagement and potential for lifelong musical activity. Although guitars, keyboards, and various folk instruments are useful for this purpose, orchestral instruments can also provide significant solo and ensemble…

Orchestrating Literacies: Print Literacy Learning Opportunities within Multimodal Intergenerational Ensembles

ERIC Educational Resources Information Center

McKee, Lori L.; Heydon, Rachel M.

2015-01-01

This exploratory case study considered the opportunities for print literacy learning within multimodal ensembles that featured art, singing and digital media within the context of an intergenerational programme that brought together 13 kindergarten children (4 and 5 years) with seven elder companions. Study questions concerned how reading and…

Educating Orchestral Musicians

ERIC Educational Resources Information Center

Calissendorff, Maria; Hannesson, Haukur F.

2017-01-01

This article examines research on the specific training of musicians before they begin work as players in professional orchestras. Most of the research is in the area of education. The present article suggests that little research exists that is specific to the development of a traditional orchestra musician from an early age through the music…

Settling the 'Score' with Heart Disease

NASA Technical Reports Server (NTRS)

2004-01-01

Technology and medicine forged a bond in 1986 when a group of dedicated NASA scientists, University of Southern California (USC) medical professors, and a Dutch cardiologist joined forces to prevent heart attacks, using ultrasound images of astronauts blood-flow patterns and the supercomputer depended upon to orchestrate the "Star Wars" Strategic Defense Initiative.

Improving Collaborative Learning in the Classroom: Text Mining Based Grouping and Representing

ERIC Educational Resources Information Center

Erkens, Melanie; Bodemer, Daniel; Hoppe, H. Ulrich

2016-01-01

Orchestrating collaborative learning in the classroom involves tasks such as forming learning groups with heterogeneous knowledge and making learners aware of the knowledge differences. However, gathering information on which the formation of appropriate groups and the creation of graphical knowledge representations can be based is very effortful…

Temporal expression of pecan allergens during nut development

USDA-ARS?s Scientific Manuscript database

Pecan nuts and other tree nuts are among a group of eight foods that most commonly cause food allergy. The growth of pecan nuts is a highly complex process orchestrated by the temporal and spatial expression of specific genes. Three conserved seed-storage proteins from the prolamin and cupin super...

Marketing Climate: New Considerations for Target Marketing in Graduate Student Enrollment Management

ERIC Educational Resources Information Center

Kranzow, Jeannine; Hyland, Nancy

2011-01-01

Lewison and Hawes (1997) discuss target marketing strategies of differentiated, concentrated or orchestrated marketing in their article "Student Marketing Strategies for Universities." While the authors agree with some of the suggested strategies and reasons behind them, their perspective as faculty teaching in a graduate education program offers…

The Secret Talents of Fundraisers

ERIC Educational Resources Information Center

Pulley, John

2010-01-01

A significant but unknown number of performing artists have redirected their creativity and passion into development. They are ballet and contemporary dancers, jazz and orchestral musicians, actors and comedians, opera divas and gospel belters. None of them set out to become fundraisers. Yet here they are, and they partly credit their success in…

Metacognitive Awareness and Monitoring in Adult and College Readers.

ERIC Educational Resources Information Center

Rinehart, Steve D.; Platt, Jennifer M.

1984-01-01

A literature review was undertaken to demonstrate how knowledge of one's cognitive processes, the orchestration of strategic effort, and the monitoring of one's cognitive activities can enhance reading performance. The findings indicate that while older readers exercise more awareness of their own learning processes and greater self-control or…

Approximations of Practice in the Preparation of Prospective Elementary Science Teachers

ERIC Educational Resources Information Center

Nelson, Michele M.

2011-01-01

Elementary teacher education involves learning to teach science. Even in elementary school, teaching science is demanding work--teachers must orchestrate a complex set of teaching practices to support students' science learning. This dissertation examines the application of Grossman and colleagues' (2009) cross-professional learning framework,…

Teacher Education: Interface Between Practices and Policies: The Malaysian Experience 1979-1997.

ERIC Educational Resources Information Center

Ratnavadivel, Nagendralingan

1999-01-01

Describes preservice teacher education in Malaysia, focusing on the interface between policies and practices as orchestrated by the Teacher Education Division of the Ministry of Education. Looks at changes in the political, economic, and sociocultural spheres, both locally and internationally, that have helped ensure qualitative and quantitative…

Orchestrating Productive Whole Class Discussions: The Role of Designed Student Responses

ERIC Educational Resources Information Center

Evans, Sheila; Dawson, Clare

2017-01-01

The value of students publicly sharing and discussing their solutions to unstructured problems is widely recognized. This can, however, be pedagogically challenging. The solutions may be partial, unclear and unpredictable. For many teachers, particularly those new to working with such problems with their students, the improvisation needed to…

Methodological Reflections: Designing and Understanding Computer-Supported Collaborative Learning

ERIC Educational Resources Information Center

Hamalainen, Raija

2012-01-01

Learning involves more than just a small group of participants, which makes designing and managing collaborative learning processes in higher education a challenging task. As a result, emerging concerns in current research have pointed increasingly to teacher orchestrated learning processes in naturalistic learning settings. In line with this…

Computational Systems Toxicology: recapitulating the logistical dynamics of cellular response networks in virtual tissue models (Eurotox_2017)

EPA Science Inventory

Translating in vitro data and biological information into a predictive model for human toxicity poses a significant challenge. This is especially true for complex adaptive systems such as the embryo where cellular dynamics are precisely orchestrated in space and time. Computer ce...

The Role of Ki 'Im in Orchestrating Contrastive Focus in Biblical Hebrew

ERIC Educational Resources Information Center

Park, Grace Jeongyeon

2011-01-01

The so-called compound use of ki 'im has been interpreted mainly either with exceptive ("except" or "unless") or adversative meaning ("but" or "rather"), although it has sometimes also been interpreted in other ways such as "only" or "surely". These various meanings have been applied…

Model-Driven Design: Systematically Building Integrated Blended Learning Experiences

ERIC Educational Resources Information Center

Laster, Stephen

2010-01-01

Developing and delivering curricula that are integrated and that use blended learning techniques requires a highly orchestrated design. While institutions have demonstrated the ability to design complex curricula on an ad-hoc basis, these projects are generally successful at a great human and capital cost. Model-driven design provides a…

The Play of Psychotherapy

ERIC Educational Resources Information Center

Marks-Tarlow, Terry

2012-01-01

The author reviews the role of play within psychotherapy. She does not discuss the formal play therapy especially popular for young children, nor play from the Jungian perspective that encourages the use of the sand tray with adults. Instead, she focuses on the informal use of play during psychotherapy as it is orchestrated intuitively. Because…

Toxic plants: Effects on reproduction and fetal and embryonic development in livestock

USDA-ARS?s Scientific Manuscript database

Reproductive success is dependent on a large number of carefully orchestrated biological events that must occur in a specifically timed sequence. The interference with one of more of these sequences or events may result in total reproductive failure or a more subtle reduction in reproductive potent...

DCASR (Defense Contract Administration Services Region) Boston, Strategic/Total Quality Management Master Plan Using Management by Planning (MBP)

DTIC Science & Technology

1989-06-01

employees. A policy consists of targets, plans, and target values. Policy Deployment: One English translation for hoshin kanri . (Others are management by...policy and hoshin planning.) Policy deployment orchestrates continuous improvement in a way that fosters individual initiative and alignment. Process

OMA-gosh, where's that TAF?

PubMed

Blackwell, T Keith; Walker, Amy K

2008-10-03

How transcription is silenced in early embryos has long been a mystery. In this issue, Guven-Ozkan et al. (2008) report that transcriptional repression during worm embryogenesis is mediated through sequestration of the general transcription factor TAF-4 and is regulated by mechanisms that orchestrate the transition between maternal and zygotic gene expression.

Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit

USDA-ARS?s Scientific Manuscript database

Little is known about how plants regulate their folate content, including whether the expression of folate biosynthesis genes is orchestrated during development or modulated by folate levels. Nor is much known about how folate levels impact the expression of other genes. These points were addressed ...

Interconnecting Networks of Practice for Professional Learning

ERIC Educational Resources Information Center

Mackey, Julie; Evans, Terry

2011-01-01

The article explores the complementary connections between communities of practice and the ways in which individuals orchestrate their engagement with others to further their professional learning. It does so by reporting on part of a research project conducted in New Zealand on teachers' online professional learning in a university graduate…

Platelets Orchestrate Remote Tissue Damage After Mesenteric Ischemia-Reperfusion

DTIC Science & Technology

2012-02-02

Medicine , Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., CLS-928, Boston, MA 02115 (e-mail: gtsokos@bidmc.harvard.edu). Am...Guikema BJ, Fritzinger DC, Vogel CW, Stahl GL. Humanized cobra venom factor decreases myocardial ischemia-reperfu- sion injury. Mol Immunol 47: 506–510

How School Principals Can Foster Effective Literacy Instruction: A Ten-Step Plan

ERIC Educational Resources Information Center

Hinchman, Kathleen A.

2009-01-01

School principals can foster effective literacy instruction by orchestrating community collaboration in an ongoing cycle of literacy program development, implementation, evaluation, and revision outlined in this ten-step plan. The steps address forming a community advisory board, appointing a building literacy leader, forming a literacy team,…

Supporting Teacher Orchestration in Ubiquitous Learning Environments: A Study in Primary Education

ERIC Educational Resources Information Center

Muñoz-Cristóbal, Juan A.; Jorrín-Abellán, Iván M.; Asensio-Pérez, Juan I.; Martínez-Monés, Alejandra; Prieto, Luis P.; Dimitriadis, Yannis

2015-01-01

During the last decades, educational contexts have transformed into complex technological and social ecologies, with mobile devices expanding the scope of education beyond the traditional classroom, creating so-called Ubiquitous Learning Environments (ULEs). However, these new technological opportunities entail an additional burden for teachers,…

An Argument Everyone Wins: Shared Learning Unites Teachers across Schools and Grade Levels

ERIC Educational Resources Information Center

Goldberg, Lauren; Siegel, Brad; Goldberg, Gravity

2015-01-01

The three authors of this article--a K-12 regional director of curriculum, instruction, and assessment responsible for orchestrating professional learning, a high school English teacher who participated in the professional learning, and an independent literacy consultant who supports four districts' professional learning--share their experiences…

Clergy Views on Evolution, Creationism, Science, and Religion

ERIC Educational Resources Information Center

Colburn, Alan; Henriques, Laura

2006-01-01

Spurred by students who felt conflicted accepting evolution and the tenets of their faiths, yet knowing their faiths supported science and evolution, we began a study to determine the views clergy espouse on issues related to evolution, creationism, science, and religion. The resulting study included structured interviews with eight clergy and a…

Management of natural crises with choreography and orchestration of federated warning-systems

NASA Astrophysics Data System (ADS)

Haener, Rainer; Waechter, Joachim; Hammitzsch, Martin

2013-04-01

The project Collaborative, Complex and Critical Decision-Support in Evolving Crises (TRIDEC), co-funded by the European Commission in its Seventh Framework Programme focuses on real-time intelligent information management in earth management. The addressed challenges include the design and implementation of a robust and scalable service infrastructure supporting the integration of existing resources, components and systems. Key challenge for TRIDEC is establishing a network of independent systems, cooperatively interacting as a collective in a system-of-systems (SoS). For this purpose TRIDEC adopts enhancements of service-oriented architecture (SOA) principles in terms of an event-driven architecture (EDA) design (SOA 2.0). In this way TRIDEC establishes large-scale concurrent and intelligent information management of a manifold of crisis types by focusing on the integration of autonomous, task-oriented and geographically distributed systems. To this end TRIDEC adapts both ways SOA 2.0 offers: orchestration and choreography. In orchestration, a central knowledge-based processing framework takes control over the involved services and coordinates their execution. Choreography on the other hand avoids central coordination. Rather, each system involved in the SoS follows a global scenario without a single point of control but specifically defined (enacted, agreed upon) trigger conditions. More than orchestration choreography allows collaborative business processes of various heterogeneous sub-systems (e.g. cooperative decision making) by concurrent Complex Event Processing (CEP) and asynchronous communication. These types of interaction adapt the concept of decoupled relationships between information producers (e.g. sensors and sensor systems) and information consumers (e.g. warning systems and warning dissemination systems). Asynchronous communication is useful if a participant wants to trigger specific actions by delegating the responsibility (separation of concerns) for the action to a dedicated participant. Implementing CEP, none of the participants has to know anything about the others. Information is filtered from a stream of manifold events (triggers) assigned to certain and well-defined topics. Both, orchestration and choreography are based on the specification of conversations, which comprise the information model, the roles and responsibilities of all participants, services and business processes, and interaction scenarios. By the maintenance of conversations in commonly available and semantically enabled registries it is possible to establish a federation of systems that is able to provide dynamic, yet coherent behaviour. TRIDEC establishes a reliable and adaptive SoS (concurrent processing of events and activities) which exposes emergent behaviour (e.g. intelligent and adaptive monitoring strategies, cooperative decision making or dynamic system configuration) even in case of partly system failures. In a process of self-organising (task balancing and dynamic delegation of responsibilities) as SoS is able to secure the reliability and responsiveness for real-time, long running & durable monitoring activities. Concepts like Design by Contract (DbC), service level agreements (SLA), redundancy- and failover-strategies as well as a comprehensive knowledge-based description of all facets of all potential interactions ensure the interoperability, robustness and expected behaviour of the TRIDEC SoS even if it is composed of managerial independent sub-systems. Beyond these features, the adaptability of a SoS offers scalability and virtualization regarding both, systems and domains. Composability and re-use of functionality can be achieved easily even across domain-boundaries.

A life prediction model for laminated composite structural components

NASA Technical Reports Server (NTRS)

Allen, David H.

1990-01-01

A life prediction methodology for laminated continuous fiber composites subjected to fatigue loading conditions was developed. A summary is presented of research completed. A phenomenological damage evolution law was formulated for matrix cracking which is independent of stacking sequence. Mechanistic and physical support was developed for the phenomenological evolution law proposed above. The damage evolution law proposed above was implemented to a finite element computer program. And preliminary predictions were obtained for a structural component undergoing fatigue loading induced damage.

Object Recognition and Random Image Structure Evolution

ERIC Educational Resources Information Center

Sadr, Jvid; Sinha, Pawan

2004-01-01

We present a technique called Random Image Structure Evolution (RISE) for use in experimental investigations of high-level visual perception. Potential applications of RISE include the quantitative measurement of perceptual hysteresis and priming, the study of the neural substrates of object perception, and the assessment and detection of subtle…

Local structure of numerically generated worm hole spacetime.

NASA Astrophysics Data System (ADS)

Siino, M.

The author investigates the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, he interprets the evolution of the worm hole structure.

A Teaching Module about Stellar Structure and Evolution

ERIC Educational Resources Information Center

Colantonio, Arturo; Galano, Silvia; Leccia, Silvio; Puddu, Emanuella; Testa, Italo

2017-01-01

In this paper, we present a teaching module about stellar structure, functioning and evolution. Drawing from literature in astronomy education, we designed the activities around three key ideas: spectral analysis, mechanical and thermal equilibrium, energy and nuclear reactions. The module is divided into four phases, in which the key ideas for…

Graph Structured Program Evolution: Evolution of Loop Structures

NASA Astrophysics Data System (ADS)

Shirakawa, Shinichi; Nagao, Tomoharu

Recently, numerous automatic programming techniques have been developed and applied in various fields. A typical example is genetic programming (GP), and various extensions and representations of GP have been proposed thus far. Complex programs and hand-written programs, however, may contain several loops and handle multiple data types. In this chapter, we propose a new method called Graph Structured Program Evolution (GRAPE). The representation of GRAPE is a graph structure; therefore, it can represent branches and loops using this structure. Each programis constructed as an arbitrary directed graph of nodes and a data set. The GRAPE program handles multiple data types using the data set for each type, and the genotype of GRAPE takes the form of a linear string of integers. We apply GRAPE to three test problems, factorial, exponentiation, and list sorting, and demonstrate that the optimum solution in each problem is obtained by the GRAPE system.

Genetic variability, individuality and the evolution of the mammalian brain.

PubMed

Lipp, H P

1995-12-01

The neo-Darwinian theory of evolution has difficulty in explaining the rapid evolution of mammalian brain and behavior. I shall argue that the plasticity mechanisms of the brain (i.e., system homeostasis, developmental reorganization, structural adult plasticity, and cognition and learning) have evolved primarily as genetic buffer systems which protect subtle mutations influencing brain structures from natural selection. These buffer systems permit accumulation of genetic variation in the higher system levels of the brain (simply defined as structures with late differentiation), while low-level systems are kept constant by natural selection. The organization of this intrinsic genetic buffering system provides several features facilitating neo-Darwinian evolution: In conclusion, the evolutionary appearance of cognition and intelligence is an ordinary biological mechanism compensating evolutionary drags such as long lifespans and fewer offspring. The concept has heuristic value for identifying gene-brain-behavior relationships and for explaining behavioral consequences of artifical gene deletions.

Improvisation in evolution of genes and genomes: whose structure is it anyway?

PubMed

Shakhnovich, Boris E; Shakhnovich, Eugene I

2008-06-01

Significant progress has been made in recent years in a variety of seemingly unrelated fields such as sequencing, protein structure prediction, and high-throughput transcriptomics and metabolomics. At the same time, new microscopic models have been developed that made it possible to analyze the evolution of genes and genomes from first principles. The results from these efforts enable, for the first time, a comprehensive insight into the evolution of complex systems and organisms on all scales--from sequences to organisms and populations. Every newly sequenced genome uncovers new genes, families, and folds. Where do these new genes come from? How do gene duplication and subsequent divergence of sequence and structure affect the fitness of the organism? What role does regulation play in the evolution of proteins and folds? Emerging synergism between data and modeling provides first robust answers to these questions.

A modified Lax-Phillips scattering theory for quantum mechanics

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

Strauss, Y., E-mail: ystrauss@cs.bgu.ac.il

The Lax-Phillips scattering theory is an appealing abstract framework for the analysis of scattering resonances. Quantum mechanical adaptations of the theory have been proposed. However, since these quantum adaptations essentially retain the original structure of the theory, assuming the existence of incoming and outgoing subspaces for the evolution and requiring the spectrum of the generator of evolution to be unbounded from below, their range of applications is rather limited. In this paper, it is shown that if we replace the assumption regarding the existence of incoming and outgoing subspaces by the assumption of the existence of Lyapunov operators for themore » quantum evolution (the existence of which has been proved for certain classes of quantum mechanical scattering problems), then it is possible to construct a structure analogous to the Lax-Phillips structure for scattering problems for which the spectrum of the generator of evolution is bounded from below.« less

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Traumatic Brain Injury: At the Crossroads of Neuropathology and Common Metabolic Endocrinopathies

PubMed Central

Li, Melanie

2018-01-01

Building on the seminal work by Geoffrey Harris in the 1970s, the neuroendocrinology field, having undergone spectacular growth, has endeavored to understand the mechanisms of hormonal connectivity between the brain and the rest of the body. Given the fundamental role of the brain in the orchestration of endocrine processes through interactions among neurohormones, it is thus not surprising that the structural and/or functional alterations following traumatic brain injury (TBI) can lead to endocrine changes affecting the whole organism. Taking into account that systemic hormones also act on the brain, modifying its structure and biochemistry, and can acutely and chronically affect several neurophysiological endpoints, the question is to what extent preexisting endocrine dysfunction may set the stage for an adverse outcome after TBI. In this review, we provide an overview of some aspects of three common metabolic endocrinopathies, e.g., diabetes mellitus, obesity, and thyroid dysfunction, and how these could be triggered by TBI. In addition, we discuss how the complex endocrine networks are woven into the responses to sudden changes after TBI, as well as some of the potential mechanisms that, separately or synergistically, can influence outcomes after TBI. PMID:29538298

Rational drug design and synthesis of molecules targeting the angiotensin II type 1 and type 2 receptors.

PubMed

Kellici, Tahsin F; Tzakos, Andreas G; Mavromoustakos, Thomas

2015-03-02

The angiotensin II (Ang II) type 1 and type 2 receptors (AT1R and AT2R) orchestrate an array of biological processes that regulate human health. Aberrant function of these receptors triggers pathophysiological responses that can ultimately lead to death. Therefore, it is important to design and synthesize compounds that affect beneficially these two receptors. Cardiovascular disease, which is attributed to the overactivation of the vasoactive peptide hormone Αng II, can now be treated with commercial AT1R antagonists. Herein, recent achievements in rational drug design and synthesis of molecules acting on the two AT receptors are reviewed. Quantitative structure activity relationships (QSAR) and molecular modeling on the two receptors aim to assist the search for new active compounds. As AT1R and AT2R are GPCRs and drug action is localized in the transmembrane region the role of membrane bilayers is exploited. The future perspectives in this field are outlined. Tremendous progress in the field is expected if the two receptors are crystallized, as this will assist the structure based screening of the chemical space and lead to new potent therapeutic agents in cardiovascular and other diseases.

A chromatin link to caste identity in the carpenter ant Camponotus floridanus

PubMed Central

Simola, Daniel F.; Ye, Chaoyang; Mutti, Navdeep S.; Dolezal, Kelly; Bonasio, Roberto; Liebig, Jürgen; Reinberg, Danny; Berger, Shelley L.

2013-01-01

In many ant species, sibling larvae follow alternative ontogenetic trajectories that generate striking variation in morphology and behavior among adults. These organism-level outcomes are often determined by environmental rather than genetic factors. Therefore, epigenetic mechanisms may mediate the expression of adult polyphenisms. We produced the first genome-wide maps of chromatin structure in a eusocial insect and found that gene-proximal changes in histone modifications, notably H3K27 acetylation, discriminate two female worker and male castes in Camponotus floridanus ants and partially explain differential gene expression between castes. Genes showing coordinated changes in H3K27ac and RNA implicate muscle development, neuronal regulation, and sensory responses in modulating caste identity. Binding sites of the acetyltransferase CBP harbor the greatest caste variation in H3K27ac, are enriched with motifs for conserved transcription factors, and show evolutionary expansion near developmental and neuronal genes. These results suggest that environmental effects on caste identity may be mediated by differential recruitment of CBP to chromatin. We propose that epigenetic mechanisms that modify chromatin structure may help orchestrate the generation and maintenance of polyphenic caste morphology and social behavior in ants. PMID:23212948

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

PubMed Central

Kiosze-Becker, Kristin; Ori, Alessandro; Gerovac, Milan; Heuer, André; Nürenberg-Goloub, Elina; Rashid, Umar Jan; Becker, Thomas; Beckmann, Roland; Beck, Martin; Tampé, Robert

2016-01-01

Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final—or the first—step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix–loop–helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling. PMID:27824037

Temporomandibular Joint Regenerative Medicine

PubMed Central

Van Bellinghen, Xavier; Idoux-Gillet, Ysia; Pugliano, Marion; Strub, Marion; Bornert, Fabien; Clauss, Francois; Schwinté, Pascale; Keller, Laetitia; Benkirane-Jessel, Nadia; Lutz, Jean Christophe; Fioretti, Florence

2018-01-01

The temporomandibular joint (TMJ) is an articulation formed between the temporal bone and the mandibular condyle which is commonly affected. These affections are often so painful during fundamental oral activities that patients have lower quality of life. Limitations of therapeutics for severe TMJ diseases have led to increased interest in regenerative strategies combining stem cells, implantable scaffolds and well-targeting bioactive molecules. To succeed in functional and structural regeneration of TMJ is very challenging. Innovative strategies and biomaterials are absolutely crucial because TMJ can be considered as one of the most difficult tissues to regenerate due to its limited healing capacity, its unique histological and structural properties and the necessity for long-term prevention of its ossified or fibrous adhesions. The ideal approach for TMJ regeneration is a unique scaffold functionalized with an osteochondral molecular gradient containing a single stem cell population able to undergo osteogenic and chondrogenic differentiation such as BMSCs, ADSCs or DPSCs. The key for this complex regeneration is the functionalization with active molecules such as IGF-1, TGF-β1 or bFGF. This regeneration can be optimized by nano/micro-assisted functionalization and by spatiotemporal drug delivery systems orchestrating the 3D formation of TMJ tissues. PMID:29393880

Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains.

PubMed

Müllenbroich, M Caroline; Silvestri, Ludovico; Onofri, Leonardo; Costantini, Irene; Hoff, Marcel Van't; Sacconi, Leonardo; Iannello, Giulio; Pavone, Francesco S

2015-10-01

Comprehensive mapping and quantification of neuronal projections in the central nervous system requires high-throughput imaging of large volumes with microscopic resolution. To this end, we have developed a confocal light-sheet microscope that has been optimized for three-dimensional (3-D) imaging of structurally intact clarified whole-mount mouse brains. We describe the optical and electromechanical arrangement of the microscope and give details on the organization of the microscope management software. The software orchestrates all components of the microscope, coordinates critical timing and synchronization, and has been written in a versatile and modular structure using the LabVIEW language. It can easily be adapted and integrated to other microscope systems and has been made freely available to the light-sheet community. The tremendous amount of data routinely generated by light-sheet microscopy further requires novel strategies for data handling and storage. To complete the full imaging pipeline of our high-throughput microscope, we further elaborate on big data management from streaming of raw images up to stitching of 3-D datasets. The mesoscale neuroanatomy imaged at micron-scale resolution in those datasets allows characterization and quantification of neuronal projections in unsectioned mouse brains.

Evolution: Tracing the origins of centrioles, cilia, and flagella.

PubMed

Carvalho-Santos, Zita; Azimzadeh, Juliette; Pereira-Leal, José B; Bettencourt-Dias, Mónica

2011-07-25

Centrioles/basal bodies (CBBs) are microtubule-based cylindrical organelles that nucleate the formation of centrosomes, cilia, and flagella. CBBs, cilia, and flagella are ancestral structures; they are present in all major eukaryotic groups. Despite the conservation of their core structure, there is variability in their architecture, function, and biogenesis. Recent genomic and functional studies have provided insight into the evolution of the structure and function of these organelles.

Structure and evolution of plant centromeres.

PubMed

Nagaki, Kiyotaka; Walling, Jason; Hirsch, Cory; Jiang, Jiming; Murata, Minoru

2009-01-01

Investigations of centromeric DNA and proteins and centromere structures in plants have lagged behind those conducted with yeasts and animals; however, many attractive results have been obtained from plants during this decade. In particular, intensive investigations have been conducted in Arabidopsis and Gramineae species. We will review our understanding of centromeric components, centromere structures, and the evolution of these attributes of centromeres among plants using data mainly from Arabidopsis and Gramineae species.

The relativistic equations of stellar structure and evolution. Stars with degenerate neutron cores. 1: Structure of equilibrium models

NASA Technical Reports Server (NTRS)

Thorne, K. S.; Zytkow, A. N.

1976-01-01

The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. Also, a general relativistic version of the mixing-length formalism for convection is presented. Finally, it is argued that in previous work on spherical systems general relativity theorists have identified the wrong quantity as "total mass-energy inside radius r."

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses.

PubMed

Ocker, Gabriel Koch; Litwin-Kumar, Ashok; Doiron, Brent

2015-08-01

The synaptic connectivity of cortical networks features an overrepresentation of certain wiring motifs compared to simple random-network models. This structure is shaped, in part, by synaptic plasticity that promotes or suppresses connections between neurons depending on their joint spiking activity. Frequently, theoretical studies focus on how feedforward inputs drive plasticity to create this network structure. We study the complementary scenario of self-organized structure in a recurrent network, with spike timing-dependent plasticity driven by spontaneous dynamics. We develop a self-consistent theory for the evolution of network structure by combining fast spiking covariance with a slow evolution of synaptic weights. Through a finite-size expansion of network dynamics we obtain a low-dimensional set of nonlinear differential equations for the evolution of two-synapse connectivity motifs. With this theory in hand, we explore how the form of the plasticity rule drives the evolution of microcircuits in cortical networks. When potentiation and depression are in approximate balance, synaptic dynamics depend on weighted divergent, convergent, and chain motifs. For additive, Hebbian STDP these motif interactions create instabilities in synaptic dynamics that either promote or suppress the initial network structure. Our work provides a consistent theoretical framework for studying how spiking activity in recurrent networks interacts with synaptic plasticity to determine network structure.

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses

PubMed Central

Ocker, Gabriel Koch; Litwin-Kumar, Ashok; Doiron, Brent

2015-01-01

The synaptic connectivity of cortical networks features an overrepresentation of certain wiring motifs compared to simple random-network models. This structure is shaped, in part, by synaptic plasticity that promotes or suppresses connections between neurons depending on their joint spiking activity. Frequently, theoretical studies focus on how feedforward inputs drive plasticity to create this network structure. We study the complementary scenario of self-organized structure in a recurrent network, with spike timing-dependent plasticity driven by spontaneous dynamics. We develop a self-consistent theory for the evolution of network structure by combining fast spiking covariance with a slow evolution of synaptic weights. Through a finite-size expansion of network dynamics we obtain a low-dimensional set of nonlinear differential equations for the evolution of two-synapse connectivity motifs. With this theory in hand, we explore how the form of the plasticity rule drives the evolution of microcircuits in cortical networks. When potentiation and depression are in approximate balance, synaptic dynamics depend on weighted divergent, convergent, and chain motifs. For additive, Hebbian STDP these motif interactions create instabilities in synaptic dynamics that either promote or suppress the initial network structure. Our work provides a consistent theoretical framework for studying how spiking activity in recurrent networks interacts with synaptic plasticity to determine network structure. PMID:26291697

Dissipative structures, machines, and organisms: A perspective

NASA Astrophysics Data System (ADS)

Kondepudi, Dilip; Kay, Bruce; Dixon, James

2017-10-01

Self-organization in nonequilibrium systems resulting in the formation of dissipative structures has been studied in a variety of systems, most prominently in chemical systems. We present a study of a voltage-driven dissipative structure consisting of conducting beads immersed in a viscous medium of oil. In this simple system, we observed remarkably complex organism-like behavior. The dissipative structure consists of a tree structure that spontaneously forms and moves like a worm and exhibits many features characteristic of living organisms. The complex motion of the beads driven by the applied field, the dipole-dipole interaction between the beads, and the hydrodynamic flow of the viscous medium result in a time evolution of the tree structure towards states of lower resistance or higher dissipation and thus higher rates of entropy production. The resulting end-directed evolution manifests as the tree moving to locations seeking higher current, the current that sustains its structure and dynamics. The study of end-directed evolution in the dissipative structure gives us a means to distinguish the fundamental difference between machines and organisms and opens a path for the formulation of physics of organisms.

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

Structural evolution of Li{sub x}Mn{sub 2}O{sub 4} in lithium-ion battery cells measured in situ using synchrotron X-ray diffraction techniques

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

Mukerjee, S.; Thurston, T.R.; Jisrawi, N.M.

The authors describe synchrotron based X-ray diffraction techniques and issues related to in situ studies of intercalation processes in battery electrodes. They then demonstrate the utility of this technique, through a study of two batches of Li{sub x}Mn{sub 2}O{sub 4} cathode materials. The structural evolution of these spinel materials was monitored in situ during the initial charge of these electrodes in actual battery cells. Significant differences were observed in the two batches, particularly in the intercalation range of x = 0.45 to 0.20. The first-order structural transitions in this region indicated coexistence of two cubic phases in the batch 2more » material, whereas the batch 1 material showed suppressed two-phase coexistence. Batch 2 cells also indicated structural evolution in the low-potential region below 3.0 V in contrast to the batch 1 material. Differences in structural evolution between batches of Li{sub x}Mn{sub 2}O{sub 4} could have important ramifications in their cycle life and stability characteristics.« less

Convergent evolution of modularity in metabolic networks through different community structures.

PubMed

Zhou, Wanding; Nakhleh, Luay

2012-09-14

It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxonomy. We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism's metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new measures of modularity and network communities that better correspond to functional categorizations.

Complex quantum network geometries: Evolution and phase transitions

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Complex quantum network geometries: Evolution and phase transitions.

PubMed

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

PubMed

Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

2003-08-14

The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

A spatial analysis of hierarchical waste transport structures under growing demand.

PubMed

Tanguy, Audrey; Glaus, Mathias; Laforest, Valérie; Villot, Jonathan; Hausler, Robert

2016-10-01

The design of waste management systems rarely accounts for the spatio-temporal evolution of the demand. However, recent studies suggest that this evolution affects the planning of waste management activities like the choice and location of treatment facilities. As a result, the transport structure could also be affected by these changes. The objective of this paper is to study the influence of the spatio-temporal evolution of the demand on the strategic planning of a waste transport structure. More particularly this study aims at evaluating the effect of varying spatial parameters on the economic performance of hierarchical structures (with one transfer station). To this end, three consecutive generations of three different spatial distributions were tested for hierarchical and non-hierarchical transport structures based on costs minimization. Results showed that a hierarchical structure is economically viable for large and clustered spatial distributions. The distance parameter was decisive but the loading ratio of trucks and the formation of clusters of sources also impacted the attractiveness of the transfer station. Thus the territories' morphology should influence strategies as regards to the installation of transfer stations. The use of spatial-explicit tools such as the transport model presented in this work that take into account the territory's evolution are needed to help waste managers in the strategic planning of waste transport structures. © The Author(s) 2016.

Dislocation density evolution in the process of high-temperature treatment and creep of EK-181 steel

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

Vershinina, Tatyana, E-mail: vershinina@bsu.edu.ru

2017-03-15

X-ray diffraction has been used to study the dislocation structure in ferrite-martensite high-chromium steel EK-181 in the states after heat treatment and high-temperature creep. The influence of heat treatment and stress on evolution of lath martensite structure was investigated by and electron back-scattered diffraction. The effect of nitrogen content on the total dislocation density, fraction of edge and screw dislocation segments are analyzed. - Highlights: •Fraction of edge dislocation in quenched state depends on nitrogen concentration. •Nitrogen affects the character of dislocation structure evolution during annealing. •Edge dislocations fraction influences on dislocation density after aging and creep.

Modeling the mesozoic-cenozoic structural evolution of east texas

USGS Publications Warehouse

Pearson, Ofori N.; Rowan, Elisabeth L.; Miller, John J.

2012-01-01

The U.S. Geological Survey (USGS) recently assessed the undiscovered technically recoverable oil and gas resources within Jurassic and Cretaceous strata of the onshore coastal plain and State waters of the U.S. Gulf Coast. Regional 2D seismic lines for key parts of the Gulf Coast basin were interpreted in order to examine the evolution of structural traps and the burial history of petroleum source rocks. Interpretation and structural modeling of seismic lines from eastern Texas provide insights into the structural evolution of this part of the Gulf of Mexico basin. Since completing the assessment, the USGS has acquired additional regional seismic lines in east Texas; interpretation of these new lines, which extend from the Texas-Oklahoma state line to the Gulf Coast shoreline, show how some of the region's prominent structural elements (e.g., the Talco and Mount Enterprise fault zones, the East Texas salt basin, and the Houston diapir province) vary along strike. The interpretations also indicate that unexplored structures may lie beneath the current drilling floor. Structural restorations based upon interpretation of these lines illustrate the evolution of key structures and show the genetic relation between structural growth and movement of the Jurassic Louann Salt. 1D thermal models that integrate kinetics and burial histories were also created for the region's two primary petroleum source rocks, the Oxfordian Smackover Formation and the Cenomanian-Turonian Eagle Ford Shale. Integrating results from the thermal models with the structural restorations provides insights into the distribution and timing of petroleum expulsion from the Smackover Formation and Eagle Ford Shale in eastern Texas.

EVOLUTION OF FAST MAGNETOACOUSTIC PULSES IN RANDOMLY STRUCTURED CORONAL PLASMAS

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

Yuan, D.; Li, B.; Pascoe, D. J.

2015-02-01

We investigate the evolution of fast magnetoacoustic pulses in randomly structured plasmas, in the context of large-scale propagating waves in the solar atmosphere. We perform one-dimensional numerical simulations of fast wave pulses propagating perpendicular to a constant magnetic field in a low-β plasma with a random density profile across the field. Both linear and nonlinear regimes are considered. We study how the evolution of the pulse amplitude and width depends on their initial values and the parameters of the random structuring. Acting as a dispersive medium, a randomly structured plasma causes amplitude attenuation and width broadening of the fast wavemore » pulses. After the passage of the main pulse, secondary propagating and standing fast waves appear. Width evolution of both linear and nonlinear pulses can be well approximated by linear functions; however, narrow pulses may have zero or negative broadening. This arises because narrow pulses are prone to splitting, while broad pulses usually deviate less from their initial Gaussian shape and form ripple structures on top of the main pulse. Linear pulses decay at an almost constant rate, while nonlinear pulses decay exponentially. A pulse interacts most efficiently with a random medium with a correlation length of about half of the initial pulse width. This detailed model of fast wave pulses propagating in highly structured media substantiates the interpretation of EIT waves as fast magnetoacoustic waves. Evolution of a fast pulse provides us with a novel method to diagnose the sub-resolution filamentation of the solar atmosphere.« less

Molecular evolution of the vertebrate mechanosensory cell and ear.

PubMed

Fritzsch, Bernd; Beisel, Kirk W; Pauley, Sarah; Soukup, Garrett

2007-01-01

The molecular basis of mechanosensation, mechanosensory cell development and mechanosensory organ development is reviewed with an emphasis on its evolution. In contrast to eye evolution and development, which apparently modified a genetic program through intercalation of genes between the master control genes on the top (Pax6, Eya1, Six1) of the hierarchy and the structural genes (rhodopsin) at the bottom, the as yet molecularly unknown mechanosensory channel precludes such a firm conclusion for mechanosensors. However, recent years have seen the identification of several structural genes which are involved in mechanosensory tethering and several transcription factors controlling mechanosensory cell and organ development; these warrant the interpretation of available data in very much the same fashion as for eye evolution: molecular homology combined with potential morphological parallelism. This assertion of molecular homology is strongly supported by recent findings of a highly conserved set of microRNAs that appear to be associated with mechanosensory cell development across phyla. The conservation of transcription factors and their regulators fits very well to the known or presumed mechanosensory specializations which can be mostly grouped as variations of a common cellular theme. Given the widespread distribution of the molecular ability to form mechanosensory cells, it comes as no surprise that structurally different mechanosensory organs evolved in different phyla, presenting a variation of a common theme specified by a conserved set of transcription factors in their cellular development. Within vertebrates and arthropods, some mechanosensory organs evolved into auditory organs, greatly increasing sensitivity to sound through modifications of accessory structures to direct sound to the specific sensory epithelia. However, while great attention has been paid to the evolution of these accessory structures in vertebrate fossils, comparatively less attention has been spent on the evolution of the inner ear and the central auditory system. Recent advances in our molecular understanding of ear and brain development provide novel avenues to this neglected aspect of auditory neurosensory evolution.

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

PubMed Central

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

Pressure-Induced Structural Evolution and Band Gap Shifts of Organometal Halide Perovskite-Based Methylammonium Lead Chloride.

PubMed

Wang, Lingrui; Wang, Kai; Xiao, Guanjun; Zeng, Qiaoshi; Zou, Bo

2016-12-15

Organometal halide perovskites are promising materials for optoelectronic devices. Further development of these devices requires a deep understanding of their fundamental structure-property relationships. The effect of pressure on the structural evolution and band gap shifts of methylammonium lead chloride (MAPbCl 3 ) was investigated systematically. Synchrotron X-ray diffraction and Raman experiments provided structural information on the shrinkage, tilting distortion, and amorphization of the primitive cubic unit cell. In situ high pressure optical absorption and photoluminescence spectra manifested that the band gap of MAPbCl 3 could be fine-tuned to the ultraviolet region by pressure. The optical changes are correlated with pressure-induced structural evolution of MAPbCl 3 , as evidenced by band gap shifts. Comparisons between Pb-hybrid perovskites and inorganic octahedra provided insights on the effects of halogens on pressure-induced transition sequences of these compounds. Our results improve the understanding of the structural and optical properties of organometal halide perovskites.

Evolution of specialization in resource utilization in structured metapopulations.

PubMed

Nurmi, Tuomas; Geritz, Stefan; Parvinen, Kalle; Gyllenberg, Mats

2008-07-01

We study the evolution of resource utilization in a structured discrete-time metapopulation model with an infinite number of patches, prone to local catastrophes. The consumer faces a trade-off in the abilities to consume two resources available in different amounts in each patch. We analyse how the evolution of specialization in the utilization of the resources is affected by different ecological factors: migration, local growth, local catastrophes, forms of the trade-off and distribution of the resources in the patches. Our modelling approach offers a natural way to include more than two patch types into the models. This has not been usually possible in the previous spatially heterogeneous models focusing on the evolution of specialization.

Joint evolution of specialization and dispersal in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2011-04-21

We study the joint evolution of dispersal and specialization concerning resource usage in a mechanistically underpinned structured discrete-time metapopulation model. We show that dispersal significantly affects the evolution of specialization and that specialization is a key factor that determines the possibility of evolutionary branching in dispersal propensity. Allowing both dispersal propensity and specialization to evolve as a consequence of natural selection is necessary in order to understand the evolutionary dynamics. The joint evolution of dispersal and specialization forms a natural evolutionary path leading to the coexistence of generalists and specialists. We show that in this process, the number of different patch types and the resource distribution are essential. Copyright © 2011 Elsevier Ltd. All rights reserved.

Tectono-sedimentary events and geodynamic evolution of the Mesozoic and Cenozoic basins of the Alpine Margin, Gulf of Tunis, north-eastern Tunisia offshore

NASA Astrophysics Data System (ADS)

Melki, Fetheddine; Zouaghi, Taher; Chelbi, Mohamed Ben; Bédir, Mourad; Zargouni, Fouad

2010-09-01

The structural pattern, tectono-sedimentary framework and geodynamic evolution for Mesozoic and Cenozoic deep structures of the Gulf of Tunis (north-eastern Tunisia) are proposed using petroleum well data and a 2-D seismic interpretation. The structural system of the study area is marked by two sets of faults that control the Mesozoic subsidence and inversions during the Paleogene and Neogene times: (i) a NE-SW striking set associated with folds and faults, which have a reverse component; and (ii) a NW-SE striking set active during the Tertiary extension episodes and delineating grabens and subsiding synclines. In order to better characterize the tectono-sedimentary evolution of the Gulf of Tunis structures, seismic data interpretations are compared to stratigraphic and structural data from wells and neighbouring outcrops. The Atlas and external Tell belonged to the southernmost Tethyan margin record a geodynamic evolution including: (i) rifting periods of subsidence and Tethyan oceanic accretions from Triassic until Early Cretaceous: we recognized high subsiding zones (Raja and Carthage domains), less subsiding zones (Gamart domain) and a completely emerged area (Raouad domain); (ii) compressive events during the Cenozoic with relaxation periods of the Oligocene-Aquitanian and Messinian-Early Pliocene. The NW-SE Late Eocene and Tortonian compressive events caused local inversions with sealed and eroded folded structures. During Middle to Late Miocene and Early Pliocene, we have identified depocentre structures corresponding to half-grabens and synclines in the Carthage and Karkouane domains. The north-south contractional events at the end of Early Pliocene and Late Pliocene periods are associated with significant inversion of subsidence and synsedimentary folded structures. Structuring and major tectonic events, recognized in the Gulf of Tunis, are linked to the common geodynamic evolution of the north African and western Mediterranean basins.

Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.

PubMed

Greenman, C D; Cooke, S L; Marshall, J; Stratton, M R; Campbell, P J

2016-01-01

Breakage-fusion-bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. Here we study the evolution space of breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are [Formula: see text] qualitatively distinct evolutions involving [Formula: see text] breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the process to show these evolutions are not equally likely, and also describe how amplicons become localized. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples.

Structural Changes in PEO-PPO-PEO Gels Induced by Methylparaben and Dexamethasone Observed Using Time-Resolved SAXS

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

Meznarich, Norman A.K.; Juggernauth, K Anne; Batzli, Kiersten M

2011-11-17

Aqueous solutions of polyoxyethylene-polyoxypropylene-polyoxyethylene (PEO-PPO-PEO) triblock copolymers (commercially available as Pluronic surfactants) micellize and structurally arrange into cubic quasicrystalline lattices as their temperature is raised. This structural evolution is seen macroscopically as a gelation, and the presence of these ordered phases can be controlled through both polymer concentration and temperature. The presence of added solutes within the dispersions can also affect the onset and kinetics of structure formation. Here we investigate the structures formed in Pluronic F127 solutions ranging from 20 to 30% with two pharmaceutical additives [methylparaben (MP) and dexamethasone (DX)] using small-angle X-ray scattering (SAXS). We observe bothmore » the progressive evolution and breakdown of these structures as the temperature is increased from 0 to 80 °C. Additionally, we conducted time-resolved SAXS measurements to elucidate the kinetics of the structural evolution. On the basis of the evolution of scattering peaks as the samples were being heated, we suggest that added MP changes the nucleation behavior of fcc phases within the sample from a heterogeneous process to a more homogeneous distribution of nucleated species. MP and DX also stabilize the micelle lattices, allowing them to persevere at higher temperatures. We observed the unusual result that the presence of DX caused the primary peaks of the structure factor to be suppressed, while preserving the higher order peaks. The primary peaks reappeared at the highest temperatures tested.« less

Cloning the Professor, an Alternative to Ineffective Teaching in a Large Course

ERIC Educational Resources Information Center

Nelson, Jennifer; Robison, Diane F.; Bell, John D.; Bradshaw, William S.

2009-01-01

Pedagogical strategies have been experimentally applied in large-enrollment biology courses in an attempt to amplify what teachers do best in effecting deep learning, thus more closely approximating a one-on-one interaction with students. Carefully orchestrated in-class formative assessments were conducted to provide frequent, high-quality…

A Model for Integrating Assessment across an Undergraduate Political Science Major

ERIC Educational Resources Information Center

Mills, Shala; Bennett, Bryan; Crawford, C. B.; Gould, Lawrence

2009-01-01

A call to engagement at Fort Hays State University (FHSU) led to significant curricular and assessment changes in the university's Department of Political Science. The university unveiled the Year of the Department (YOTD) as "an ongoing strategic initiative for orchestrating change and aligning people, systems and culture at the basic unit…

Orchestrating French Music Conservatories: European Political Interventions and Local Governance

ERIC Educational Resources Information Center

Raevskikh, Elena

2017-01-01

Supported by the omnipresent State in the past, French music education leans increasingly towards a more liberal and competitive model. In the current context of a decentralized economy and European integration, music conservatories are called upon to contribute to regional and municipal development and enhance European student mobility. How do…

Orchestral Stalls, Honore Daumier

ERIC Educational Resources Information Center

Lucero-Criswell, Amber

2004-01-01

Honore Daumier is probably best known as a politically motivated artist. Born in Marseilles in 1808, the French artist lived through one of the most turbulent eras of his country's history. With his artistic prowess and biting wit, he recorded the 1848 revolution, the rise and fall of the Second Empire, the Crimean and Franco-Prussian Wars, and…

Innovations in Higher Education. Singapore at the Competitive Edge. World Bank Technical Paper No. 222.

ERIC Educational Resources Information Center

Selvaratnam, Viswanathan

This report provides an overview of Singapore's strategy for human resource development and the country's concerted effort to successfully orchestrate the many separate initiatives between 1960s to 1980s into an effective market-driven, three-tiered higher education system emphasizing technology and modernization. The study highlights the…

Molecular mechanisms involved in the early steps of flavivirus cell entry.

PubMed

Kaufmann, Bärbel; Rossmann, Michael G

2011-01-01

Flaviviruses enter their host cells by receptor-mediated endocytosis, a well-orchestrated process of receptor recognition, penetration and uncoating. Recent findings on these early steps in the life cycle of flaviviruses are the focus of this review. Copyright © 2010 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

The Hidden Curriculum--Faculty-Made Tests in Science. Part 1: Lower-Division Courses. Innovations in Science and Technology.

ERIC Educational Resources Information Center

Tobias, Sheila; Raphael, Jacqueline

Successful reform of science education requires careful orchestration of a number of factors including technological developments, organizational issues, teacher preparation and enhancement, and advances in the scientific disciplines themselves. Exemplary innovations in exam practices that assess scientific understanding in new and more…

The Story of Carora: The Origins of El Sistema

ERIC Educational Resources Information Center

Carlson, Alexandra

2016-01-01

Venezuela's youth symphony program, the Fundación Musical Simón Bolívar, commonly referred to as "El Sistema," combines musical achievement with learning important life skills through orchestral practice and performance. Although the history most commonly reported outside Venezuela is of the program's director, José Antonio Abreu,…

Application of Online Discussion and Cooperative Learning Strategies to Online and Blended College Courses

ERIC Educational Resources Information Center

Lynch, Douglas J.

2010-01-01

Effective online instructional practices may be applied to online and blended college courses. Carefully orchestrated online discussions support learning well beyond the limited face-to-face course time. Students gain greater depth of academic understanding and leadership skills if cooperative learning groups use research-based process and…

Forced-Attention Dichotic Listening with University Students with Dyslexia: Search for a Core Deficit

ERIC Educational Resources Information Center

Kershner, John R.

2016-01-01

Rapidly changing environments in day-to-day activities, enriched with stimuli competing for attention, require a cognitive control mechanism to select relevant stimuli, ignore irrelevant stimuli, and shift attention between alternative features of the environment. Such attentional orchestration is essential to the acquisition of reading skills. In…

How Learners' Interactions Sustain Engagement: A MOOC Case Study

ERIC Educational Resources Information Center

Sunar, Ayse Saliha; White, Su; Abdullah, Nor Aniza; Davis, Hugh C.

2017-01-01

In 2015, 35 million learners participated online in 4,200 MOOCs organized by over 500 universities. Learning designers orchestrate MOOC content to engage learners at scale and retain interest by carefully mixing videos, lectures, readings, quizzes, and discussions. Universally, far fewer people actually participate in MOOCs than originally sign up…

School Violence and Theoretically Atypical Schools: The Principal's Centrality in Orchestrating Safe Schools

ERIC Educational Resources Information Center

Astor, Ron Avi; Benbenishty, Rami; Estrada, Jose Nunez

2009-01-01

Theories often assume that schools in communities with high violence also have high rates of school violence, yet there are schools with very low violence in high violence communities. Organizational variables within these schools may buffer community influences. Nine "atypical" schools are selected from a national database in Israel.…

Organic or Orchestrated: The Nature of Leadership in Rural Australia

ERIC Educational Resources Information Center

Davies, Amanda

2007-01-01

Over the last decade, rural leadership policies and programmes have attracted substantial support from all tiers of government. These policies are promulgated as a support mechanism for enhancing the internal capacity of rural communities to adjust to changes in the social and political-economic landscape. Leadership training programmes have been…

Orchestrating a New Approach to Learning

ERIC Educational Resources Information Center

Kaplan, Michael

2017-01-01

In 2011, the directors of the Phoenix Symphony came up with a bold plan to improve and expand their community outreach programs. Inspired by the growing movement to integrate the arts with the other subjects in the K-12 curriculum, they created a thriving program called Mind Over Music, which pairs professional musicians with local elementary…

Presidential Prescriptions for State Policy: Obama's Race to the Top Initiative

ERIC Educational Resources Information Center

Howell, William G.; Magazinnik, Asya

2017-01-01

With increasing frequency, U.S. presidents have orchestrated relations between federal and state governments. A defining feature of this "executive federalism" is a pragmatic willingness to both borrow from and reconstitute very different types of past federalisms. A case in point is President Barack Obama's Race to the Top (RttT)…

Pharmacodynamic Assay Panel for Monitoring Phospho-Signaling Networks | Office of Cancer Clinical Proteomics Research

Cancer.gov

The DNA damage response (DDR) is a highly regulated signal transduction network that orchestrates the temporal and spatial organization of protein complexes required to repair (or tolerate) DNA damage (e.g., nucleotide excision repair, base excision repair, homologous recombination, non-homologous end joining, post-replication repair).

Mashups by Orchestration and Widget-Based Personal Environments: Key Challenges, Solution Strategies, and an Application

ERIC Educational Resources Information Center

Soylu, Ahmet; Modritscher, Felix; Wild, Fridolin; De Causmaecker, Patrick; Desmet, Piet

2012-01-01

Purpose: Mashups have been studied extensively in the literature; nevertheless, the large body of work in this area focuses on service/data level integration and leaves UI level integration, hence UI mashups, almost unexplored. The latter generates digital environments in which participating sources exist as individual entities; member…