Digital and analog chemical evolution.

PubMed

Goodwin, Jay T; Mehta, Anil K; Lynn, David G

2012-12-18

Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution. Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.

Biological robustness.

PubMed

Kitano, Hiroaki

2004-11-01

Robustness is a ubiquitously observed property of biological systems. It is considered to be a fundamental feature of complex evolvable systems. It is attained by several underlying principles that are universal to both biological organisms and sophisticated engineering systems. Robustness facilitates evolvability and robust traits are often selected by evolution. Such a mutually beneficial process is made possible by specific architectural features observed in robust systems. But there are trade-offs between robustness, fragility, performance and resource demands, which explain system behaviour, including the patterns of failure. Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design.

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language

PubMed Central

Scharff, Constance; Petri, Jana

2011-01-01

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the ‘evo-devo’ conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this ‘deep homology’. Recently, ‘evo-devo’ has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can ‘descend with modification’. PMID:21690130

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language.

PubMed

Scharff, Constance; Petri, Jana

2011-07-27

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the 'evo-devo' conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this 'deep homology'. Recently, 'evo-devo' has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can 'descend with modification'.

Transforming graduate nursing education in the context of complex adaptive systems: implications for master's and DNP curricula.

PubMed

Lis, Gail A; Hanson, Patricia; Burgermeister, Diane; Banfield, Barbara

2014-01-01

The purpose of this article is to describe the evolution and implementation of a graduate nursing program's curricular framework. A number of factors contributed to the realization that the curricular framework needed revision. These factors included the rapid changes occurring in the U.S. health care system, the publication of the 2011 edition of the Essentials of Master's Education in Nursing, and the publication of the Institute of Medicine's report entitled The Future of Nursing: Leading Change, Advancing Health (2010). A careful analysis of key guiding documents resulted in the development of three central, interrelated concepts to guide this revision, namely, relationship-based care, creative inquiry, and leadership. Copyright © 2014 Elsevier Inc. All rights reserved.

A two-fluid study of oblique tearing modes in a force-free current sheet

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

Akçay, Cihan, E-mail: akcay@lanl.gov; Daughton, William; Lukin, Vyacheslav S.

2016-01-15

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Since kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. The resulting theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

A two-fluid study of oblique tearing modes in a force-free current sheet

DOE PAGES

Akçay, Cihan; Daughton, William; Lukin, Vyacheslav S.; ...

2016-01-01

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Because kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. As a results this theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

ABC estimation of unit costs for emergency department services.

PubMed

Holmes, R L; Schroeder, R E

1996-04-01

Rapid evolution of the health care industry forces managers to make cost-effective decisions. Typical hospital cost accounting systems do not provide emergency department managers with the information needed, but emergency department settings are so complex and dynamic as to make the more accurate activity-based costing (ABC) system prohibitively expensive. Through judicious use of the available traditional cost accounting information and simple computer spreadsheets. managers may approximate the decision-guiding information that would result from the much more costly and time-consuming implementation of ABC.

Self-assembly of metal nanostructures on binary alloy surfaces

PubMed Central

Duguet, T.; Han, Yong; Yuen, Chad; Jing, Dapeng; Ünal, Barış; Evans, J. W.; Thiel, P. A.

2011-01-01

Deposition of metals on binary alloy surfaces offers new possibilities for guiding the formation of functional metal nanostructures. This idea is explored with scanning tunneling microscopy studies and atomistic-level analysis and modeling of nonequilibrium island formation. For Au/NiAl(110), complex monolayer structures are found and compared with the simple fcc(110) bilayer structure recently observed for Ag/NiAl(110). We also consider a more complex codeposition system, (Ni + Al)/NiAl(110), which offers the opportunity for fundamental studies of self-growth of alloys including deviations for equilibrium ordering. A general multisite lattice-gas model framework enables analysis of structure selection and morphological evolution in these systems. PMID:21097706

Towards a Framework for Evolvable Network Design

NASA Astrophysics Data System (ADS)

Hassan, Hoda; Eltarras, Ramy; Eltoweissy, Mohamed

The layered Internet architecture that had long guided network design and protocol engineering was an “interconnection architecture” defining a framework for interconnecting networks rather than a model for generic network structuring and engineering. We claim that the approach of abstracting the network in terms of an internetwork hinders the thorough understanding of the network salient characteristics and emergent behavior resulting in impeding design evolution required to address extreme scale, heterogeneity, and complexity. This paper reports on our work in progress that aims to: 1) Investigate the problem space in terms of the factors and decisions that influenced the design and development of computer networks; 2) Sketch the core principles for designing complex computer networks; and 3) Propose a model and related framework for building evolvable, adaptable and self organizing networks We will adopt a bottom up strategy primarily focusing on the building unit of the network model, which we call the “network cell”. The model is inspired by natural complex systems. A network cell is intrinsically capable of specialization, adaptation and evolution. Subsequently, we propose CellNet; a framework for evolvable network design. We outline scenarios for using the CellNet framework to enhance legacy Internet protocol stack.

Field guide to the Mesozoic arc and accretionary complex of South-Central Alaska, Indian to Hatcher Pass

USGS Publications Warehouse

Karl, Susan M.; Oswald, P.J.; Hults, Chad P.

2015-01-01

This field trip traverses exposures of a multi-generation Mesozoic magmatic arc and subduction-accretion complex that had a complicated history of magmatic activity and experienced variations in composition and deformational style in response to changes in the tectonic environment. This Mesozoic arc formed at an unknown latitude to the south, was accreted to North America, and was subsequently transported along faults to its present location (Plafker and others, 1989; Hillhouse and Coe, 1994). Some of these faults are still active. Similar tectonic, igneous, and sedimentary processes to those that formed the Mesozoic arc complex persist today in southern Alaska, building on, and deforming the Mesozoic arc. The rocks we will see on this field trip provide insights on the three-dimensional composition of the modern arc, and the processes involved in the evolution of an arc and its companion accretionary complex.

Application of Optical Forces in Microphotonic Systems

DTIC Science & Technology

2013-05-01

Experiments are carried out to optically characterize the high-Q guided resonance modes with slot confinement. The evolution of the measured wavelengths...the guided resonant device. Two cross polarizers (PC) are applied before and after the device to cancel out Fabry-Perot noise. TL: tunable laser; MO...carried out to optically characterize the high-Q guided resonance modes with slot confinement. The evolution of the measured wavelengths and quality

KSC-99pp0495

NASA Image and Video Library

1999-05-04

While a crane lifts NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite, workers at Hangar AE, Cape Canaveral Air Station, help guide it toward the circular Payload Attach Fitting (PAF) in front of it. FUSE is undergoing a functional test of its systems, plus installation of flight batteries and solar arrays. Developed by The Johns Hopkins University under contract to Goddard Space Flight Center, Greenbelt, Md., FUSE will investigate the origin and evolution of the lightest elements in the universe hydrogen and deuterium. In addition, the FUSE satellite will examine the forces and process involved in the evolution of the galaxies, stars and planetary systems by investigating light in the far ultraviolet portion of the electromagnetic spectrum. FUSE is scheduled to be launched May 27 aboard a Boeing Delta II rocket at Launch Complex 17

Evolution: A Programmed Text [And] Pronunciation Guide for Evolution. Publications No. 71-8 and 71-1.

ERIC Educational Resources Information Center

Thomas, Georgelle; Fishburne, Robert P.

Part of the Anthropology Curriculum Project, the document contains a programmed text on evolution and a vocabulary pronunciation guide. The unit is intended for use by students in social studies and science courses in the 5th, 6th, and 7th grades. The bulk of the document, the programmed text, is organized in a question answer format. Students are…

Review of Nearshore Morphologic Prediction

NASA Astrophysics Data System (ADS)

Plant, N. G.; Dalyander, S.; Long, J.

2014-12-01

The evolution of the world's erodible coastlines will determine the balance between the benefits and costs associated with human and ecological utilization of shores, beaches, dunes, barrier islands, wetlands, and estuaries. So, we would like to predict coastal evolution to guide management and planning of human and ecological response to coastal changes. After decades of research investment in data collection, theoretical and statistical analysis, and model development we have a number of empirical, statistical, and deterministic models that can predict the evolution of the shoreline, beaches, dunes, and wetlands over time scales of hours to decades, and even predict the evolution of geologic strata over the course of millennia. Comparisons of predictions to data have demonstrated that these models can have meaningful predictive skill. But these comparisons also highlight the deficiencies in fundamental understanding, formulations, or data that are responsible for prediction errors and uncertainty. Here, we review a subset of predictive models of the nearshore to illustrate tradeoffs in complexity, predictive skill, and sensitivity to input data and parameterization errors. We identify where future improvement in prediction skill will result from improved theoretical understanding, and data collection, and model-data assimilation.

Networks as systems.

PubMed

Best, Allan; Berland, Alex; Greenhalgh, Trisha; Bourgeault, Ivy L; Saul, Jessie E; Barker, Brittany

2018-03-19

Purpose The purpose of this paper is to present a case study of the World Health Organization's Global Healthcare Workforce Alliance (GHWA). Based on a commissioned evaluation of GHWA, it applies network theory and key concepts from systems thinking to explore network emergence, effectiveness, and evolution to over a ten-year period. The research was designed to provide high-level strategic guidance for further evolution of global governance in human resources for health (HRH). Design/methodology/approach Methods included a review of published literature on HRH governance and current practice in the field and an in-depth case study whose main data sources were relevant GHWA background documents and key informant interviews with GHWA leaders, staff, and stakeholders. Sampling was purposive and at a senior level, focusing on board members, executive directors, funders, and academics. Data were analyzed thematically with reference to systems theory and Shiffman's theory of network development. Findings Five key lessons emerged: effective management and leadership are critical; networks need to balance "tight" and "loose" approaches to their structure and processes; an active communication strategy is key to create and maintain support; the goals, priorities, and membership must be carefully focused; and the network needs to support shared measurement of progress on agreed-upon goals. Shiffman's middle-range network theory is a useful tool when guided by the principles of complex systems that illuminate dynamic situations and shifting interests as global alliances evolve. Research limitations/implications This study was implemented at the end of the ten-year funding cycle. A more continuous evaluation throughout the term would have provided richer understanding of issues. Experience and perspectives at the country level were not assessed. Practical implications Design and management of large, complex networks requires ongoing attention to key issues like leadership, and flexible structures and processes to accommodate the dynamic reality of these networks. Originality/value This case study builds on growing interest in the role of networks to foster large-scale change. The particular value rests on the longitudinal perspective on the evolution of a large, complex global network, and the use of theory to guide understanding.

The development and application of landscape evolution models to coupled coast-estuarine environments

NASA Astrophysics Data System (ADS)

Morris, Chloe; Coulthard, Tom; Parsons, Daniel R.; Manson, Susan; Barkwith, Andrew

2017-04-01

Landscape Evolution Models (LEMs) are proven to be useful tools in understanding the morphodynamics of coast and estuarine systems. However, perhaps owing to the lack of research in this area, current models are not capable of simulating the dynamic interactions between these systems and their co-evolution at the meso-scale. Through a novel coupling of numerical models, this research is designed to explore coupled coastal-estuarine interactions, controls on system behaviour and the influence that environmental change could have. This will contribute to the understanding of the morphodynamics of these systems and how they may behave and evolve over the next century in response to climate changes, with the aim of informing management practices. This goal is being achieved through the modification and coupling of the one-line Coastline Evolution Model (CEM) with the hydrodynamic LEM CAESAR-Lisflood (C-L). The major issues faced with coupling these programs are their differing complexities and the limited graphical visualisations produced by the CEM that hinder the dissemination of results. The work towards overcoming these issues and reported here, include a new version of the CEM that incorporates a range of more complex geomorphological processes and boasts a graphical user interface that guides users through model set-up and projects a live output during model runs. The improved version is a stand-alone tool that can be used for further research projects and for teaching purposes. A sensitivity analysis using the Morris method has been completed to identify which key variables, including wave climate, erosion and weathering values, dominate the control of model behaviour. The model is being applied and tested using the evolution of the Holderness Coast, Humber Estuary and Spurn Point on the east coast of England (UK), which possess diverse geomorphologies and complex, co-evolving sediment pathways. Simulations using the modified CEM are currently being completed to ascertain the processes influential to the morphodynamics and evolution of these systems; presently this includes increasing sea levels and changing wave climate patterns. Outputs and findings from these runs will be presented and discussed, with the aid of the improved graphical visualisations and animations that illustrate the evolution of simulated environments.

Marr's levels and the minimalist program.

PubMed

Johnson, Mark

2017-02-01

A simple change to a cognitive system at Marr's computational level may entail complex changes at the other levels of description of the system. The implementational level complexity of a change, rather than its computational level complexity, may be more closely related to the plausibility of a discrete evolutionary event causing that change. Thus the formal complexity of a change at the computational level may not be a good guide to the plausibility of an evolutionary event introducing that change. For example, while the Minimalist Program's Merge is a simple formal operation (Berwick & Chomsky, 2016), the computational mechanisms required to implement the language it generates (e.g., to parse the language) may be considerably more complex. This has implications for the theory of grammar: theories of grammar which involve several kinds of syntactic operations may be no less evolutionarily plausible than a theory of grammar that involves only one. A deeper understanding of human language at the algorithmic and implementational levels could strengthen Minimalist Program's account of the evolution of language.

Evolution. Teacher's Guide.

ERIC Educational Resources Information Center

Bershad, Carol

This teacher's guide was developed to assist teachers in the use of multimedia resources for the Public Broadcasting System (PBS) program, "Evolution." Each unit uses an inquiry-based approach to meet the National Science Education Standards. Units include: (1) "What is the Nature of Science?"; (2) "Who Was Charles Darwin?"; (3) "What is the…

Systems Integration Challenges for a National Space Launch System

NASA Technical Reports Server (NTRS)

May, Todd A.

2011-01-01

System Integration was refined through the complexity and early failures experienced in rocket flight. System Integration encompasses many different viewpoints of the system development. System Integration must ensure consistency in development and operations activities. Human Space Flight tends toward large, complex systems. Understanding the system fs operational and use context is the guiding principle for System Integration: (1) Sizeable costs can be driven into systems by not fully understanding context (2). Adhering to the system context throughout the system fs life cycle is essential to maintaining efficient System Integration. System Integration exists within the System Architecture. Beautiful systems are simple in use and operation -- Block upgrades facilitate manageable steps in functionality evolution. Effective System Integration requires a stable system concept. Communication is essential to system simplicity

The evolution of syntactic communication

NASA Astrophysics Data System (ADS)

Nowak, Martin A.; Plotkin, Joshua B.; Jansen, Vincent A. A.

2000-03-01

Animal communication is typically non-syntactic, which means that signals refer to whole situations. Human language is syntactic, and signals consist of discrete components that have their own meaning. Syntax is a prerequisite for taking advantage of combinatorics, that is, ``making infinite use of finite means''. The vast expressive power of human language would be impossible without syntax, and the transition from non-syntactic to syntactic communication was an essential step in the evolution of human language. We aim to understand the evolutionary dynamics of this transition and to analyse how natural selection can guide it. Here we present a model for the population dynamics of language evolution, define the basic reproductive ratio of words and calculate the maximum size of a lexicon. Syntax allows larger repertoires and the possibility to formulate messages that have not been learned beforehand. Nevertheless, according to our model natural selection can only favour the emergence of syntax if the number of required signals exceeds a threshold value. This result might explain why only humans evolved syntactic communication and hence complex language.

Significant differences in ion and electron guiding through highly insulating capillaries

NASA Astrophysics Data System (ADS)

Stolterfoht, N.; Tanis, J.

2018-04-01

Outstanding phenomena of capillary guiding are discussed in accordance with a recent review in the field. Experiments concerning highly charged ions of a few keV energy guided through insulating nanocapillaries are shown. Studies of the temporal evolution of ion transmission are presented. Attention is focused on oscillatory structures in the ion emission and the independence of the ion guiding on the beam intensity. A few experiments of electron guiding are presented showing a significantly different temporal evolution of the transmitted intensity. The onset of the electron transmission is very sudden accompanied by a considerable energy loss within the capillary. To achieve more insight into the different guiding mechanisms, theoretical aspects of the capillary guiding are analyzed. A scenario is offered to explain the abrupt rise of transmitted electrons. Altogether, these studies show that ion and electron guiding are accomplished through different manifestations of the charge build up that underlies both.

The Physical Processes of CME/ICME Evolution

NASA Astrophysics Data System (ADS)

Manchester, Ward; Kilpua, Emilia K. J.; Liu, Ying D.; Lugaz, Noé; Riley, Pete; Török, Tibor; Vršnak, Bojan

2017-11-01

As observed in Thomson-scattered white light, coronal mass ejections (CMEs) are manifest as large-scale expulsions of plasma magnetically driven from the corona in the most energetic eruptions from the Sun. It remains a tantalizing mystery as to how these erupting magnetic fields evolve to form the complex structures we observe in the solar wind at Earth. Here, we strive to provide a fresh perspective on the post-eruption and interplanetary evolution of CMEs, focusing on the physical processes that define the many complex interactions of the ejected plasma with its surroundings as it departs the corona and propagates through the heliosphere. We summarize the ways CMEs and their interplanetary CMEs (ICMEs) are rotated, reconfigured, deformed, deflected, decelerated and disguised during their journey through the solar wind. This study then leads to consideration of how structures originating in coronal eruptions can be connected to their far removed interplanetary counterparts. Given that ICMEs are the drivers of most geomagnetic storms (and the sole driver of extreme storms), this work provides a guide to the processes that must be considered in making space weather forecasts from remote observations of the corona.

Algorithm for cellular reprogramming.

PubMed

Ronquist, Scott; Patterson, Geoff; Muir, Lindsey A; Lindsly, Stephen; Chen, Haiming; Brown, Markus; Wicha, Max S; Bloch, Anthony; Brockett, Roger; Rajapakse, Indika

2017-11-07

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle-synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes. Copyright © 2017 the Author(s). Published by PNAS.

Clonal evolution in myelodysplastic syndromes

PubMed Central

da Silva-Coelho, Pedro; Kroeze, Leonie I.; Yoshida, Kenichi; Koorenhof-Scheele, Theresia N.; Knops, Ruth; van de Locht, Louis T.; de Graaf, Aniek O.; Massop, Marion; Sandmann, Sarah; Dugas, Martin; Stevens-Kroef, Marian J.; Cermak, Jaroslav; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; de Witte, Theo; Blijlevens, Nicole M. A.; Muus, Petra; Huls, Gerwin; van der Reijden, Bert A.; Ogawa, Seishi; Jansen, Joop H.

2017-01-01

Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5–11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions. PMID:28429724

Evolution of design considerations in complex craniofacial reconstruction using patient-specific implants.

PubMed

Peel, Sean; Bhatia, Satyajeet; Eggbeer, Dominic; Morris, Daniel S; Hayhurst, Caroline

2017-06-01

Previously published evidence has established major clinical benefits from using computer-aided design, computer-aided manufacturing, and additive manufacturing to produce patient-specific devices. These include cutting guides, drilling guides, positioning guides, and implants. However, custom devices produced using these methods are still not in routine use, particularly by the UK National Health Service. Oft-cited reasons for this slow uptake include the following: a higher up-front cost than conventionally fabricated devices, material-choice uncertainty, and a lack of long-term follow-up due to their relatively recent introduction. This article identifies a further gap in current knowledge - that of design rules, or key specification considerations for complex computer-aided design/computer-aided manufacturing/additive manufacturing devices. This research begins to address the gap by combining a detailed review of the literature with first-hand experience of interdisciplinary collaboration on five craniofacial patient case studies. In each patient case, bony lesions in the orbito-temporal region were segmented, excised, and reconstructed in the virtual environment. Three cases translated these digital plans into theatre via polymer surgical guides. Four cases utilised additive manufacturing to fabricate titanium implants. One implant was machined from polyether ether ketone. From the literature, articles with relevant abstracts were analysed to extract design considerations. In all, 19 frequently recurring design considerations were extracted from previous publications. Nine new design considerations were extracted from the case studies - on the basis of subjective clinical evaluation. These were synthesised to produce a design considerations framework to assist clinicians with prescribing and design engineers with modelling. Promising avenues for further research are proposed.

The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex.

PubMed

Merker, Matthias; Kohl, Thomas A; Niemann, Stefan; Supply, Philip

2017-01-01

Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.

Can Random Mutation Mimic Design?: A Guided Inquiry Laboratory for Undergraduate Students

PubMed Central

Kalinowski, Steven T.; Taper, Mark L.; Metz, Anneke M.

2006-01-01

Complex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results. PMID:16951065

Determination of the performance of the Kaplan hydraulic turbines through simplified procedure

NASA Astrophysics Data System (ADS)

Pădureanu, I.; Jurcu, M.; Campian, C. V.; Haţiegan, C.

2018-01-01

A simplified procedure has been developed, compared to the complex one recommended by IEC 60041 (i.e. index samples), for measurement of the performance of the hydraulic turbines. The simplified procedure determines the minimum and maximum powers, the efficiency at maximum power, the evolution of powers by head and flow and to determine the correct relationship between runner/impeller blade angle and guide vane opening for most efficient operation of double-regulated machines. The simplified procedure can be used for a rapid and partial estimation of the performance of hydraulic turbines for repair and maintenance work.

Characterization of the dynamic behaviour of flax fibre reinforced composites using vibration measurements

NASA Astrophysics Data System (ADS)

El-Hafidi, Ali; Birame Gning, Papa; Piezel, Benoit; Fontaine, Stéphane

2017-10-01

Experimental and numerical methods to identify the linear viscoelastic properties of flax fibre reinforced epoxy (FFRE) composite are presented in this study. The method relies on the evolution of storage modulus and loss factor as observed through the frequency response. Free-free symmetrically guided beams were excited on the dynamic range of 10 Hz to 4 kHz with a swept sine excitation focused around their first modes. A fractional derivative Zener model has been identified to predict the complex moduli. A modified ply constitutive law has been then implemented in a classical laminates theory calculation (CLT) routine.

8. The development and evolution of division of labor and foraging specialization in a social insect (Apis mellifera L.).

PubMed

Page, Robert E; Scheiner, Ricarda; Erber, Joachim; Amdam, Gro V

2006-01-01

How does complex social behavior evolve? What are the developmental building blocks of division of labor and specialization, the hallmarks of insect societies? Studies have revealed the developmental origins in the evolution of division of labor and specialization in foraging worker honeybees, the hallmarks of complex insect societies. Selective breeding for a single social trait, the amount of surplus pollen stored in the nest (pollen hoarding) revealed a phenotypic architecture of correlated traits at multiple levels of biological organization in facultatively sterile female worker honeybees. Verification of this phenotypic architecture in "wild-type" bees provided strong support for a "pollen foraging syndrome" that involves increased senso-motor responses, motor activity, associative learning, reproductive status, and rates of behavioral development, as well as foraging behavior. This set of traits guided further research into reproductive regulatory systems that were co-opted by natural selection during the evolution of social behavior. Division of labor, characterized by changes in the tasks performed by bees, as they age, is controlled by hormones linked to ovary development. Foraging specialization on nectar and pollen results also from different reproductive states of bees where nectar foragers engage in pre-reproductive behavior, foraging for nectar for self-maintenance, while pollen foragers perform foraging tasks associated with reproduction and maternal care, collecting protein.

The origin of cellular life.

PubMed

Ingber, D E

2000-12-01

This essay presents a scenario of the origin of life that is based on analysis of biological architecture and mechanical design at the microstructural level. My thesis is that the same architectural and energetic constraints that shape cells today also guided the evolution of the first cells and that the molecular scaffolds that support solid-phase biochemistry in modern cells represent living microfossils of past life forms. This concept emerged from the discovery that cells mechanically stabilize themselves using tensegrity architecture and that these same building rules guide hierarchical self-assembly at all size scales (Sci. Amer 278:48-57;1998). When combined with other fundamental design principles (e.g., energy minimization, topological constraints, structural hierarchies, autocatalytic sets, solid-state biochemistry), tensegrity provides a physical basis to explain how atomic and molecular elements progressively self-assembled to create hierarchical structures with increasingly complex functions, including living cells that can self-reproduce.

The origin of cellular life

NASA Technical Reports Server (NTRS)

Ingber, D. E.

2000-01-01

This essay presents a scenario of the origin of life that is based on analysis of biological architecture and mechanical design at the microstructural level. My thesis is that the same architectural and energetic constraints that shape cells today also guided the evolution of the first cells and that the molecular scaffolds that support solid-phase biochemistry in modern cells represent living microfossils of past life forms. This concept emerged from the discovery that cells mechanically stabilize themselves using tensegrity architecture and that these same building rules guide hierarchical self-assembly at all size scales (Sci. Amer 278:48-57;1998). When combined with other fundamental design principles (e.g., energy minimization, topological constraints, structural hierarchies, autocatalytic sets, solid-state biochemistry), tensegrity provides a physical basis to explain how atomic and molecular elements progressively self-assembled to create hierarchical structures with increasingly complex functions, including living cells that can self-reproduce.

Field-trip guide to volcanic and volcaniclastic deposits of the lower Jurassic Talkeetna formation, Sheep Mountain, south-central Alaska

USGS Publications Warehouse

Draut, Amy E.; Clift, Peter D.; Blodgett, Robert B.

2006-01-01

This guide provides information for a one-day field trip in the vicinity of Sheep Mountain, just north of the Glenn Highway in south-central Alaska. The Lower Jurassic Talkeetna Formation, consisting of extrusive volcanic and volcaniclastic sedimentary rocks of the Talkeetna arc complex, is exposed on and near Sheep Mountain. Field-trip stops within short walking distance of the Glenn Highway (approximately two hours’ drive from Anchorage) are described, which will be visited during the Geological Society of America Penrose meeting entitled Crustal Genesis and Evolution: Focus on Arc Lower Crust and Shallow Mantle, held in Valdez, Alaska, in July 2006. Several additional exposures of the Talkeetna Formation on other parts of Sheep Mountain that would need to be accessed with longer and more strenuous walking or by helicopter are also mentioned.

Life in the Universe: Foundation for exciting multidisciplinary science activities for middle and elementary school classes

NASA Technical Reports Server (NTRS)

Milne, D.; O'Sullivan, K.

1994-01-01

Young students find extra-terrestrial life one of the most intriguing of all topics. A project funded by the National Science Foundation and NASA, and administered by the SETI Institute, is underway to devise science lessons for grades 3-9 that draw upon this fascination. The lessons are designed by teachers and persons with long experience at curriculum design, tested in classrooms, revised and retested. Six guides, each containing some 6-10 science lessons, will be finished by summer, 1994.The theme Life in the Universe lends itself naturally to integrated treatment of facts and concepts from many scientific disciplines. The lessons for two completed guides span the origin of planet systems, evolution of complex life, chemical makeup of life, astronomy, spectroscopy, continental drift, mathematics and SETI (Search for Extra-Terrestrial Intelligence). All lessons are hands-on, interesting, and successful.

Life in the universe: foundation for exciting multidisciplinary science activities for middle and elementary school classes.

PubMed

Milne, D; O'Sullivan, K

1994-01-01

Young students find extra-terrestrial life one of the most intriguing of all topics. A project funded by the National Science Foundation and NASA, and administered by the SETI Institute, is underway to devise science lessons for grades 3-9 that draw upon this fascination. The lessons are designed by teachers and persons with long experience at curriculum design, tested in classrooms, revised and retested. Six guides, each containing some 6-10 science lessons, will be finished by summer, 1994. The theme Life in the Universe lends itself naturally to integrated treatment of facts and concepts from many scientific disciplines. The lessons for two completed guides span the origin of planet systems, evolution of complex life, chemical makeup of life, astronomy, spectroscopy, continental drift, mathematics and SETI (Search for Extra-Terrestrial Intelligence). All lessons are hands-on, interesting, and successful.

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

PubMed

Citorik, Robert J; Mimee, Mark; Lu, Timothy K

2014-11-01

Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

MRI-guided robotics at the U of Houston: evolving methodologies for interventions and surgeries.

PubMed

Tsekos, Nikolaos V

2009-01-01

Currently, we witness the rapid evolution of minimally invasive surgeries (MIS) and image guided interventions (IGI) for offering improved patient management and cost effectiveness. It is well recognized that sustaining and expand this paradigm shift would require new computational methodology that integrates sensing with multimodal imaging, actively controlled robotic manipulators, the patient and the operator. Such approach would include (1) assessing in real-time tissue deformation secondary to the procedure and physiologic motion, (2) monitoring the tool(s) in 3D, and (3) on-the-fly update information about the pathophysiology of the targeted tissue. With those capabilities, real time image guidance may facilitate a paradigm shift and methodological leap from "keyhole" visualization (i.e. endoscopy or laparoscopy) to one that uses a volumetric and informational rich perception of the Area of Operation (AoO). This capability may eventually enable a wider range and level of complexity IGI and MIS.

Eukaryotic systematics: a user's guide for cell biologists and parasitologists.

PubMed

Walker, Giselle; Dorrell, Richard G; Schlacht, Alexander; Dacks, Joel B

2011-11-01

Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

Dynamic self-guiding analysis of Alzheimer's disease

PubMed Central

Kurakin, Alexei; Bredesen, Dale E.

2015-01-01

We applied a self-guiding evolutionary algorithm to initiate the synthesis of the Alzheimer's disease-related data and literature. A protein interaction network associated with amyloid-beta precursor protein (APP) and a seed model that treats Alzheimer's disease as progressive dysregulation of APP-associated signaling were used as dynamic “guides” and structural “filters” in the recursive search, analysis, and assimilation of data to drive the evolution of the seed model in size, detail, and complexity. Analysis of data and literature across sub-disciplines and system-scale discovery platforms suggests a key role of dynamic cytoskeletal connectivity in the stability, plasticity, and performance of multicellular networks and architectures. Chronic impairment and/or dysregulation of cell adhesions/synapses, cytoskeletal networks, and/or reversible epithelial-to-mesenchymal-like transitions, which enable and mediate the stable and coherent yet dynamic and reconfigurable multicellular architectures, may lead to the emergence and persistence of the disordered, wound-like pockets/microenvironments of chronically disconnected cells. Such wound-like microenvironments support and are supported by pro-inflammatory, pro-secretion, de-differentiated cellular phenotypes with altered metabolism and signaling. The co-evolution of wound-like microenvironments and their inhabitants may lead to the selection and stabilization of degenerated cellular phenotypes, via acquisition of epigenetic modifications and mutations, which eventually result in degenerative disorders such as cancer and Alzheimer's disease. PMID:26041885

On the Improvement of Convergence Performance for Integrated Design of Wind Turbine Blade Using a Vector Dominating Multi-objective Evolution Algorithm

NASA Astrophysics Data System (ADS)

Wang, L.; Wang, T. G.; Wu, J. H.; Cheng, G. P.

2016-09-01

A novel multi-objective optimization algorithm incorporating evolution strategies and vector mechanisms, referred as VD-MOEA, is proposed and applied in aerodynamic- structural integrated design of wind turbine blade. In the algorithm, a set of uniformly distributed vectors is constructed to guide population in moving forward to the Pareto front rapidly and maintain population diversity with high efficiency. For example, two- and three- objective designs of 1.5MW wind turbine blade are subsequently carried out for the optimization objectives of maximum annual energy production, minimum blade mass, and minimum extreme root thrust. The results show that the Pareto optimal solutions can be obtained in one single simulation run and uniformly distributed in the objective space, maximally maintaining the population diversity. In comparison to conventional evolution algorithms, VD-MOEA displays dramatic improvement of algorithm performance in both convergence and diversity preservation for handling complex problems of multi-variables, multi-objectives and multi-constraints. This provides a reliable high-performance optimization approach for the aerodynamic-structural integrated design of wind turbine blade.

Supercomputations and big-data analysis in strong-field ultrafast optical physics: filamentation of high-peak-power ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Voronin, A. A.; Panchenko, V. Ya; Zheltikov, A. M.

2016-06-01

High-intensity ultrashort laser pulses propagating in gas media or in condensed matter undergo complex nonlinear spatiotemporal evolution where temporal transformations of optical field waveforms are strongly coupled to an intricate beam dynamics and ultrafast field-induced ionization processes. At the level of laser peak powers orders of magnitude above the critical power of self-focusing, the beam exhibits modulation instabilities, producing random field hot spots and breaking up into multiple noise-seeded filaments. This problem is described by a (3  +  1)-dimensional nonlinear field evolution equation, which needs to be solved jointly with the equation for ultrafast ionization of a medium. Analysis of this problem, which is equivalent to solving a billion-dimensional evolution problem, is only possible by means of supercomputer simulations augmented with coordinated big-data processing of large volumes of information acquired through theory-guiding experiments and supercomputations. Here, we review the main challenges of supercomputations and big-data processing encountered in strong-field ultrafast optical physics and discuss strategies to confront these challenges.

The evolution of organic matter in space.

PubMed

Ehrenfreund, Pascale; Spaans, Marco; Holm, Nils G

2011-02-13

Carbon, and molecules made from it, have already been observed in the early Universe. During cosmic time, many galaxies undergo intense periods of star formation, during which heavy elements like carbon, oxygen, nitrogen, silicon and iron are produced. Also, many complex molecules, from carbon monoxide to polycyclic aromatic hydrocarbons, are detected in these systems, like they are for our own Galaxy. Interstellar molecular clouds and circumstellar envelopes are factories of complex molecular synthesis. A surprisingly high number of molecules that are used in contemporary biochemistry on the Earth are found in the interstellar medium, planetary atmospheres and surfaces, comets, asteroids and meteorites and interplanetary dust particles. Large quantities of extra-terrestrial material were delivered via comets and asteroids to young planetary surfaces during the heavy bombardment phase. Monitoring the formation and evolution of organic matter in space is crucial in order to determine the prebiotic reservoirs available to the early Earth. It is equally important to reveal abiotic routes to prebiotic molecules in the Earth environments. Materials from both carbon sources (extra-terrestrial and endogenous) may have contributed to biochemical pathways on the Earth leading to life's origin. The research avenues discussed also guide us to extend our knowledge to other habitable worlds.

A novel procedure for the identification of chaos in complex biological systems

NASA Astrophysics Data System (ADS)

Bazeia, D.; Pereira, M. B. P. N.; Brito, A. V.; Oliveira, B. F. De; Ramos, J. G. G. S.

2017-03-01

We demonstrate the presence of chaos in stochastic simulations that are widely used to study biodiversity in nature. The investigation deals with a set of three distinct species that evolve according to the standard rules of mobility, reproduction and predation, with predation following the cyclic rules of the popular rock, paper and scissors game. The study uncovers the possibility to distinguish between time evolutions that start from slightly different initial states, guided by the Hamming distance which heuristically unveils the chaotic behavior. The finding opens up a quantitative approach that relates the correlation length to the average density of maxima of a typical species, and an ensemble of stochastic simulations is implemented to support the procedure. The main result of the work shows how a single and simple experimental realization that counts the density of maxima associated with the chaotic evolution of the species serves to infer its correlation length. We use the result to investigate others distinct complex systems, one dealing with a set of differential equations that can be used to model a diversity of natural and artificial chaotic systems, and another one, focusing on the ocean water level.

A Resource Guide for Teachers of Hindu Literature.

ERIC Educational Resources Information Center

Meehan, John L., Ed.; And Others

Focusing on Hinduism, India, and Indian literature, this course guide offers help in organizing a course or units of instruction. The guide contains a historical outline of the evolution of Hinduism over a period of 3,000 years; a glossary listing terms in the guide and in Hindu literature; five courses of different time lengths (the literature of…

Lifting the Markov blankets of socio-cultural evolution. A comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Désormeau Ramstead et al.

NASA Astrophysics Data System (ADS)

Leydesdorff, Loet

2018-03-01

Ramstead et al. [8] claim an encompassing ontology which can be used as a heuristics for studying life, mind, and society both empirically and in terms of computer simulations. The systems levels are self-organizing into a hierarchy; "Markov blankets" close the various levels for one another. Homo sapiens sapiens is placed at the top of this hierarchy as "the world's most complex living systems." Humans are said to generate "(epi)genetically-specified expectations that have been shaped by selection to guide action-perception cycles toward adaptive or unsurprising states."

Physical Complexity and Cognitive Evolution

NASA Astrophysics Data System (ADS)

Jedlicka, Peter

Our intuition tells us that there is a general trend in the evolution of nature, a trend towards greater complexity. However, there are several definitions of complexity and hence it is difficult to argue for or against the validity of this intuition. Christoph Adami has recently introduced a novel measure called physical complexity that assigns low complexity to both ordered and random systems and high complexity to those in between. Physical complexity measures the amount of information that an organism stores in its genome about the environment in which it evolves. The theory of physical complexity predicts that evolution increases the amount of `knowledge' an organism accumulates about its niche. It might be fruitful to generalize Adami's concept of complexity to the entire evolution (including the evolution of man). Physical complexity fits nicely into the philosophical framework of cognitive biology which considers biological evolution as a progressing process of accumulation of knowledge (as a gradual increase of epistemic complexity). According to this paradigm, evolution is a cognitive `ratchet' that pushes the organisms unidirectionally towards higher complexity. Dynamic environment continually creates problems to be solved. To survive in the environment means to solve the problem, and the solution is an embodied knowledge. Cognitive biology (as well as the theory of physical complexity) uses the concepts of information and entropy and views the evolution from both the information-theoretical and thermodynamical perspective. Concerning humans as conscious beings, it seems necessary to postulate an emergence of a new kind of knowledge - a self-aware and self-referential knowledge. Appearence of selfreflection in evolution indicates that the human brain reached a new qualitative level in the epistemic complexity.

Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition

PubMed Central

Madina, Bhaskara R.; Kumar, Vikas; Metz, Richard; Mooers, Blaine H.M.; Bundschuh, Ralf; Cruz-Reyes, Jorge

2014-01-01

Mitochondrial mRNAs in kinetoplastids require extensive U-insertion/deletion editing that progresses 3′-to-5′ in small blocks, each directed by a guide RNA (gRNA), and exhibits substrate and developmental stage-specificity by unsolved mechanisms. Here, we address compositionally related factors, collectively known as the mitochondrial RNA-binding complex 1 (MRB1) or gRNA-binding complex (GRBC), that contain gRNA, have a dynamic protein composition, and transiently associate with several mitochondrial factors including RNA editing core complexes (RECC) and ribosomes. MRB1 controls editing by still unknown mechanisms. We performed the first next-generation sequencing study of native subcomplexes of MRB1, immunoselected via either RNA helicase 2 (REH2), that binds RNA and associates with unwinding activity, or MRB3010, that affects an early editing step. The particles contain either REH2 or MRB3010 but share the core GAP1 and other proteins detected by RNA photo-crosslinking. Analyses of the first editing blocks indicate an enrichment of several initiating gRNAs in the MRB3010-purified complex. Our data also indicate fast evolution of mRNA 3′ ends and strain-specific alternative 3′ editing within 3′ UTR or C-terminal protein-coding sequence that could impact mitochondrial physiology. Moreover, we found robust specific copurification of edited and pre-edited mRNAs, suggesting that these particles may bind both mRNA and gRNA editing substrates. We propose that multiple subcomplexes of MRB1 with different RNA/protein composition serve as a scaffold for specific assembly of editing substrates and RECC, thereby forming the editing holoenzyme. The MRB3010-subcomplex may promote early editing through its preferential recruitment of initiating gRNAs. PMID:24865612

Model criticism based on likelihood-free inference, with an application to protein network evolution.

PubMed

Ratmann, Oliver; Andrieu, Christophe; Wiuf, Carsten; Richardson, Sylvia

2009-06-30

Mathematical models are an important tool to explain and comprehend complex phenomena, and unparalleled computational advances enable us to easily explore them without any or little understanding of their global properties. In fact, the likelihood of the data under complex stochastic models is often analytically or numerically intractable in many areas of sciences. This makes it even more important to simultaneously investigate the adequacy of these models-in absolute terms, against the data, rather than relative to the performance of other models-but no such procedure has been formally discussed when the likelihood is intractable. We provide a statistical interpretation to current developments in likelihood-free Bayesian inference that explicitly accounts for discrepancies between the model and the data, termed Approximate Bayesian Computation under model uncertainty (ABCmicro). We augment the likelihood of the data with unknown error terms that correspond to freely chosen checking functions, and provide Monte Carlo strategies for sampling from the associated joint posterior distribution without the need of evaluating the likelihood. We discuss the benefit of incorporating model diagnostics within an ABC framework, and demonstrate how this method diagnoses model mismatch and guides model refinement by contrasting three qualitative models of protein network evolution to the protein interaction datasets of Helicobacter pylori and Treponema pallidum. Our results make a number of model deficiencies explicit, and suggest that the T. pallidum network topology is inconsistent with evolution dominated by link turnover or lateral gene transfer alone.

Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery

PubMed Central

2018-01-01

Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA). Here, small molecules from phenotypic screens with demonstrated antiparasitic activity are used in genome-based target discovery methods. In this Review, we discuss the newest, most promising druggable targets discovered or further validated by evolution-based methods, as well as some exceptions. PMID:29451780

Nonlinear evolution of three-dimensional instabilities of thin and thick electron scale current sheets: Plasmoid formation and current filamentation

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

Jain, Neeraj; Büchner, Jörg; Max Planck Institute for Solar System Research, Justus-Von-Liebig-Weg-3, Göttingen

Nonlinear evolution of three dimensional electron shear flow instabilities of an electron current sheet (ECS) is studied using electron-magnetohydrodynamic simulations. The dependence of the evolution on current sheet thickness is examined. For thin current sheets (half thickness =d{sub e}=c/ω{sub pe}), tearing mode instability dominates. In its nonlinear evolution, it leads to the formation of oblique current channels. Magnetic field lines form 3-D magnetic spirals. Even in the absence of initial guide field, the out-of-reconnection-plane magnetic field generated by the tearing instability itself may play the role of guide field in the growth of secondary finite-guide-field instabilities. For thicker current sheetsmore » (half thickness ∼5 d{sub e}), both tearing and non-tearing modes grow. Due to the non-tearing mode, current sheet becomes corrugated in the beginning of the evolution. In this case, tearing mode lets the magnetic field reconnect in the corrugated ECS. Later thick ECS develops filamentary structures and turbulence in which reconnection occurs. This evolution of thick ECS provides an example of reconnection in self-generated turbulence. The power spectra for both the thin and thick current sheets are anisotropic with respect to the electron flow direction. The cascade towards shorter scales occurs preferentially in the direction perpendicular to the electron flow.« less

Effect of users' opinion evolution on information diffusion in online social networks

NASA Astrophysics Data System (ADS)

Zhu, Hengmin; Kong, Yuehan; Wei, Jing; Ma, Jing

2018-02-01

The process of topic propagation always interweaves information diffusion and opinion evolution, but most previous works studied the models of information diffusion and opinion evolution separately, and seldom focused on their interaction of each other. To shed light on the effect of users' opinion evolution on information diffusion in online social networks, we proposed a model which incorporates opinion evolution into the process of topic propagation. Several real topics propagating on Sina Microblog were collected to analyze individuals' propagation intentions, and different propagation intentions were considered in the model. The topic propagation was simulated to explore the impact of different opinion distributions and intervention with opposite opinion on information diffusion. Results show that the topic with one-sided opinions can spread faster and more widely, and intervention with opposite opinion is an effective measure to guide the topic propagation. The earlier to intervene, the more effectively the topic propagation would be guided.

Detection of structural damage in multiwire cables by monitoring the entropy evolution of wavelet coefficients

NASA Astrophysics Data System (ADS)

Ibáñez, Flor; Baltazar, Arturo; Mijarez, Rito; Aranda, Jorge

2015-03-01

Multiwire cables are widely used in important civil structures. Since they are exposed to several dynamic and static loads, their structural health can be compromised. The cables can also be submitted to mechanical contact, tension and energy propagation in addition to changes in size and material within their wires. Due to the critical role played by multiwire cables, it is necessary to develop a non-destructive health monitoring method to maintain their structure and proper performance. Ultrasonic inspection using guided waves is a promising non-destructive damage monitoring technique for rods, single wires and multiwire cables. The propagated guided waves are composed by an infinite number of vibrational modes making their analysis difficult. In this work, an entropy-based method to identify small changes in non-stationary signals is proposed. A system to capture and post-process acoustic signals is implemented. The Discrete Wavelet Transform (DWT) is computed in order to obtain the reconstructed wavelet coefficients of the signals and to analyze the energy at different scales. The feasibility of using the concept of entropy evolution of non-stationary signals to detect damage in multiwire cables is evaluated. The results show that there is a high correlation between the entropy value and damage level of the cable. The proposed method has low sensitivity to noise and reduces the computational complexity found in a typical time-frequency analysis.

Interdisciplinary Studies Program. Teacher's Guide: Part IV.

ERIC Educational Resources Information Center

Valencia Community Coll., Orlando, FL.

This teacher's guide was developed for the last of four courses in Valencia Community College's Interdisciplinary Studies program, a 2-year core general education curriculum which chronologically examines the major developments in the evolution of human knowledge. The guide provides an introductory overview of the semester's content (i.e., the…

Interdisciplinary Studies Program. Teacher's Guide: Part II.

ERIC Educational Resources Information Center

Valencia Community Coll., Orlando, FL.

This teacher's guide was developed for the second of four courses in Valencia Community College's Interdisciplinary Studies Program, a 2-year core general education curriculum which chronologically examines the major developments in the evolution of human knowledge. The guide provides an introductory overview of the semester's topic (i.e., the…

Interdisciplinary Studies Program. Teacher's Guide: Part III.

ERIC Educational Resources Information Center

Valencia Community Coll., Orlando, FL.

This teacher's guide was developed for the third of four courses in Valencia Community College's Interdisciplinary Studies program, a 2-year core general education curriculum which chronologically examines the major developments in the evolution of human knowledge. The guide provides an introductory overview of the course's topic (i.e., Western…

Interdisciplinary Studies Program. Teacher's Guide: Part I.

ERIC Educational Resources Information Center

Valencia Community Coll., Orlando, FL.

This teacher's guide was developed for the first of four courses in Valencia Community College's Interdisciplinary Studies Program, a 2-year core general education curriculum which chronologically examines the major developments in the evolution of human knowledge. The guide provides an introductory overview of the semester's topic (i.e., the…

Evolution of biological complexity

PubMed Central

Adami, Christoph; Ofria, Charles; Collier, Travis C.

2000-01-01

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural “Maxwell Demon,” within a fixed environment, genomic complexity is forced to increase. PMID:10781045

From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.

PubMed

Böttcher, Thomas

2018-01-01

Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

Evolving gene regulation networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system

PubMed Central

Fritzsch, Bernd; Jahan, Israt; Pan, Ning; Elliott, Karen L.

2014-01-01

Understanding the evolution of the neurosensory system of man, able to reflect on its own origin, is one of the major goals of comparative neurobiology. Details of the origin of neurosensory cells, their aggregation into central nervous systems and associated sensory organs, their localized patterning into remarkably different cell types aggregated into variably sized parts of the central nervous system begin to emerge. Insights at the cellular and molecular level begin to shed some light on the evolution of neurosensory cells, partially covered in this review. Molecular evidence suggests that high mobility group (HMG) proteins of pre-metazoans evolved into the definitive Sox [SRY (sex determining region Y)-box] genes used for neurosensory precursor specification in metazoans. Likewise, pre-metazoan basic helix-loop-helix (bHLH) genes evolved in metazoans into the group A bHLH genes dedicated to neurosensory differentiation in bilaterians. Available evidence suggests that the Sox and bHLH genes evolved a cross-regulatory network able to synchronize expansion of precursor populations and their subsequent differentiation into novel parts of the brain or sensory organs. Molecular evidence suggests metazoans evolved patterning gene networks early and not dedicated to neuronal development. Only later in evolution were these patterning gene networks tied into the increasing complexity of diffusible factors, many of which were already present in pre-metazoans, to drive local patterning events. It appears that the evolving molecular basis of neurosensory cell development may have led, in interaction with differentially expressed patterning genes, to local network modifications guiding unique specializations of neurosensory cells into sensory organs and various areas of the central nervous system. PMID:25416504

Evolving gene regulatory networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system.

PubMed

Fritzsch, Bernd; Jahan, Israt; Pan, Ning; Elliott, Karen L

2015-01-01

Understanding the evolution of the neurosensory system of man, able to reflect on its own origin, is one of the major goals of comparative neurobiology. Details of the origin of neurosensory cells, their aggregation into central nervous systems and associated sensory organs and their localized patterning leading to remarkably different cell types aggregated into variably sized parts of the central nervous system have begun to emerge. Insights at the cellular and molecular level have begun to shed some light on the evolution of neurosensory cells, partially covered in this review. Molecular evidence suggests that high mobility group (HMG) proteins of pre-metazoans evolved into the definitive Sox [SRY (sex determining region Y)-box] genes used for neurosensory precursor specification in metazoans. Likewise, pre-metazoan basic helix-loop-helix (bHLH) genes evolved in metazoans into the group A bHLH genes dedicated to neurosensory differentiation in bilaterians. Available evidence suggests that the Sox and bHLH genes evolved a cross-regulatory network able to synchronize expansion of precursor populations and their subsequent differentiation into novel parts of the brain or sensory organs. Molecular evidence suggests metazoans evolved patterning gene networks early, which were not dedicated to neuronal development. Only later in evolution were these patterning gene networks tied into the increasing complexity of diffusible factors, many of which were already present in pre-metazoans, to drive local patterning events. It appears that the evolving molecular basis of neurosensory cell development may have led, in interaction with differentially expressed patterning genes, to local network modifications guiding unique specializations of neurosensory cells into sensory organs and various areas of the central nervous system.

Rarely at rest

PubMed Central

Hardwick, Steven W.; Luisi, Ben F.

2013-01-01

RNA helicases are compact, machine-like proteins that can harness the energy of nucleoside triphosphate binding and hydrolysis to dynamically remodel RNA structures and protein-RNA complexes. Through such activities, helicases participate in virtually every process associated with the expression of genetic information. Often found as components of multi-enzyme assemblies, RNA helicases facilitate the processivity of RNA degradation, the remodeling of protein interactions during maturation of structured RNA precursors, and fidelity checks of RNA quality. In turn, the assemblies modulate and guide the activities of the helicases. We describe the roles of RNA helicases with a conserved “DExD/H box” sequence motif in representative examples of such machineries from bacteria, archaea and eukaryotes. The recurrent occurrence of such helicases in complex assemblies throughout the course of evolution suggests a common requirement for their activities to meet cellular demands for the dynamic control of RNA metabolism. PMID:23064154

Evolution and complexity: the double-edged sword.

PubMed

Miconi, Thomas

2008-01-01

We attempt to provide a comprehensive answer to the question of whether, and when, an arrow of complexity emerges in Darwinian evolution. We note that this expression can be interpreted in different ways, including a passive, incidental growth, or a pervasive bias towards complexification. We argue at length that an arrow of complexity does indeed occur in evolution, which can be most reasonably interpreted as the result of a passive trend rather than a driven one. What, then, is the role of evolution in the creation of this trend, and under which conditions will it emerge? In the later sections of this article we point out that when certain proper conditions (which we attempt to formulate in a concise form) are met, Darwinian evolution predictably creates a sustained trend of increase in maximum complexity (that is, an arrow of complexity) that would not be possible without it; but if they are not, evolution will not only fail to produce an arrow of complexity, but may actually prevent any increase in complexity altogether. We conclude that, with regard to the growth of complexity, evolution is very much a double-edged sword.

A Teaching Guide to Evolution

ERIC Educational Resources Information Center

Gregg, Thomas G.; Janssen, Gary R.; Bhattacharjee, J.K.

2003-01-01

Evolution is considered by virtually all biologists to be the central unifying principle of biology, yet its fundamental concepts are not widely understood or widely disseminated. Teaching evolution--defined as descent with modification from a common ancestor as a result of natural selection acting on genetic variation--has traditionally been a…

Using the Situated Clinical Decision-Making framework to guide analysis of nurses' clinical decision-making.

PubMed

Gillespie, Mary

2010-11-01

Nurses' clinical decision-making is a complex process that holds potential to influence the quality of care provided and patient outcomes. The evolution of nurses' decision-making that occurs with experience has been well documented. In addition, literature includes numerous strategies and approaches purported to support development of nurses' clinical decision-making. There has been, however, significantly less attention given to the process of assessing nurses' clinical decision-making and novice clinical educators are often challenged with knowing how to best support nurses and nursing students in developing their clinical decision-making capacity. The Situated Clinical Decision-Making framework is presented for use by clinical educators: it provides a structured approach to analyzing nursing students' and novice nurses' decision-making in clinical nursing practice, assists educators in identifying specific issues within nurses' clinical decision-making, and guides selection of relevant strategies to support development of clinical decision-making. A series of questions is offered as a guide for clinical educators when assessing nurses' clinical decision-making. The discussion presents key considerations related to analysis of various decision-making components, including common sources of challenge and errors that may occur within nurses' clinical decision-making. An exemplar illustrates use of the framework and guiding questions. Implications of this approach for selection of strategies that support development of clinical decision-making are highlighted. Copyright © 2010 Elsevier Ltd. All rights reserved.

Contract Management or Self-Operation: A Decision-Making Guide for Higher Education.

ERIC Educational Resources Information Center

Goldstein, Philip J.; And Others

This guide offers an objective framework for deciding whether self-operation or contract management (also known as privatization or "outsourcing") will best serve the goals and objectives of an individual institution of higher education. The guide is organized into four chapters. Chapter 1 briefly outlines the evolution of contract…

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

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

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.

PubMed

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-11-24

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.

Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

PubMed Central

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-01-01

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci. PMID:26596461

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

PubMed Central

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; Li, Jinyang; Schwab, Mark J.; Brudvig, Gary W.; Taylor, André D.

2016-01-01

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. However, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. Here, we show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O2 batteries. The heme's oxygen binding capability facilitates battery recharge by accepting and releasing dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. This study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage. PMID:27759005

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

DOE PAGES

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; ...

2016-10-19

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

The evolution of complex life.

PubMed

Billingham, J

1989-01-01

In considering the probabilities that intelligent life might exist elsewhere in the Universe, it is important to ask questions about the factors governing the emergence of complex living organisms in the context of evolutionary biology, planetary environments and events in space. Two important problems arise. First, what can be learned about the general laws governing the evolution of complex life anywhere in space by studying its history on the Earth? Second, how is the evolution of complex life affected by events in space? To address these problems, a series of Science Workshops on the Evolution of Complex Life was held at the Ames Research Center. Included in this paper are highlights of those workshops, with particular emphasis on the first question, namely the evolution of complex extraterrestrial life.

Leveraging Human Insights by Combining Multi-Objective Optimization with Interactive Evolution

DTIC Science & Technology

2015-03-26

application, a program that used human selections to guide the evolution of insect -like images. He was able to demonstrate that humans provide key insights...LEVERAGING HUMAN INSIGHTS BY COMBINING MULTI-OBJECTIVE OPTIMIZATION WITH INTERACTIVE EVOLUTION THESIS Joshua R. Christman, Second Lieutenant, USAF...COMBINING MULTI-OBJECTIVE OPTIMIZATION WITH INTERACTIVE EVOLUTION THESIS Presented to the Faculty Department of Electrical and Computer Engineering

Monitoring microstructural evolution of alloy 617 with non-linear acoustics for remaining useful life prediction; multiaxial creep-fatigue and creep-ratcheting

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

Lissenden, Cliff; Hassan, Tasnin; Rangari, Vijaya

The research built upon a prior investigation to develop a unified constitutive model for design-­by-­analysis of the intermediate heat exchanger (IHX) for a very high temperature reactor (VHTR) design of next generation nuclear plants (NGNPs). Model development requires a set of failure data from complex mechanical experiments to characterize the material behavior. Therefore uniaxial and multiaxial creep-­fatigue and creep-­ratcheting tests were conducted on the nickel-­base Alloy 617 at 850 and 950°C. The time dependence of material behavior, and the interaction of time dependent behavior (e.g., creep) with ratcheting, which is an increase in the cyclic mean strain under load-­controlled cycling,more » are major concerns for NGNP design. This research project aimed at characterizing the microstructure evolution mechanisms activated in Alloy 617 by mechanical loading and dwell times at elevated temperature. The acoustic harmonic generation method was researched for microstructural characterization. It is a nonlinear acoustics method with excellent potential for nondestructive evaluation, and even online continuous monitoring once high temperature sensors become available. It is unique because it has the ability to quantitatively characterize microstructural features well before macroscale defects (e.g., cracks) form. The nonlinear acoustics beta parameter was shown to correlate with microstructural evolution using a systematic approach to handle the complexity of multiaxial creep-­fatigue and creep-­ratcheting deformation. Mechanical testing was conducted to provide a full spectrum of data for: thermal aging, tensile creep, uniaxial fatigue, uniaxial creep-­fatigue, uniaxial creep-ratcheting, multiaxial creep-fatigue, and multiaxial creep-­ratcheting. Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), and Optical Microscopy were conducted to correlate the beta parameter with individual microstructure mechanisms. We researched application of the harmonic generation method to tubular mechanical test specimens and pipes for nondestructive evaluation. Tubular specimens and pipes act as waveguides, thus we applied the acoustic harmonic generation method to guided waves in both plates and shells. Magnetostrictive transducers were used to generate and receive guided wave modes in the shell sample and the received signals were processed to show the sensitivity of higher harmonic generation to microstructure evolution. Modeling was initiated to correlate higher harmonic generation with the microstructure that will lead to development of a life prediction model that is informed by the nonlinear acoustics measurements.« less

Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

PubMed Central

Ord, Terry J.; Garcia-Porta, Joan

2012-01-01

Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

Origin and evolution of planetary atmospheres

NASA Technical Reports Server (NTRS)

Pollack, J. B.; Yung, Y. L.

1980-01-01

The current understanding of the origin and evolution of the atmospheres of solar system objects is reviewed. Physical processes that control this evolution are described in an attempt to develop a set of general principles that can help guide studies of specific objects. Particular emphasis is placed on the planetary and satellite atmospheres of the inner solar system objects; current hypotheses on the origin and evolution of these objects are critically considered.

The evolution of life cycle complexity in aphids: Ecological optimization or historical constraint?

PubMed

Hardy, Nate B; Peterson, Daniel A; von Dohlen, Carol D

2015-06-01

For decades, biologists have debated why many parasites have obligate multihost life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, that is, change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (nonaphidines)-groups that differ in the intensity of their relationships with primary hosts. Next, we test specific mechanisms by which life cycle complexity could be adaptive or a constraint. We find that among aphidines there is a strong association between complex life cycles and polyphagy but only a weak correlation between life cycle complexity and reproductive mode. In contrast, among nonaphidines the relationship between life cycle complexity and host breadth is weak but the association between complex life cycles and sexual reproduction is strong. Thus, although the adaptiveness of life cycle complexity appears to be lineage specific, across aphids, life cycle evolution appears to be tightly linked with the evolution of other important natural history traits. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

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

Wang, Yanli; Juranek, Stefan; Li, Haitao

Here we report on a 3.0 {angstrom} crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formationmore » of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.« less

Solar Physics and Terrestrial Effects: A Curriculum Guide for Teachers Grades 7-12, 2nd Edition.

ERIC Educational Resources Information Center

Briggs, Roger P.; Carlisle, Robert J.

This curriculum guide includes a brief textbook, a hands-on activity guide, and resource listings. The textbook provides background information in solar physics for teachers and contains problems suitable for advanced students at the end of each chapter. Topics covered in the textbook include stellar evolution, the structure of the sun, methods of…

Origin of Man: Problems in the Interpretation of New Evidence. Test Edition. AAAS Study Guides on Contemporary Problems.

ERIC Educational Resources Information Center

Almquist, Alan J.; Cronin, John E.

This is one of several study guides on contemporary problems produced by the American Association for the Advancement of Science with support of the National Science Foundation. This guide focuses on the origin of man. Part I, The Biochemical Evidence for Human Evolution, contains four sections: (1) Introduction; (2) Macromolecular Data; (3)…

Simulating evolution of protein complexes through gene duplication and co-option.

PubMed

Haarsma, Loren; Nelesen, Serita; VanAndel, Ethan; Lamine, James; VandeHaar, Peter

2016-06-21

We present a model of the evolution of protein complexes with novel functions through gene duplication, mutation, and co-option. Under a wide variety of input parameters, digital organisms evolve complexes of 2-5 bound proteins which have novel functions but whose component proteins are not independently functional. Evolution of complexes with novel functions happens more quickly as gene duplication rates increase, point mutation rates increase, protein complex functional probability increases, protein complex functional strength increases, and protein family size decreases. Evolution of complexity is inhibited when the metabolic costs of making proteins exceeds the fitness gain of having functional proteins, or when point mutation rates get so large the functional proteins undergo deleterious mutations faster than new functional complexes can evolve. Copyright © 2016 Elsevier Ltd. All rights reserved.

Statistical Determinants of Selective Ionic Complexation: Ions in Solvent, Transport Proteins, and Other “Hosts”

PubMed Central

Bostick, David L.; Brooks, Charles L.

2009-01-01

To provide utility in understanding the molecular evolution of ion-selective biomembrane channels/transporters, globular proteins, and ionophoric compounds, as well as in guiding their modification and design, we present a statistical mechanical basis for deconstructing the impact of the coordination structure and chemistry of selective multidentate ionic complexes. The deconstruction augments familiar ideas in liquid structure theory to realize the ionic complex as an open ion-ligated system acting under the influence of an “external field” provided by the host (or surrounding medium). Using considerations derived from this basis, we show that selective complexation arises from exploitation of a particular ion's coordination preferences. These preferences derive from a balance of interactions much like that which dictates the Hofmeister effect. By analyzing the coordination-state space of small family IA and VIIA ions in simulated fluid media, we derive domains of coordinated states that confer selectivity for a given ion upon isolating and constraining particular attributes (order parameters) of a complex comprised of a given type of ligand. We demonstrate that such domains may be used to rationalize the ion-coordinated environments provided by selective ionophores and biological ion channels/transporters of known structure, and that they can serve as a means toward deriving rational design principles for ion-selective hosts. PMID:19486671

Human Origins: Problems in the Interpretation of New Evidence. Third Edition. AAAS Study Guides on Contemporary Problems.

ERIC Educational Resources Information Center

Almquist, Alan J.; Cronin, John E.

This Chautauqua-type short course in human evolution is divided into two parts: The Biochemical Evidence for Human Evolution, and the Fossil Evidence for Human Evolution. The first part covers the comparison of macromolecular differences between species. This includes comparison of DNA base-ratios and amino acid substitution in enzymes and other…

Crustal Movement: A Major Force in Evolution. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Composite Agency: Semiotics of Modularity and Guiding Interactions.

PubMed

Sharov, Alexei A

2017-07-01

Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call "guiding", do not have immediate effects and do not disrupt the evolution and learning capacity of partner agents. However, they modify the extent of learning and evolutionary possibilities of partners via establishment of scaffolds and constraints. As a result, subagents construct reciprocal scaffolding for each other to rebalance their communal evolution and learning. As an example, I discuss guiding interactions between the body and mind of animals, where the pain system adjusts mind-based learning to the physical and physiological constraints of the body. Reciprocal effects of mind and behaviors on the development and evolution of the body includes the effects of Lamarck and Baldwin.

Rigorous simulations of a helical core fiber by the use of transformation optics formalism.

PubMed

Napiorkowski, Maciej; Urbanczyk, Waclaw

2014-09-22

We report for the first time on rigorous numerical simulations of a helical-core fiber by using a full vectorial method based on the transformation optics formalism. We modeled the dependence of circular birefringence of the fundamental mode on the helix pitch and analyzed the effect of a birefringence increase caused by the mode displacement induced by a core twist. Furthermore, we analyzed the complex field evolution versus the helix pitch in the first order modes, including polarization and intensity distribution. Finally, we show that the use of the rigorous vectorial method allows to better predict the confinement loss of the guided modes compared to approximate methods based on equivalent in-plane bending models.

Honing Theory: A Complex Systems Framework for Creativity.

PubMed

Gabora, Liane

2017-01-01

This paper proposes a theory of creativity, referred to as honing theory, which posits that creativity fuels the process by which culture evolves through communal exchange amongst minds that are self-organizing, self-maintaining, and self-reproducing. According to honing theory, minds, like other self-organizing systems, modify their contents and adapt to their environments to minimize entropy. Creativity begins with detection of high psychological entropy material, which provokes uncertainty and is arousal-inducing. The creative process involves recursively considering this material from new contexts until it is sufficiently restructured that arousal dissipates. Restructuring involves neural synchrony and dynamic binding, and may be facilitated by temporarily shifting to a more associative mode of thought. A creative work may similarly induce restructuring in others, and thereby contribute to the cultural evolution of more nuanced worldviews. Since lines of cultural descent connecting creative outputs may exhibit little continuity, it is proposed that cultural evolution occurs at the level of self-organizing minds; outputs reflect their evolutionary state. Honing theory addresses challenges not addressed by other theories of creativity, such as the factors that guide restructuring, and in what sense creative works evolve. Evidence comes from empirical studies, an agent-based computational model of cultural evolution, and a model of concept combination.

Trace elements at the intersection of marine biological and geochemical evolution

USGS Publications Warehouse

Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

2016-01-01

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

Prototype of a laser guide star wavefront sensor for the Extremely Large Telescope

NASA Astrophysics Data System (ADS)

Patti, M.; Lombini, M.; Schreiber, L.; Bregoli, G.; Arcidiacono, C.; Cosentino, G.; Diolaiti, E.; Foppiani, I.

2018-06-01

The new class of large telescopes, like the future Extremely Large Telescope (ELT), are designed to work with a laser guide star (LGS) tuned to a resonance of atmospheric sodium atoms. This wavefront sensing technique presents complex issues when applied to big telescopes for many reasons, mainly linked to the finite distance of the LGS, the launching angle, tip-tilt indetermination and focus anisoplanatism. The implementation of a laboratory prototype for the LGS wavefront sensor (WFS) at the beginning of the phase study of MAORY (Multi-conjugate Adaptive Optics Relay) for ELT first light has been indispensable in investigating specific mitigation strategies for the LGS WFS issues. This paper presents the test results of the LGS WFS prototype under different working conditions. The accuracy within which the LGS images are generated on the Shack-Hartmann WFS has been cross-checked with the MAORY simulation code. The experiments show the effect of noise on centroiding precision, the impact of LGS image truncation on wavefront sensing accuracy as well as the temporal evolution of the sodium density profile and LGS image under-sampling.

Approaches to Legacy System Evolution.

DTIC Science & Technology

1997-12-01

such as migrating legacy systems, to more distributed open environments. This framework draws out the important global issues early in the planning...ongoing system evolution initiatives, for drawing out important global issues early in the planning cycle using the checklists as a guide, and for

Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence.

PubMed

Hernández-Orozco, Santiago; Hernández-Quiroz, Francisco; Zenil, Hector

2018-01-01

Is undecidability a requirement for open-ended evolution (OEE)? Using methods derived from algorithmic complexity theory, we propose robust computational definitions of open-ended evolution and the adaptability of computable dynamical systems. Within this framework, we show that decidability imposes absolute limits on the stable growth of complexity in computable dynamical systems. Conversely, systems that exhibit (strong) open-ended evolution must be undecidable, establishing undecidability as a requirement for such systems. Complexity is assessed in terms of three measures: sophistication, coarse sophistication, and busy beaver logical depth. These three complexity measures assign low complexity values to random (incompressible) objects. As time grows, the stated complexity measures allow for the existence of complex states during the evolution of a computable dynamical system. We show, however, that finding these states involves undecidable computations. We conjecture that for similar complexity measures that assign low complexity values, decidability imposes comparable limits on the stable growth of complexity, and that such behavior is necessary for nontrivial evolutionary systems. We show that the undecidability of adapted states imposes novel and unpredictable behavior on the individuals or populations being modeled. Such behavior is irreducible. Finally, we offer an example of a system, first proposed by Chaitin, that exhibits strong OEE.

Intuition and logic in human evolution

PubMed Central

Campbell, Robert

2012-01-01

Modern science has come to be regarded as an exclusively objective endeavor employing explicit language that attempts to exclude subjective anthropomorphic biases. In doing so it has run the risk of becoming a purely materialistic bias itself, according no proper place to the human spirit or to intuitive insights that have guided the evolution of human cultures, even though this includes the guiding insights of the most important contributors to the sciences. Although this may have been necessary to exclude rampant superstition in the past, a summary overview of the historical evidence indicates a current pressing need to restore a proper balance. PMID:23181155

The Great Evolution Trial: Use of Role-Play in the Classroom.

ERIC Educational Resources Information Center

Duveen, Jonathan; Solomon, Joan

1994-01-01

Provides both the pedagogic and scientific thinking that guided the construction of a classroom role play called "The Great Evolution Debate," which is about the publication of Darwin's "The Origin of Species." Provides tentative findings regarding learning from role playing. (ZWH)

An insight into the sialome of the bed bug, Cimex lectularius

PubMed Central

Francischetti, Ivo M.B.; Calvo, Eric; Andersen, John F.; Pham, Van M.; Favreau, Amanda J.; Barbian, Kent D.; Romero, Alvaro; Valenzuela, Jesus G.; Ribeiro., José M.C.

2010-01-01

The evolution of insects to a blood diet leads to the development of a saliva that antagonizes their hosts' hemostasis and inflammation. Hemostasis and inflammation are redundant processes, and thus a complex salivary potion comprised of dozens or near one hundred different polypeptides is commonly found by transcriptome or proteome analysis of these organisms. Several insect orders or families evolved independently to hematophagy creating unique salivary potions in the form of novel pharmacological use of endogenous substances, and in the form of unique proteins not matching other known proteins, these probably arriving by fast evolution of salivary proteins as they evade their hosts' immune response. In this work we present a preliminary description of the sialome (from the Greek Sialo = saliva) of the common bed bug Cimex lectularius, the first such work from a member of the Cimicidae family. This manuscript is a guide for the supplemental database files http://exon.niaid.nih.gov/transcriptome/C_lectularius/S1/Cimex-S1.zip and http://exon.niaid.nih.gov/transcriptome/C_lectularius/S2/Cimex-S2.xls PMID:20441151

Insight into the Sialome of the Bed Bug, Cimex lectularius.

PubMed

Francischetti, Ivo M B; Calvo, Eric; Andersen, John F; Pham, Van M; Favreau, Amanda J; Barbian, Kent D; Romero, Alvaro; Valenzuela, Jesus G; Ribeiro, José M C

2010-08-06

The evolution of insects to a blood diet leads to the development of a saliva that antagonizes their hosts' hemostasis and inflammation. Hemostasis and inflammation are redundant processes, and thus a complex salivary potion composed of dozens or near 100 different polypeptides is commonly found by transcriptome or proteome analysis of these organisms. Several insect orders or families evolved independently to hematophagy, creating unique salivary potions in the form of novel pharmacological use of endogenous substances and in the form of unique proteins not matching other known proteins, these probably arriving by fast evolution of salivary proteins as they evade their hosts' immune response. In this work we present a preliminary description of the sialome (from the Greek Sialo = saliva) of the common bed bug Cimex lectularius, the first such work from a member of the Cimicidae family. This manuscript is a guide for the supplemental database files http://exon.niaid.nih.gov/transcriptome/C_lectularius/S1/Cimex-S1.zip and http://exon.niaid.nih.gov/transcriptome/C_lectularius/S2/Cimex-S2.xls.

Modelling and analysis of the wetting characteristics of ink for display applications with the surface evolution technique

NASA Astrophysics Data System (ADS)

Shin, Dong-Youn; Brakke, Kenneth A.

2009-06-01

Piezo drop-on-demand inkjet printing technology has attracted the attention of display industries for the production of colour filters for thin film transistor liquid crystal displays (TFT LCD) because of the opportunity of reducing manufacturing cost. Colourant ink droplets ejected from inkjet nozzles selectively fill subpixels surrounded with black matrix (BM). Surface energy differences between the glass substrate and the BM generally guide this ink filling process. This colourant ink filling process, however, results from the complex hydrodynamic interaction of ink with the substrate and the BM. Neither computationally expensive numerical methods nor time and cost expensive experiments are suitable for the derivation of optimum surface conditions at the early development stage. In this study, a more concise surface evolution technique is proposed and ways to find the optimum surface conditions for the fabrication of TFT LCD colour filters and polymer light emitting devices are discussed, which might be useful for chemists and developers of ink and BM material, as well as for process engineers in display industries.

Career Education Resource Guide for Biology. Working Draft.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge.

The resource guide integrates learning activities in biological science with an exploration of careers in biology or related fields. The materials are divided into seven units: tools of the scientist, basis for life, diversity (protists, plants, animals), structure and function, continuity (reproduction, development, and genetics), evolution, and…

Creating Professional Development School Partnerships. A Resource Guide.

ERIC Educational Resources Information Center

Teitel, Lee; Del Prete, Tom

This three-part guide presents information and recommendations from the Massachusetts Professional Development School Network Steering Committee on how to develop a professional development school (PDS) partnership. Part 1 defines the PDS concept, presents a brief background account of its evolution, and discusses its potential for simultaneously…

Guide to Federal Resources for the Developmentally Disabled.

ERIC Educational Resources Information Center

Russem, Wendy, Ed.; And Others

The guide presents information on available federal resources to improve services for developmentally disabled persons. An introductory chapter provides an overview of the creation and evolution of the Developmental Disabilities Program. Chapter two focuses on federal funding and appropriations, including methods of awarding grants and contracts.…

Cosmic evolution: the context for astrobiology and its cultural implications

NASA Astrophysics Data System (ADS)

Dick, Steven J.

2012-10-01

Astrobiology must be seen in the context of cosmic evolution, the 13.7 billion-year master narrative of the universe. The idea of an evolving universe dates back only to the 19th century, and became a guiding principle for astronomical research only in the second half of the 20th century. The modern synthesis in evolutionary biology hastened the acceptance of the idea in its cosmic setting, as did the confirmation of the Big Bang theory for the origin of the universe. NASA programmes such as Origins incorporated it as a guiding principle. Cosmic evolution encompasses physical, biological and cultural evolution, and may result in a physical, biological or postbiological universe, each with its own implications for long-term human destiny, and each imbuing the meaning of life with different values. It has the status of an increasingly accepted worldview that is beginning to have a profound effect not only in science but also in religion and philosophy.

Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms

PubMed Central

2016-01-01

A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large—but not intermediate-sized—populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations. PMID:27923053

Accelerated Evolution in the Death Galaxy

NASA Astrophysics Data System (ADS)

Austin, Robert; Tung, Chih-Kuan; Gong, Xiu-Quing; Lambert, Guillaume; Liao, David

2010-03-01

We recall 4 main guiding principles of evolution: 1) instability of defections, 2) stress induced non-random mutations, 3) genetic heterogeneity, and 4) fragmented populations. Our previous preliminary experiments have been relatively simple 1-D stress experiments. We are proceeding with 2-D experiments whose design is guided by these principles. Our new experiment we have dubbed the Death Galaxy because of it's use of these design principles. The ``galaxy'' name comes from the fact that the structure is designed as an interconnected array of micro-ecologies, these micro-ecologies are similar to the stars that comprise an astronomical galaxy, and provide the fragmented small populations. A gradient of the antibiotic Cipro is introduced across the galaxy, and we will present results which show how bacterial evolution resulting in resistance to Cipro is accelerated by the physics principles underlying the device.

A Teachers' Guide to the Whales of the Gulf of Maine.

ERIC Educational Resources Information Center

Elk, Catherine Kiorpes; Lignell, Kathleen, Ed.

This guide provides: (1) background information for teachers on whales; (2) 10 interdisciplinary activities; (3) teacher resources; (4) a bibliography; and (5) "pocket materials." Topic areas addressed in the first section include evolution and adaptation to an aquatic environment, diversity of whales, functional anatomy of feeding and…

A complex guided spectral transform Lanczos method for studying quantum resonance states

DOE PAGES

Yu, Hua-Gen

2014-12-28

A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos (cFOL) polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the originalmore » Hamiltonian in the spectral range of interest. Therefore the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO₂, and compared to previous calculations.« less

An analysis of microsystems development at Sandia National Laboratories

NASA Astrophysics Data System (ADS)

Herrera, Gilbert V.; Myers, David R.

2011-06-01

While Sandia initially was motivated to investigate emergent microsystem technology to miniaturize existing macroscale structures, present designs embody innovative approaches that directly exploit the fundamentally different material properties of a new technology at the micro- and nano-scale. Direct, hands-on experience with the emerging technology gave Sandia engineers insights that not only guided the evolution of the technology but also enabled them to address new applications that enlarged the customer base for the new technology. Sandia's early commitment to develop complex microsystems demonstrated the advantages that early adopters gain by developing an extensive design and process tool kit and a shared awareness of multiple approaches to achieve the multiple goals. As with any emergent technology, Sandia's program benefited from interactions with the larger technical community. However, custom development followed a spiral path of direct trial-and-error experience, analysis, quantification of materials properties at the micro- and nano-scale, evolution of design tools and process recipes, and an understanding of reliability factors and failure mechanisms even in extreme environments. The microsystems capability at Sandia relied on three key elements. The first was people: a mix of mechanical and semiconductor engineers, chemists, physical scientists, designers, and numerical analysts. The second was a unique facility that enabled the development of custom technologies without contaminating mainline product deliveries. The third was the arrival of specialized equipment as part of a Cooperative Research And Development Agreement (CRADA) enabled by the National Competitiveness Technology Transfer Act of 1989. Underpinning all these, the program was guided and sustained through the research and development phases by accomplishing intermediate milestones addressing direct mission needs.

The Development of Man and His Culture: Old World Prehistory. Grade 5. Teacher Guide [And] Pupil Text [And] Pupil Guide [And] Teacher Background Material [And] A Sequential Curriculum in Anthropology. Test Form 5, Composite Form for Pre- and Post-Test. Revised, January 1968. Publications No. 25, 31, 23, 24 and 43.

ERIC Educational Resources Information Center

Potterfield, James E.; And Others

This social studies unit includes a teaching guide, student text, study guide, teacher background material, and composite pretest/posttest covering archaeological methods, evolution, fossils and man, and development of culture during the prehistoric periods in the Old World. It is part of the Anthropology Curriculum Project and is designed for…

The evolution of genital complexity and mating rates in sexually size dimorphic spiders.

PubMed

Kuntner, Matjaž; Cheng, Ren-Chung; Kralj-Fišer, Simona; Liao, Chen-Pan; Schneider, Jutta M; Elgar, Mark A

2016-11-09

Genital diversity may arise through sexual conflict over polyandry, where male genital features function to manipulate female mating frequency against her interest. Correlated genital evolution across animal groups is consistent with this view, but a link between genital complexity and mating rates remains to be established. In sexually size dimorphic spiders, golden orbweaving spiders (Nephilidae) males mutilate their genitals to form genital plugs, but these plugs do not always prevent female polyandry. In a comparative framework, we test whether male and female genital complexity coevolve, and how these morphologies, as well as sexual cannibalism, relate to the evolution of mating systems. Using a combination of comparative tests, we show that male genital complexity negatively correlates with female mating rates, and that levels of sexual cannibalism negatively correlate with male mating rates. We also confirm a positive correlation between male and female genital complexity. The macroevolutionary trajectory is consistent with a repeated evolution from polyandry to monandry coinciding with the evolution towards more complex male genitals. These results are consistent with the predictions from sexual conflict theory, although sexual conflict may not be the only mechanism responsible for the evolution of genital complexity and mating systems. Nevertheless, our comparative evidence suggests that in golden orbweavers, male genital complexity limits female mating rates, and sexual cannibalism by females coincides with monogyny.

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation

PubMed Central

Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

2017-01-01

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA–DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA–DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs. PMID:28484024

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation.

PubMed

Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

2017-05-23

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA-DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA-DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs.

Evolution of complex adaptations in molecular systems

PubMed Central

Pál, Csaba; Papp, Balázs

2017-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular ’springboards’, such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. PMID:28782044

Power-induced evolution and increased dimensionality of nonlinear modes in reorientational soft matter.

PubMed

Laudyn, Urszula A; Jung, Paweł S; Zegadło, Krzysztof B; Karpierz, Miroslaw A; Assanto, Gaetano

2014-11-15

We demonstrate the evolution of higher order one-dimensional guided modes into two-dimensional solitary waves in a reorientational medium. The observations, carried out at two different wavelengths in chiral nematic liquid crystals, are in good agreement with a simple nonlocal nonlinear model.

Reflexions sur L'Evolution de L'Enseignement de la Biologie en Afrique.

ERIC Educational Resources Information Center

Sasson, A.

1980-01-01

Reviews the main stages of the evolution of biology teaching in Africa. Discusses the UNESCO pilot project, the teaching aids produced for English- and French-speaking countries of Africa, and the "Teacher's Guide on the Biology of Human Populations" and projects needs for further assistance. (CS)

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

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

PubMed Central

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

2013-01-01

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

Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.

PubMed

Conlin, Peter L; Chandler, Josephine R; Kerr, Benjamin

2014-10-01

In this review, we demonstrate how game theory can be a useful first step in modeling and understanding interactions among bacteria that produce and resist antibiotics. We introduce the basic features of evolutionary game theory and explore model microbial systems that correspond to some classical games. Each game discussed defines a different category of social interaction with different resulting population dynamics (exclusion, coexistence, bistability, cycling). We then explore how the framework can be extended to incorporate some of the complexity of natural microbial communities. Overall, the game theoretical perspective helps to guide our expectations about the evolution of some forms of antibiotic resistance and production because it makes clear the precise nature of social interaction in this context. Copyright © 2014 Elsevier Ltd. All rights reserved.

Washington: Symbol and City. An Educator's Guide to the Exhibit.

ERIC Educational Resources Information Center

Toby Levine Communications, Inc., Bethesda, MD.

Designed to make a visit to Washington, D.C. a successful learning experience for students by helping them understand the evolution of the city into what it is today, this teacher's guide presents themes and activities to accommodate many teaching and learning styles. Three sections of activities explore how the built environment symbolizes…

Consciousness of Unification: The Mind-Matter Phallacy Bites the Dust

NASA Astrophysics Data System (ADS)

Beichler, James E.

A complete theoretical model of how consciousness arises in neural nets can be developed based on a mixed quantum/classical basis. Both mind and consciousness are multi-leveled scalar and vector electromagnetic complexity patterns, respectively, which emerge within all living organisms through the process of evolution. Like life, the mind and consciousness patterns extend throughout living organisms (bodies), but the neural nets and higher level groupings that distinguish higher levels of consciousness only exist in the brain so mind and consciousness have been traditionally associated with the brain alone. A close study of neurons and neural nets in the brain shows that the microtubules within axons are classical bio-magnetic inductors that emit and absorb electromagnetic pulses from each other. These pulses establish interference patterns that influence the quantized vector potential patterns of interstitial water molecules within the neurons as well as create the coherence within neurons and neural nets that scientists normally associate with more complex memories, thought processes and streams of thought. Memory storage and recall are guided by the microtubules and the actual memory patterns are stored as magnetic vector potential complexity patterns in the points of space at the quantum level occupied by the water molecules. This model also accounts for the plasticity of the brain and implies that mind and consciousness, like life itself, are the result of evolutionary processes. However, consciousness can evolve independent of an organism's birth genetics once it has evolved by normal bottom-up genetic processes and thus force a new type of top-down evolution on living organisms and species as a whole that can be explained by expanding the laws of thermodynamics to include orderly systems.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards physical principles of biological evolution

NASA Astrophysics Data System (ADS)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.

An integrated zircon geochronological and geochemical investigation into the Miocene plutonic evolution of the Cyclades, Aegean Sea, Greece: part 2—geochemistry

NASA Astrophysics Data System (ADS)

Bolhar, Robert; Ring, Uwe; Kemp, Anthony I. S.; Whitehouse, Martin J.; Weaver, Steve D.; Woodhead, Jon D.; Uysal, I. Tonguc; Turnbull, Rose

2012-12-01

Zircons from 14 compositionally variable granitic rocks were examined in detail using CL image-guided micro-analysis to unravel the complex magmatic history above the southward retreating Hellenic subduction zone system in the Aegean Sea. Previously published U-Pb ages document an episodic crystallisation history from 17 to 11 Ma, with peraluminous (S-type) granitic rocks systematically older than closely associated metaluminous (I-type) granitic rocks. Zircon O- and Hf isotopic data, combined with trace element compositions, are highly variable within and between individual samples, indicative of open-system behaviour involving mantle-derived melts and evolved supracrustal sources. Pronounced compositional and thermal fluctuations highlight the role of magma mixing and mingling, in accord with field observations, and incremental emplacement of distinct melt batches coupled with variable degrees of crustal assimilation. In the course of partial fusion, more fertile supracrustal sources dominated in the earlier stages of Aegean Miocene magmatism, consistent with systematically older crystallisation ages of peraluminous granitic rocks. Differences between zircon saturation and crystallisation temperatures (deduced from zircon Ti concentrations), along with multimodal crystallisation age spectra for individual plutons, highlight the complex and highly variable physico-compositional and thermal evolution of silicic magma systems. The transfer of heat and juvenile melts from the mantle varied probably in response to episodic rollback of the subducting lithospheric slab, as suggested by punctuated crystallisation age spectra within and among individual granitic plutons.

A catalyst for system change: a case study of child health network formation, evolution and sustainability in Canada.

PubMed

McPherson, Charmaine; Ploeg, Jenny; Edwards, Nancy; Ciliska, Donna; Sword, Wendy

2017-02-01

The purpose of this study was to examine key processes and supportive and inhibiting factors involved in the development, evolution, and sustainability of a child health network in rural Canada. This study contributes to a relatively new research agenda aimed at understanding inter-organizational and cross-sectoral health networks. These networks encourage collaboration focusing on complex issues impacting health - issues that individual agencies cannot effectively address alone. This paper presents an overview of the study findings. An explanatory qualitative case study approach examined the Network's 13-year lifespan. Data sources were documents and Network members, including regional and 71 provincial senior managers from 11 child and youth service sectors. Data were collected through 34 individual interviews and a review of 127 documents. Interview data were analyzed using framework analysis methods; Prior's approach guided document analysis. Three themes related to network development, evolution and sustainability were identified: (a) Network relationships as system triggers, (b) Network-mediated system responsiveness, and (c) Network practice as political. Study findings have important implications for network organizational development, collaborative practice, interprofessional education, public policy, and public system responsiveness research. Findings suggest it is important to explicitly focus on relationships and multi-level socio-political contexts, such as supportive policy environments, in understanding health networks. The dynamic interplay among the Network members; central supportive and inhibiting factors; and micro-, meso-, and macro-organizational contexts was identified.

Re-Engaging At-Risk Youth through Art -- The Evolution Program

ERIC Educational Resources Information Center

Brown, Robert; Jeanneret, Neryl

2015-01-01

Many studies have highlighted the capacity of community arts programs to re-engage those young people considered at-risk of disconnection from future education and/or employment. "Evolution" is an artist-guided visual arts program established for young people challenged by mental health and social issues that aims to foster re-engagement…

Revisiting the Great Lessons. Spotlight: Cosmic Education.

ERIC Educational Resources Information Center

Chattin-McNichols, John

2002-01-01

Considers the role of the Great Lessons--formation of the universe, evolution of life, evolution of humans, and discovery of language and mathematics--in the Montessori elementary curriculum. Discusses how the Great Lessons guide and organize the curriculum, as well as the timing of the lessons across the 6-12 age span. (JPB)

Low-Resolution Vision-at the Hub of Eye Evolution.

PubMed

Nilsson, Dan-E; Bok, Michael J

2017-11-01

Simple roles for photoreception are likely to have preceded more demanding ones such as vision. The driving force behind this evolution is the improvement and elaboration of animal behaviors using photoreceptor input. Because the basic role for all senses aimed at the external world is to guide behavior, we argue here that understanding this "behavioral drive" is essential for unraveling the evolutionary past of the senses. Photoreception serves many different types of behavior, from simple shadow responses to visual communication. Based on minimum performance requirements for different types of tasks, photoreceptors have been argued to have evolved from non-directional receptors, via directional receptors, to low-resolution vision, and finally to high-resolution vision. Through this sequence, the performance requirements on the photoreceptors have gradually changed from broad to narrow angular sensitivity, from slow to fast response, and from low to high contrast sensitivity during the evolution from simple to more advanced and demanding behaviors. New behaviors would only evolve if their sensory performance requirements to some degree overlap with the requirements of already existing behaviors. This need for sensory "performance continuity" must have determined the order by which behaviors have evolved and thus been an important factor guiding animal evolution. Naturally, new behaviors are most likely to evolve from already existing behaviors with similar neural processing needs and similar motor responses, pointing to "neural continuity" as another guiding factor in sensory evolution. Here we use these principles to derive an evolutionary tree for behaviors driven by photoreceptor input. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Four-dimensional computed tomography based respiratory-gated radiotherapy with respiratory guidance system: analysis of respiratory signals and dosimetric comparison.

PubMed

Lee, Jung Ae; Kim, Chul Yong; Yang, Dae Sik; Yoon, Won Sup; Park, Young Je; Lee, Suk; Kim, Young Bum

2014-01-01

To investigate the effectiveness of respiratory guidance system in 4-dimensional computed tomography (4 DCT) based respiratory-gated radiation therapy (RGRT) by comparing respiratory signals and dosimetric analysis of treatment plans. The respiratory amplitude and period of the free, the audio device-guided, and the complex system-guided breathing were evaluated in eleven patients with lung or liver cancers. The dosimetric parameters were assessed by comparing free breathing CT plan and 4 DCT-based 30-70% maximal intensity projection (MIP) plan. The use of complex system-guided breathing showed significantly less variation in respiratory amplitude and period compared to the free or audio-guided breathing regarding the root mean square errors (RMSE) of full inspiration (P = 0.031), full expiration (P = 0.007), and period (P = 0.007). The dosimetric parameters including V(5 Gy), V(10 Gy), V(20 Gy), V(30 Gy), V(40 Gy), and V(50 Gy) of normal liver or lung in 4 DCT MIP plan were superior over free breathing CT plan. The reproducibility and regularity of respiratory amplitude and period were significantly improved with the complex system-guided breathing compared to the free or the audio-guided breathing. In addition, the treatment plan based on the 4D CT-based MIP images acquired with the complex system guided breathing showed better normal tissue sparing than that on the free breathing CT.

Field Guide to Fossils. Earth Science Curriculum Project Pamphlet Series PS-4.

ERIC Educational Resources Information Center

Beerbower, James R.

This guide introduces the study of fossils and means through which this study may provide clues to ancient environments and geology. Presented are discussions about the origin of many types of organisms, origin of organic communities, evolution, and extinction of species. Suggestions are provided for likely collection sites, methods of collection,…

Reporter's Guide: Drugs, Drug Abuse Issues, Resources.

ERIC Educational Resources Information Center

Parachini, Allan

The purposes of this booklet are: (1) to serve as a commentary on the evolution, state and problems of drug reporting; (2) to make the journalist aware of the prominent issues and some of the major misconceptions common among reporters, readers and/or listeners; (3) to serve as a guide to the fundamental background literature of the field; (4) to…

BioCore Guide: A Tool for Interpreting the Core Concepts of Vision and Change for Biology Majors

ERIC Educational Resources Information Center

Brownell, Sara E.; Freeman, Scott; Wenderoth, Mary Pat; Crowe, Alison J.

2014-01-01

"Vision and Change in Undergraduate Biology Education" outlined five core concepts intended to guide undergraduate biology education: 1) evolution; 2) structure and function; 3) information flow, exchange, and storage; 4) pathways and transformations of energy and matter; and 5) systems. We have taken these general recommendations and…

Hybrid surgical guidance based on the integration of radionuclear and optical technologies

PubMed Central

Valdés-Olmos, Renato; Buckle, Tessa; Vidal-Sicart, Sergi

2016-01-01

With the evolution of imaging technologies and tracers, the applications for nuclear molecular imaging are growing rapidly. For example, nuclear medicine is increasingly being used to guide surgical resections in complex anatomical locations. Here, a future workflow is envisioned that uses a combination of pre-operative diagnostics, navigation and intraoperative guidance. Radioguidance can provide means for pre-operative and intraoperative identification of “hot” lesions, forming the basis of a virtual data set that can be used for navigation. Luminescence guidance has shown great potential in the intraoperative setting by providing optical feedback, in some cases even in real time. Both of these techniques have distinct drawbacks, which include inaccuracy in areas that contain a background signal (radioactivity) or a limited degree of signal penetration (luminescence). We, and others, have reasoned that hybrid/multimodal approaches that integrate the use of these complementary modalities may help overcome their individual weaknesses. Ultimately, this will lead to advancement of the field of interventional molecular imaging/image-guided surgery. In this review, an overview of clinically applied hybrid surgical guidance technologies is given, whereby the focus is placed on tracers and hardware. PMID:26943463

Hydrogen storage and evolution catalysed by metal hydride complexes.

PubMed

Fukuzumi, Shunichi; Suenobu, Tomoyoshi

2013-01-07

The storage and evolution of hydrogen are catalysed by appropriate metal hydride complexes. Hydrogenation of carbon dioxide by hydrogen is catalysed by a [C,N] cyclometalated organoiridium complex, [Ir(III)(Cp*)(4-(1H-pyrazol-1-yl-κN(2))benzoic acid-κC(3))(OH(2))](2)SO(4) [Ir-OH(2)](2)SO(4), under atmospheric pressure of H(2) and CO(2) in weakly basic water (pH 7.5) at room temperature. The reverse reaction, i.e., hydrogen evolution from formate, is also catalysed by [Ir-OH(2)](+) in acidic water (pH 2.8) at room temperature. Thus, interconversion between hydrogen and formic acid in water at ambient temperature and pressure has been achieved by using [Ir-OH(2)](+) as an efficient catalyst in both directions depending on pH. The Ir complex [Ir-OH(2)](+) also catalyses regioselective hydrogenation of the oxidised form of β-nicotinamide adenine dinucleotide (NAD(+)) to produce the 1,4-reduced form (NADH) under atmospheric pressure of H(2) at room temperature in weakly basic water. In weakly acidic water, the complex [Ir-OH(2)](+) also catalyses the reverse reaction, i.e., hydrogen evolution from NADH to produce NAD(+) at room temperature. Thus, interconversion between NADH (and H(+)) and NAD(+) (and H(2)) has also been achieved by using [Ir-OH(2)](+) as an efficient catalyst and by changing pH. The iridium hydride complex formed by the reduction of [Ir-OH(2)](+) by H(2) and NADH is responsible for the hydrogen evolution. Photoirradiation (λ > 330 nm) of an aqueous solution of the Ir-hydride complex produced by the reduction of [Ir-OH(2)](+) with alcohols resulted in the quantitative conversion to a unique [C,C] cyclometalated Ir-hydride complex, which can catalyse hydrogen evolution from alcohols in a basic aqueous solution (pH 11.9). The catalytic mechanisms of the hydrogen storage and evolution are discussed by focusing on the reactivity of Ir-hydride complexes.

Evolution of disorder in Mediator complex and its functional relevance

PubMed Central

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K.

2016-01-01

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. PMID:26590257

Comparing wave shoaling methods used in large-scale coastal evolution modeling

NASA Astrophysics Data System (ADS)

Limber, P. W.; Adams, P. N.; Murray, A.

2013-12-01

A variety of methods are available to simulate wave propagation from the deep ocean to the surf zone. They range from simple and computationally fast (e.g. linear wave theory applied to shore-parallel bathymetric contours) to complicated and computationally intense (e.g., Delft's ';Simulating WAves Nearshore', or SWAN, model applied to complex bathymetry). Despite their differences, the goal of each method is the same with respect to coastline evolution modeling: to link offshore waves with rates of (and gradients in) alongshore sediment transport. Choosing a shoaling technique for modeling coastline evolution should be partly informed by the spatial and temporal scales of the model, as well as the model's intent (is it simulating a specific coastline, or exploring generic coastline dynamics?). However, the particular advantages and disadvantages of each technique, and how the advantages/disadvantages vary over different model spatial and temporal scales, are not always clear. We present a wave shoaling model that simultaneously computes breaking wave heights and angles using three increasingly complex wave shoaling routines: the most basic approach assuming shore-parallel bathymetric contours, a wave ray tracing method that includes wave energy convergence and divergence and non-shore-parallel contours, and a spectral wave model (SWAN). Initial results show reasonable agreement between wave models along a flat shoreline for small (1 m) wave heights, low wave angles (0 to 10 degrees), and simple bathymetry. But, as wave heights and angles increase, bathymetry becomes more variable, and the shoreline shape becomes sinuous, the model results begin to diverge. This causes different gradients in alongshore sediment transport between model runs employing different shoaling techniques and, therefore, different coastline behavior. Because SWAN does not approximate wave breaking (which drives alongshore sediment transport) we use a routine to extract grid cells from SWAN output where wave height is approximately one-half of the water depth (a standard wave breaking threshold). The goal of this modeling exercise is to understand under what conditions a simple wave model is sufficient for simulating coastline evolution, and when using a more complex shoaling routine can optimize a coastline model. The Coastline Evolution Model (CEM; Ashton and Murray, 2006) is used to show how different shoaling routines affect modeled coastline behavior. The CEM currently includes the most basic wave shoaling approach to simulate cape and spit formation. We will instead couple it to SWAN, using the insight from the comprehensive wave model (above) to guide its application. This will allow waves transformed over complex bathymetry, such as cape-associated shoals and ridges, to be input for the CEM so that large-scale coastline behavior can be addressed in less idealized environments. Ashton, A., and Murray, A.B., 2006, High-angle wave instability and emergent shoreline shapes: 1. Modeling of sand waves, flying spits, and capes: Journal of Geophysical Research, v. 111, p. F04011, doi:10.1029/2005JF000422.

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

PubMed Central

Nithianantharajah, J.; Komiyama, N.H.; McKechanie, A.; Johnstone, M.; Blackwood, D. H.; St Clair, D.; Emes, R.D.; van de Lagemaat, L. N.; Saksida, L.M.; Bussey, T.J.; Grant, S.G.N.

2014-01-01

The origins and evolution of higher cognitive functions including complex forms of learning, attention and executive functions are unknown. A potential mechanism driving the evolution of vertebrate cognition early in the vertebrate lineage (550 My ago) was genome duplication and subsequent diversification of postsynaptic genes. Here we report the first genetic analysis of a vertebrate gene family in cognitive functions measured using computerized touchscreens. Comparison of mice carrying mutations in all four Dlg paralogs show simple associative learning required Dlg4, while Dlg2 and Dlg3 diversified to play opposing roles in complex cognitive processes. Exploiting the translational utility of touchscreens in humans and mice, testing Dlg2 mutations in both species showed Dlg2’s role in complex learning, cognitive flexibility and attention has been highly conserved over 100 My. Dlg family mutations underlie psychiatric disorders suggesting genome evolution expanded the complexity of vertebrate cognition at the cost of susceptibility to mental illness. PMID:23201973

Variety and evolution of American endoscopic image management and recording systems.

PubMed

Korman, L Y

1996-03-01

The rapid evolution of computing technology has and will continue to alter the practice of gastroenterology and gastrointestinal endoscopy. Development of communication standards for text, images, and security systems will be necessary for medicine to take advantage of high-speed computing and communications. Professional societies can have an important role in guiding the development process.

Volcanoes: Where and Why? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

The Evolution of the Krebs Cycle: A Promising Subject for Meaningful Learning of Biochemistry

ERIC Educational Resources Information Center

da Costa, Caetano; Galembeck, Eduardo

2016-01-01

Evolution has been recognized as a key concept for biologists. To enhance comprehension and motivate biology undergraduates for the contents of central energetic metabolism, we addressed the Krebs cycle structure and functions in an evolutionary view. To this end, we created a study guide that contextualizes the emergence of the cyclic pathway, in…

Which Way is North? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Quake Estate (board game). Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

A new dynamic 3D virtual methodology for teaching the mechanics of atrial septation as seen in the human heart.

PubMed

Schleich, Jean-Marc; Dillenseger, Jean-Louis; Houyel, Lucile; Almange, Claude; Anderson, Robert H

2009-01-01

Learning embryology remains difficult, since it requires understanding of many complex phenomena. The temporal evolution of developmental events has classically been illustrated using cartoons, which create difficulty in linking spatial and temporal aspects, such correlation being the keystone of descriptive embryology. We synthesized the bibliographic data from recent studies of atrial septal development. On the basis of this synthesis, consensus on the stages of atrial septation as seen in the human heart has been reached by a group of experts in cardiac embryology and pediatric cardiology. This has permitted the preparation of three-dimensional (3D) computer graphic objects for the anatomical components involved in the different stages of normal human atrial septation. We have provided a virtual guide to the process of normal atrial septation, the animation providing an appreciation of the temporal and morphologic events necessary to separate the systemic and pulmonary venous returns. We have shown that our animations of normal human atrial septation increase significantly the teaching of the complex developmental processes involved, and provide a new dynamic for the process of learning.

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms.

PubMed

Yedid, G; Ofria, C A; Lenski, R E

2008-09-01

Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution's most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate 'replay' populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

Time evolution of complexity in Abelian gauge theories

NASA Astrophysics Data System (ADS)

Hashimoto, Koji; Iizuka, Norihiro; Sugishita, Sotaro

2017-12-01

Quantum complexity is conjectured to probe inside of black hole horizons (or wormholes) via gauge gravity correspondence. In order to have a better understanding of this correspondence, we study time evolutions of complexities for Abelian pure gauge theories. For this purpose, we discretize the U (1 ) gauge group as ZN and also the continuum spacetime as lattice spacetime, and this enables us to define a universal gate set for these gauge theories and to evaluate time evolutions of the complexities explicitly. We find that to achieve a large complexity ˜exp (entropy), which is one of the conjectured criteria necessary to have a dual black hole, the Abelian gauge theory needs to be maximally nonlocal.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

PubMed

Kapheim, Karen M; Pan, Hailin; Li, Cai; Salzberg, Steven L; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M; Hudson, Matthew E; Venkat, Aarti; Fischman, Brielle J; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D; Kemp, William P; Bosch, Jordi; Waterhouse, Robert M; Zdobnov, Evgeny M; Stolle, Eckart; Kraus, F Bernhard; Helbing, Sophie; Moritz, Robin F A; Glastad, Karl M; Hunt, Brendan G; Goodisman, Michael A D; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D; Barribeau, Seth M; Johnson, Reed M; Massey, Jonathan H; Southey, Bruce R; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J Spencer; Hanrahan, Shawn J; Kocher, Sarah D; Wang, Jun; Robinson, Gene E; Zhang, Guojie

2015-06-05

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. Copyright © 2015, American Association for the Advancement of Science.

Complexity in cancer stem cells and tumor evolution: Toward precision medicine.

PubMed

La Porta, Caterina A M; Zapperi, Stefano

2017-06-01

In this review, we discuss recent advances on the plasticity of cancer stem cells and highlight their relevance to understand the metastatic process and to guide therapeutic interventions. Recent results suggest that the strict hierarchical structure of cancer cell populations advocated by the cancer stem cell model must be reconsidered since the depletion of cancer stem cells leads the other tumor cells to switch back into the cancer stem cell phenotype. This plasticity has important implications for metastasis since migrating cells do not need to be cancer stem cells in order to seed a metastasis. We also discuss the important role of the immune system and the microenvironment in modulating phenotypic switching and suggest possible avenues to exploit our understanding of this process to develop an effective strategy for precision medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

The reemergence of the trampoline as a recreational activity and competitive sport.

PubMed

Esposito, Paul W; Esposito, Lisa M

2009-01-01

The recreational use of trampolines is widespread and growing rapidly around the world. The reported incidence of significant injuries continues to increase despite more than three decades of attempts to educate the public on the inherent dangers of trampolines and appropriate safety rules for their use. Competitive trampolining also is growing, although there is scant medical literature related to training issues and injuries to assist the physician in guiding and treating these athletes. It is anticipated that with the increased use of trampolines and with the evolution of ever more complex competitive techniques and routines, the potential for catastrophic injuries in competition will increase. This article discusses awareness of the risks and attempts to mitigate injuries. It remains unclear, from an injury risk standpoint, whether trampolines can be used with an acceptable degree of safety.

Analysis of non-Gaussian laser mode guidance and evolution in leaky plasma channels

NASA Astrophysics Data System (ADS)

Djordjevic, Blagoje; Benedetti, Carlo; Schroeder, Carl; Esarey, Eric; Leemans, Wim

2016-10-01

The evolution and propagation of a non-Gaussian laser pulse under varying circumstances, including a typical matched parabolic channel as well as leaky channels, are investigated. It has previously been shown for a Gaussian pulse that matched guiding can be achieved using parabolic plasma channels. In the low power regime, it can be shown directly that for multi-mode pulses there is significant transverse beating. Given the adverse behavior of non-Gaussian pulses in traditional guiding designs, we examine the use of leaky channels to filter out higher modes as a means of optimizing laser conditions. The interaction between different modes can have an adverse effect on the laser pulse as it propagates through the primary channel. To improve guiding of the pulse we propose using leaky channels. Realistic plasma channel profiles are considered. Higher order mode content is lost through the leaky channel, while the fundamental mode remains well-guided. This is demonstrated using both numerical simulations as well as the source-dependent Laguerre-Gaussian modal expansion. In conclusion, an idealized plasma lens based on leaky channels is found to filter out the higher order modes and leave a near-Gaussian profile before the pulse enters the primary channel.

Geomorphology and landscape organization of a northern peatland complex

NASA Astrophysics Data System (ADS)

Richardson, M. C.

2012-12-01

The geomorphic evolution of northern peatlands is governed by complex ecohydrological feedback mechanisms and associated hydro-climatic drivers. For example, prevailing models of bog development (i.e. Ingram's groundwater mounding hypothesis and variants) attempt to explicitly link bog dome characteristics to the regional climate based on analytical and numerical models of lateral groundwater flow and the first-order control of water table position on rates of peat accumulation. In this talk I will present new results from quantitative geomorphic analyses of a northern peatland complex at the De Beers Victor diamond mine site in the Hudson Bay Lowlands of northern Ontario. This work capitalizes on spatially-extensive, high-resolution topographic (LiDAR) data to rigorously test analytical and numerical models of bog dome development in this landscape. The analysis and discussion are then expanded beyond individual bog formations to more broadly consider ecohydrological drivers of landscape organization, with implications for understanding and modeling catchment-scale runoff response. Results show that in this landscape, drainage patterns exhibit relatively well-organized characteristics consistent with observed runoff responses in six gauged research catchments. Interpreted together, the results of these geomorphic and hydrologic analyses help refine our understanding of water balance partitioning among different landcover types within northern peatland complexes. These findings can be used to help guide the development of appropriate numerical model structures for hydrologic prediction in ungauged peatland basins of northern Canada.

Complex systems as lenses on learning and teaching

NASA Astrophysics Data System (ADS)

Hurford, Andrew C.

From metaphors to mathematized models, the complexity sciences are changing the ways disciplines view their worlds, and ideas borrowed from complexity are increasingly being used to structure conversations and guide research on teaching and learning. The purpose of this corpus of research is to further those conversations and to extend complex systems ideas, theories, and modeling to curricula and to research on learning and teaching. A review of the literatures of learning and of complexity science and a discussion of the intersections between those disciplines are provided. The work reported represents an evolving model of learning qua complex system and that evolution is the result of iterative cycles of design research. One of the signatures of complex systems is the presence of scale invariance and this line of research furnishes empirical evidence of scale invariant behaviors in the activity of learners engaged in participatory simulations. The offered discussion of possible causes for these behaviors and chaotic phase transitions in human learning favors real-time optimization of decision-making as the means for producing such behaviors. Beyond theoretical development and modeling, this work includes the development of teaching activities intended to introduce pre-service mathematics and science teachers to complex systems. While some of the learning goals for this activity focused on the introduction of complex systems as a content area, we also used complex systems to frame perspectives on learning. Results of scoring rubrics and interview responses from students illustrate attributes of the proposed model of complex systems learning and also how these pre-service teachers made sense of the ideas. Correlations between established theories of learning and a complex adaptive systems model of learning are established and made explicit, and a means for using complex systems ideas for designing instruction is offered. It is a fundamental assumption of this research and researcher that complex systems ideas and understandings can be appropriated from more complexity-developed disciplines and put to use modeling and building increasingly productive understandings of learning and teaching.

Evolution of complexity following a quantum quench in free field theory

NASA Astrophysics Data System (ADS)

Alves, Daniel W. F.; Camilo, Giancarlo

2018-06-01

Using a recent proposal of circuit complexity in quantum field theories introduced by Jefferson and Myers, we compute the time evolution of the complexity following a smooth mass quench characterized by a time scale δ t in a free scalar field theory. We show that the dynamics has two distinct phases, namely an early regime of approximately linear evolution followed by a saturation phase characterized by oscillations around a mean value. The behavior is similar to previous conjectures for the complexity growth in chaotic and holographic systems, although here we have found that the complexity may grow or decrease depending on whether the quench increases or decreases the mass, and also that the time scale for saturation of the complexity is of order δ t (not parametrically larger).

A Framework for Intentional Cultural Change

PubMed Central

Biglan, Anthony; Embry, Dennis D.

2013-01-01

We present a framework for a pragmatic science of cultural evolution. It is now possible for behavioral science to systematically influence the further evolution of cultural practices. As this science develops, it may become possible to prevent many of the problems affecting human wellbeing. By cultural practices, we refer to everything that humans do, above and beyond instinctual or unconditioned behaviors: not only art and literature, but also agriculture, manufacturing, recreation, war making, childrearing, science—everything. We can analyze cultural practices usefully in terms of the incidence and prevalence of individual behavior and group and organization actions. An effective science of intentional cultural evolution must guide efforts to influence the incidence and prevalence of individuals’ behaviors and the actions of groups and organizations. In this paper, we briefly sketch advances in scientific understanding of the influences on individual behavior. Then we describe principles that could guide efforts to influence groups and organizations. Finally, we discuss legitimate concerns about the use and misuse of a science for intentional cultural change. PMID:24363988

Darwinian evolution in the light of genomics

PubMed Central

Koonin, Eugene V.

2009-01-01

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

Evolution of disorder in Mediator complex and its functional relevance.

PubMed

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K

2016-02-29

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Continents and Ocean Basins: Floaters and Sinkers. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Deep Sea Trenches and Radioactive Water. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

When a Piece of a Continent Breaks Off. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Measuring Continental Drift: The Laser Ranging Experiment. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Drifting Continents and Wandering Poles. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

A Sea-Floor Mystery: Mapping Polarity Reversals. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Movement of the Pacific Ocean Floor. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Hot Spots in the Earth's Crust. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Iceland: The Case of the Splitting Personality. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Plate Boundaries and Earthquake Prediction. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Plotting the Shape of the Ocean Floor. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Drifting Continents and Magnetic Fields. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Why Does Sea Level Change? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

PubMed Central

Kroiss, Matthias; Schultz, Jörg; Wiesner, Julia; Chari, Ashwin; Sickmann, Albert; Fischer, Utz

2008-01-01

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction. PMID:18621711

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.

Orchid conservation: further links.

PubMed

Fay, Michael F

2016-07-01

Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here. The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Documentation & Condition Mapping for Restoration & Revitalisation of Historic Sheesh Mahal & Char Bagh Complex in Patiala (punjab), India

NASA Astrophysics Data System (ADS)

Dasgupta, S.

2017-08-01

Located in the Northern State of Punjab, the historic city of Patiala has always been a centre of culture in north India, and has seen the evolution of its own distinct style of architecture with Rajput and Mughal influences. The city is renowned for its rich architectural heritage, Music, Craft, Sports and Cuisine. The fourth Maharaja Narinder Singh was a great patron of art, architecture and music and it was during his time that several palaces like the Moti Bagh Palace, Sheesh Mahal and Banasur Bagh were designed followed by Baradari Palace. Later it was Maharaja Bhupinder Singh (1900-1938) who made Patiala State famous with his lavish lifestyle.This paper describes the process followed for Documentation and condition assessment of the historic Sheesh Mahal & Char Bagh Complex in order to restore and revitalise the palace building and the Mughal garden. The exercise included Archival research, Field surveys, Condition Mapping, inventories using traditional methods as well as GIS and preparation of restoration & conservation solutions along with post conservation management manual. The Major challenges encountered were identifying the correct documentation methodology for mapping as well as managing the large database generated on site. The Documentation and Mapping was used as a significant tool to guide towards the conservation and Management strategy of the complex.

Metabolic engineering to guide evolution - Creating a novel mode for L-valine production with Corynebacterium glutamicum.

PubMed

Schwentner, Andreas; Feith, André; Münch, Eugenia; Busche, Tobias; Rückert, Christian; Kalinowski, Jörn; Takors, Ralf; Blombach, Bastian

2018-03-06

Evolutionary approaches are often undirected and mutagen-based yielding numerous mutations, which need elaborate screenings to identify relevant targets. We here apply Metabolic engineering to Guide Evolution (MGE), an evolutionary approach evolving and identifying new targets to improve microbial producer strains. MGE is based on the idea to impair the cell's metabolism by metabolic engineering, thereby generating guided evolutionary pressure. It consists of three distinct phases: (i) metabolic engineering to create the evolutionary pressure on the applied strain followed by (ii) a cultivation phase with growth as straightforward screening indicator for the evolutionary event, and (iii) comparative whole genome sequencing (WGS), to identify mutations in the evolved strains, which are eventually re-engineered for verification. Applying MGE, we evolved the PEP and pyruvate carboxylase-deficient strain C. glutamicum Δppc Δpyc to grow on glucose as substrate with rates up to 0.31 ± 0.02 h -1 which corresponds to 80% of the growth rate of the wildtype strain. The intersection of the mutations identified by WGS revealed isocitrate dehydrogenase (ICD) as consistent target in three independently evolved mutants. Upon re-engineering in C. glutamicum Δppc Δpyc, the identified mutations led to diminished ICD activities and activated the glyoxylate shunt replenishing oxaloacetate required for growth. Intracellular relative quantitative metabolome analysis showed that the pools of citrate, isocitrate, cis-aconitate, and L-valine were significantly higher compared to the WT control. As an alternative to existing L-valine producer strains based on inactivated or attenuated pyruvate dehydrogenase complex, we finally engineered the PEP and pyruvate carboxylase-deficient C. glutamicum strains with identified ICD mutations for L-valine production by overexpression of the L-valine biosynthesis genes. Among them, C. glutamicum Δppc Δpyc ICD G407S (pJC4ilvBNCE) produced up to 8.9 ± 0.4 g L-valine L -1 , with a product yield of 0.22 ± 0.01 g L-valine per g glucose. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Environmental Influence on the Evolution of Morphological Complexity in Machines

PubMed Central

Auerbach, Joshua E.; Bongard, Josh C.

2014-01-01

Whether, when, how, and why increased complexity evolves in biological populations is a longstanding open question. In this work we combine a recently developed method for evolving virtual organisms with an information-theoretic metric of morphological complexity in order to investigate how the complexity of morphologies, which are evolved for locomotion, varies across different environments. We first demonstrate that selection for locomotion results in the evolution of organisms with morphologies that increase in complexity over evolutionary time beyond what would be expected due to random chance. This provides evidence that the increase in complexity observed is a result of a driven rather than a passive trend. In subsequent experiments we demonstrate that morphologies having greater complexity evolve in complex environments, when compared to a simple environment when a cost of complexity is imposed. This suggests that in some niches, evolution may act to complexify the body plans of organisms while in other niches selection favors simpler body plans. PMID:24391483

Time-ordered exponential on the complex plane and Gell-Mann—Low formula as a mathematical theorem

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

Futakuchi, Shinichiro; Usui, Kouta

2016-04-15

The time-ordered exponential representation of a complex time evolution operator in the interaction picture is studied. Using the complex time evolution, we prove the Gell-Mann—Low formula under certain abstract conditions, in mathematically rigorous manner. We apply the abstract results to quantum electrodynamics with cutoffs.

Acquisition of Complex Systemic Thinking: Mental Models of Evolution

ERIC Educational Resources Information Center

d'Apollonia, Sylvia T.; Charles, Elizabeth S.; Boyd, Gary M.

2004-01-01

We investigated the impact of introducing college students to complex adaptive systems on their subsequent mental models of evolution compared to those of students taught in the same manner but with no reference to complex systems. The students' mental models (derived from similarity ratings of 12 evolutionary terms using the pathfinder algorithm)…

Ornament Complexity Is Correlated with Sexual Selection: (A Comment on Raia et al., "Cope's Rule and the Universal Scaling Law of Ornament Complexity").

PubMed

Holman, Luke; Bro-Jørgensen, Jakob

2016-08-01

Raia et al. propose that the evolution of the shape and complexity of animal ornaments (e.g., deer antlers) can be explained by interspecific variation in body size and is not influenced by sexual selection. They claim to show that ornament complexity is related to body size by an 0.25-power law and argue that this finding precludes a role for sexual selection in the evolution of ornament complexity. However, their study does not test alternative hypotheses and mismeasures antler shape allometry by omitting much of the published data. We show that an index of sexual selection (sexual size dimorphism) is positively correlated with size-corrected antler complexity and that the allometric slope of complexity is substantially greater than 0.25, contra Raia et al. We conclude that sexual selection and physical constraints both affect the evolution of antler shape.

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

PubMed

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

The Role of Reticulate Evolution in Creating Innovation and Complexity

PubMed Central

Swithers, Kristen S.; Soucy, Shannon M.; Gogarten, J. Peter

2012-01-01

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity. PMID:22844638

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

The evolution of resistance genes in multi-protein plant resistance systems.

PubMed

Friedman, Aaron R; Baker, Barbara J

2007-12-01

The genomic perspective aids in integrating the analysis of single resistance (R-) genes into a higher order model of complex plant resistance systems. The majority of R-genes encode a class of proteins with nucleotide binding (NB) and leucine-rich repeat (LRR) domains. Several R-proteins act in multi-protein R-complexes that mediate interaction with pathogen effectors to induce resistance signaling. The complexity of these systems seems to have resulted from multiple rounds of plant-pathogen co-evolution. R-gene evolution is thought to be facilitated by the formation of R-gene clusters, which permit sequence exchanges via recombinatorial mispairing and generate high haplotypic diversity. This pattern of evolution may also generate diversity at other loci that contribute to the R-complex. The rate of recombination at R-clusters is not necessarily homogeneous or consistent over evolutionary time: recent evidence suggests that recombination at R-clusters is increased following pathogen infection, suggesting a mechanism that induces temporary genome instability in response to extreme stress. DNA methylation and chromatin modifications may allow this instability to be conditionally regulated and targeted to specific genome regions. Knowledge of natural R-gene evolution may contribute to strategies for artificial evolution of novel resistance specificities.

Complexity and the Arrow of Time

NASA Astrophysics Data System (ADS)

Lineweaver, Charles H.; Davies, Paul C. W.; Ruse, Michael

2013-08-01

1. What is complexity? Is it increasing? Charles H. Lineweaver, Paul C. W. Davies and Michael Ruse; 2. Directionality principles from cancer to cosmology Paul C. W. Davies; 3. A simple treatment of complexity: cosmological entropic boundary conditions on increasing complexity Charles H. Lineweaver; 4. Using complexity science to search for unity in the natural sciences Eric J. Chaisson; 5. On the spontaneous generation of complexity in the universe Seth Lloyd; 6. Emergent spatiotemporal complexity in field theory Marcelo Gleiser; 7. Life: the final frontier for complexity? Simon Conway Morris; 8. Evolution beyond Newton, Darwin, and entailing law: the origin of complexity in the evolving biosphere Stuart A. Kauffman; 9. Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere D. Eric Smith; 10. The inferential evolution of biological complexity: forgetting nature by learning to nurture David C. Krakauer; 11. Information width: a way for the second law to increase complexity David Wolpert; 12. Wrestling with biological complexity: from Darwin to Dawkins Michael Ruse; 13. The role of generative entrenchment and robustness in the evolution of complexity William C. Wimsatt; 14. On the plurality of complexity-producing mechanisms Philip Clayton; Index.

What makes the family of barred disc galaxies so rich: damping stellar bars in spinning haloes

NASA Astrophysics Data System (ADS)

Collier, Angela; Shlosman, Isaac; Heller, Clayton

2018-05-01

We model and analyse the secular evolution of stellar bars in spinning dark matter (DM) haloes with the cosmological spin λ ˜ 0-0.09. Using high-resolution stellar and DM numerical simulations, we focus on angular momentum exchange between stellar discs and DM haloes of various axisymmetric shapes - spherical, oblate, and prolate. We find that stellar bars experience a diverse evolution that is guided by the ability of parent haloes to absorb angular momentum, J, lost by the disc through the action of gravitational torques, resonant and non-resonant. We confirm that dynamical bar instability is accelerated via resonant J-transfer to the halo. Our main findings relate to the long-term secular evolution of disc-halo systems: with an increasing λ, bars experience less growth and basically dissolve after they pass through vertical buckling instability. Specifically, with increasing λ, (1) the vertical buckling instability in stellar bars colludes with inability of the inner halo to absorb J - this emerges as the main factor weakening or destroying bars in spinning haloes; (2) bars lose progressively less J, and their pattern speeds level off; (3) bars are smaller, and for λ ≳ 0.06 cease their growth completely following buckling; (4) bars in λ > 0.03 haloes have ratio of corotation-to-bar radii, RCR/Rb > 2, and represent so-called slow bars without offset dust lanes. We provide a quantitative analysis of J-transfer in disc-halo systems, and explain the reasons for absence of growth in fast spinning haloes and its observational corollaries. We conclude that stellar bar evolution is substantially more complex than anticipated, and bars are not as resilient as has been considered so far.

Double Guiding Catheters for Complex Percutaneous Coronary Intervention

PubMed Central

Chou, Shing-Hsien; Lin, Chia-Pin; Lin, Yen-Chen; Kuo, Chi-Tai; Lin, Ming-Shyan; Chang, Chi-Jen

2012-01-01

A large-lumen guiding catheter is often used for complex percutaneous coronary intervention—particularly when a final kissing-balloon or 2-stent technique is required. However, catheter insertion is sometimes restricted by diseased vascular access sites or a tortuous vascular route. We report 2 cases in which a unique double guiding catheter technique was used to create a lumen of sufficient size for complex percutaneous coronary intervention. In each patient, two 6F guiding catheters were used concurrently to engage the ostium of 1 target vessel. In 1 patient, these catheters were used for the delivery of 2 balloons to complete kissing-balloon dilation after single-stent placement. In the other patient, the catheters were used to deliver 2 stents sequentially to their respective target lesions. The stents were then deployed simultaneously as kissing stents, followed by high-pressure kissing-balloon postdilation. PMID:22412243

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.

Ultrasonic guided waves in eccentric annular pipes

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

Pattanayak, Roson Kumar; Balasubramaniam, Krishnan; Rajagopal, Prabhu

2014-02-18

This paper studies the feasibility of using ultrasonic guided waves to rapidly inspect tubes and pipes for possible eccentricity. While guided waves are well established in the long range inspection of structures such as pipes and plates, studies for more complex cross sections are limited and analytical solutions are often difficult to obtain. Recent developments have made the Semi Analytical Finite Element (SAFE) method widely accessible for researchers to study guided wave properties in complex structures. Here the SAFE method is used to study the effect of eccentricity on the modal structures and velocities of lower order guided wave modesmore » in thin pipes of diameters typically of interest to the industry. Results are validated using experiments. The paper demonstrates that even a small eccentricity in the pipe can strongly affect guided wave mode structures and velocities and hence shows potential for pipe eccentricity inspection.« less

Numerical studies of nonlinear ultrasonic guided waves in uniform waveguides with arbitrary cross sections

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

Zuo, Peng; Fan, Zheng, E-mail: ZFAN@ntu.edu.sg; Zhou, Yu

2016-07-15

Nonlinear guided waves have been investigated widely in simple geometries, such as plates, pipe and shells, where analytical solutions have been developed. This paper extends the application of nonlinear guided waves to waveguides with arbitrary cross sections. The criteria for the existence of nonlinear guided waves were summarized based on the finite deformation theory and nonlinear material properties. Numerical models were developed for the analysis of nonlinear guided waves in complex geometries, including nonlinear Semi-Analytical Finite Element (SAFE) method to identify internal resonant modes in complex waveguides, and Finite Element (FE) models to simulate the nonlinear wave propagation at resonantmore » frequencies. Two examples, an aluminum plate and a steel rectangular bar, were studied using the proposed numerical model, demonstrating the existence of nonlinear guided waves in such structures and the energy transfer from primary to secondary modes.« less

Changes and Stability in Reasoning after a Field Trip to a Natural History Museum

ERIC Educational Resources Information Center

Tenenbaum, Harriet R.; To, Cheryl; Wormald, Daniel; Pegram, Emma

2015-01-01

Darwinian evolution is difficult to understand because of conceptual barriers stemming from intuitive ideas. This study examined understanding of evolution in 52 students (M = 14.48 years, SD = 0.89) before and after a guided field trip to a natural history museum and in a comparison group of 18 students (M = 14.17 years, SD = 0.79) who did not…

Upper Secondary and First-Year University Students' Explanations of Animal Behaviour: To What Extent Are Tinbergen's Four Questions about Causation, Ontogeny, Function and Evolution, Represented?

ERIC Educational Resources Information Center

Pinxten, Rianne; Desclée, Mathieu; Eens, Marcel

2016-01-01

In 1963, the Nobel Prize-winning ethologist Niko Tinbergen proposed a framework for the scientific study of animal behaviour by outlining four questions that should be answered to have a complete understanding: causation, ontogeny, function and evolution. At present, Tinbergen's framework is still considered the best way to guide animal…

The Rise and Fall of the Bering Land Bridge. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Complex Osteotomies of Tibial Plateau Malunions Using Computer-Assisted Planning and Patient-Specific Surgical Guides.

PubMed

Fürnstahl, Philipp; Vlachopoulos, Lazaros; Schweizer, Andreas; Fucentese, Sandro F; Koch, Peter P

2015-08-01

The accurate reduction of tibial plateau malunions can be challenging without guidance. In this work, we report on a novel technique that combines 3-dimensional computer-assisted planning with patient-specific surgical guides for improving reliability and accuracy of complex intraarticular corrective osteotomies. Preoperative planning based on 3-dimensional bone models was performed to simulate fragment mobilization and reduction in 3 cases. Surgical implementation of the preoperative plan using patient-specific cutting and reduction guides was evaluated; benefits and limitations of the approach were identified and discussed. The preliminary results are encouraging and show that complex, intraarticular corrective osteotomies can be accurately performed with this technique. For selective patients with complex malunions around the tibia plateau, this method might be an attractive option, with the potential to facilitate achieving the most accurate correction possible.

Highly Complementary Target RNAs Promote Release of Guide RNAs from Human Argonaute2

PubMed Central

De, Nabanita; Young, Lisa; Lau, Pick-Wei; Meisner, Nicole-Claudia; Morrissey, David V.; MacRae, Ian J.

2013-01-01

SUMMARY Argonaute proteins use small RNAs to guide the silencing of complementary target RNAs in many eukaryotes. Although small RNA biogenesis pathways are well studied, mechanisms for removal of guide RNAs from Argonaute are poorly understood. Here we show that the Argonaute2 (Ago2) guide RNA complex is extremely stable, with a half-life on the order of days. However, highly complementary target RNAs destabilize the complex and significantly accelerate release of the guide RNA from Ago2. This “unloading” activity can be enhanced by mismatches between the target and the guide 5′ end and attenuated by mismatches to the guide 3′ end. The introduction of 3′ mismatches leads to more potent silencing of abundant mRNAs in mammalian cells. These findings help to explain why the 3′ ends of mammalian microRNAs (miRNAs) rarely match their targets, suggest a mechanism for sequence-specific small RNA turnover, and offer insights for controlling small RNAs in mammalian cells. PMID:23664376

Complex Homology and the Evolution of Nervous Systems

PubMed Central

Liebeskind, Benjamin J.; Hillis, David M.; Zakon, Harold H.; Hofmann, Hans A.

2016-01-01

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states. PMID:26746806

Quantitative Measures for Software Independent Verification and Validation

NASA Technical Reports Server (NTRS)

Lee, Alice

1996-01-01

As software is maintained or reused, it undergoes an evolution which tends to increase the overall complexity of the code. To understand the effects of this, we brought in statistics experts and leading researchers in software complexity, reliability, and their interrelationships. These experts' project has resulted in our ability to statistically correlate specific code complexity attributes, in orthogonal domains, to errors found over time in the HAL/S flight software which flies in the Space Shuttle. Although only a prototype-tools experiment, the result of this research appears to be extendable to all other NASA software, given appropriate data similar to that logged for the Shuttle onboard software. Our research has demonstrated that a more complete domain coverage can be mathematically demonstrated with the approach we have applied, thereby ensuring full insight into the cause-and-effects relationship between the complexity of a software system and the fault density of that system. By applying the operational profile we can characterize the dynamic effects of software path complexity under this same approach We now have the ability to measure specific attributes which have been statistically demonstrated to correlate to increased error probability, and to know which actions to take, for each complexity domain. Shuttle software verifiers can now monitor the changes in the software complexity, assess the added or decreased risk of software faults in modified code, and determine necessary corrections. The reports, tool documentation, user's guides, and new approach that have resulted from this research effort represent advances in the state of the art of software quality and reliability assurance. Details describing how to apply this technique to other NASA code are contained in this document.

Ongoing Search for Metal Line Emission in Intermediate and High Velocity Clouds with WHAM

NASA Astrophysics Data System (ADS)

Barger, K. A.; Haffner, L. M.; Madsen, G. J.; Hill, A. S.; Wakker, B. P.

2010-01-01

We present new observations of the ionized gas in Complexes A, K, and L obtained with the Wisconsin H-Alpha Mapper (WHAM). To date, there have been only a limited number of studies of the ionized components of intermediate and high velocity clouds. Investigating their emission provides a rare probe of the physical conditions of the clouds and the halo they are embedded within. These types of measurements will help guide discussion of the origin and evolution of these neutral halo structures. Here we follow up on the H-alpha maps we have presented elsewhere with deeper observations in H-alpha, [S II], [N II], and [O I]. Distance constraints from absorption studies place this gas in the mid to lower Galactic halo. Complex A has been constrained to a distance of 8-10 kpc (Wakker et al. 2008); Complex K has an upper limit of 6.8 kpc; and Complex L at a distance of 8-15 kpc (Wakker 2000). Some halo gas structures have clear metal line emission (e.g., Smith Cloud; Hill et al. 2009 and this meeting); however, the lack of [S II] emission toward Complex C combined with absorption-line observations demonstrates that it has very low metallically (Wakker, et al. 1999). Such discoveries reveal ongoing gas replenishment of the evolving Milky Way. Here, we find a similar lack of emission toward the high-velocity Complex A. In particular, the cores of its cloud components designated III and IV show no evidence for metal line emission in our new observations, which places new constraints on the metallically of this complex. These observations were taken with WHAM at Kitt Peak, and we thank the excellent, decade-long support from its staff. WHAM operations are supported through NSF award AST-0607512.

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

PubMed Central

Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

2015-01-01

Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

PubMed Central

Pankey, M. Sabrina; Minin, Vladimir N.; Imholte, Greg C.; Suchard, Marc A.; Oakley, Todd H.

2014-01-01

Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species’ photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them. PMID:25336755

Genomic signatures of evolutionary transitions from solitary to group living

PubMed Central

Kapheim, Karen M.; Pan, Hailin; Li, Cai; Salzberg, Steven L.; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M.; Hudson, Matthew E.; Venkat, Aarti; Fischman, Brielle J.; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D.; Kemp, William P.; Bosch, Jordi; Waterhouse, Robert M.; Zdobnov, Evgeny M.; Stolle, Eckart; Kraus, F. Bernhard; Helbing, Sophie; Moritz, Robin F. A.; Glastad, Karl M.; Hunt, Brendan G.; Goodisman, Michael A. D.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D.; Barribeau, Seth M.; Johnson, Reed M.; Massey, Jonathan H.; Southey, Bruce R.; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F.; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J. Spencer; Hanrahan, Shawn J.; Kocher, Sarah D.; Wang, Jun; Robinson, Gene E.; Zhang, Guojie

2017-01-01

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. PMID:25977371

Problem Solving: The "Wright" Math. The Centennial of Flight Special Edition. An Educator Guide with Activities in Mathematics, Science, and Technology. NASA CONNECT[TM].

ERIC Educational Resources Information Center

National Aeronautics and Space Administration, Hampton, VA. Langley Research Center.

NASA CONNECT is an annual series of integrated mathematics, science, and technology instructional distance learning programs for students in grades 6-8. This program is designed for students to learn about the evolution of flight. The program has three components--television broadcast, Web activity, and lesson guide--which are designed as an…

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

PubMed

Swarts, Daan C; van der Oost, John; Jinek, Martin

2017-04-20

The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies. Copyright © 2017 Elsevier Inc. All rights reserved.

Dementia in intellectual disability: a review of diagnostic challenges.

PubMed

Nagdee, M

2011-07-01

The evaluation of dementia in individuals with intellectual disability (ID), which will guide subsequent intervention, care and management depends on the systematic review of a number of factors: (1) the individual historical context, obtained from multiple sources, (2) evaluation of the pre-existing cognitive, behavioural, psychiatric, medical and adaptive skill profile, (3) the constellation, and pattern of evolution, of presenting signs and symptoms, (4) results of focused investigations, and (5) refinement of the differential diagnosis. In patients with ID, standard clinical methods need to be supplemented by careful, longitudinal behavioural observations, and individually tailored assessment techniques. Co-morbidity, multiple biological, psychological and socioenvironmental factors, and complex interactions among events, are the reality for many ageing people with ID. Determining the various influences is often a formidable clinical task, but should be systematically carried out using medical, cognitive, behavioural, neuropsychiatric and psycho-social frameworks.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Medical photography: current technology, evolving issues and legal perspectives.

PubMed

Harting, M T; DeWees, J M; Vela, K M; Khirallah, R T

2015-04-01

Medical photographic image capture and data management has undergone a rapid and compelling change in complexity over the last 20 years. This is because of multiple factors, including significant advances in ease of photograph capture, alongside an evolution of mechanisms of data portability/dissemination, combined with governmental focus on health information privacy. Literature to guide medical, legal, governmental and business professionals when dealing with issues related to medical photography is virtually nonexistent. Herein, we will address the breadth of uses of medical photography, device properties/specific devices utilised for image capture, methods of data transfer and dissemination and patient perceptions and attitudes regarding photography in a medical setting. In addition, we will address the legal implications, including legal precedent, copyright and privacy law, informed consent, protected health information and the Health Insurance Portability and Accountability Act (HIPAA), as they pertain to medical photography. © 2015 John Wiley & Sons Ltd.

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

PubMed

Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

2018-03-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

The systematic evolution of a NASA software technology, Appendix C

NASA Technical Reports Server (NTRS)

Deregt, M. P.; Dulfer, J. E.

1972-01-01

A long range program is described whose ultimate purpose is to make possible the production of software in NASA within predictable schedule and budget constraints and with major characteristics such as size, run-time, and correctness predictable within reasonable tolerances. As part of the program a pilot NASA computer center will be chosen to apply software development and management techniques systematically and determine a set which is effective. The techniques will be developed by a Technology Group, which will guide the pilot project and be responsible for its success. The application of the technology will involve a sequence of NASA programming tasks graduated from simpler ones at first to complex systems in late phases of the project. The evaluation of the technology will be made by monitoring the operation of the software at the users' installations. In this way a coherent discipline for software design, production maintenance, and management will be evolved.

BOND: A quantum of solace for nebular abundance determinations

NASA Astrophysics Data System (ADS)

Vale Asari, N.; Stasińska, G.; Morisset, C.; Cid Fernandes, R.

2017-11-01

The abundances of chemical elements other than hydrogen and helium in a galaxy are the fossil record of its star formation history. Empirical relations such as mass-metallicity relation are thus seen as guides for studies on the history and chemical evolution of galaxies. Those relations usually rely on nebular metallicities measured with strong-line methods, which assume that H II regions are a one- (or at most two-) parameter family where the oxygen abundance is the driving quantity. Nature is however much more complex than that, and metallicities from strong lines may be strongly biased. We have developed the method BOND (Bayesian Oxygen and Nitrogen abundance Determinations) to simultaneously derive oxygen and nitrogen abundances in giant H II regions by comparing strong and semi-strong observed emission lines to a carefully-defined, finely-meshed grid of photoionization models. Our code and results are public and available at http://bond.ufsc.br.

The accuracy of combined physical examination and ultrasonography for the detection of abdominal aorta aneurysm.

PubMed

Cârstea, Doina; Streba, Letiţia Adela Maria; Glodeanu, Adina; Cârstea, A P; Vancu, Mihaela; Ninulescu, Ana-Maria

2008-01-01

Atherosclerosis is the most frequent cause in the appearance of an abdominal aorta aneurysm (AAA) and plays an important role in his development. Most AAA does not cause any symptoms, especially when talking about elderly patients, however, many of those aneurysms can be detected during physical examination. Their detection is very important because the natural evolution and the major reason in treating AAA is their tendency to rupture. We present the case of an adult man with a complex clinical pathology, but not related to the AAA. The diagnosis of the AAA has been suspicion through palpation, and the abdominal ultrasound exam confirmed it. This case is particular interesting, as the AAA requires surgical intervention, while patient's health status was poor. An essential issue is establishing the importance of the AAA screening, when there are no symptoms present. For now, there are not satisfactory studies to be used as a guide.

Social cognitive theory of gender development and differentiation.

PubMed

Bussey, K; Bandura, A

1999-10-01

Human differentiation on the basis of gender is a fundamental phenomenon that affects virtually every aspect of people's daily lives. This article presents the social cognitive theory of gender role development and functioning. It specifies how gender conceptions are constructed from the complex mix of experiences and how they operate in concert with motivational and self-regulatory mechanisms to guide gender-linked conduct throughout the life course. The theory integrates psychological and sociostructural determinants within a unified conceptual structure. In this theoretical perspective, gender conceptions and roles are the product of a broad network of social influences operating interdependently in a variety of societal subsystems. Human evolution provides bodily structures and biological potentialities that permit a range of possibilities rather than dictate a fixed type of gender differentiation. People contribute to their self-development and bring about social changes that define and structure gender relationships through their agentic actions within the interrelated systems of influence.

Guidelines examination of victims of sexual assault harmonization of forensic and medico-legal examination of persons.

PubMed

Ludes, B; Geraut, A; Väli, M; Cusack, D; Ferrara, D; Keller, E; Mangin, P; Vieira, D N

2018-02-21

Sexual assault is a complex situation with medical, psychological, and legal aspects. Forensic experts play a major role in terms of forensic and gynecological medical examination and evidence collection in order to maintain the chain of custody. Victims should be examined by a specially trained medico-legal examiner in order to avoid multiple examinations in the surroundings that do not meet minimum health standards. The evolution and treatment of sexual assault victims are time-intensive and should optimally be provided by a team that includes a forensic medical doctor. These guidelines will be of interest to forensic medical doctors who will have responsibility for the examination and assessment of victims of sexual violence and can be used as a day-to-day service document and/or a guide to develop health service for victims of sexual violence.

Signature of a polyamorphic transition in the THz spectrum of vitreous GeO 2

DOE PAGES

Cunsolo, Alessandro; Li, Yan; Kodituwakku, Chaminda N.; ...

2015-10-13

The THz spectrum of density fluctuations, S(Q, ω), of vitreous GeO 2 at ambient temperature was measured by inelastic x-ray scattering from ambient pressure up to pressures well beyond that of the known α-quartz to rutile polyamorphic (PA) transition. We observe significant differences in the spectral shape measured below and above the PA transition, in particular, in the 30–80 meV range. Guided by first-principle lattice dynamics calculations, we interpret the changes in the phonon dispersion as the evolution from a quartz-like to a rutile-like coordination. Notably, such a crossover is accompanied by a cusp-like behavior in the pressure dependence ofmore » the elastic response of the system. Altogether, the presented results highlight the complex fingerprint of PA phenomena on the high-frequency phonon dispersion.« less

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks

PubMed Central

Grierson, Claire S.

2018-01-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli. Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution. PMID:29670941

Genomic analysis of local variation and recent evolution in Plasmodium vivax

PubMed Central

Pearson, Richard D; Miotto, Olivo; Almagro-Garcia, Jacob; Amaratunga, Chanaki; Suon, Seila; Mao, Sivanna; Noviyanti, Rintis; Trimarsanto, Hidayat; Marfurt, Jutta; Anstey, Nicholas M; William, Timothy; Boni, Maciej F; Dolecek, Christiane; Hien, Tinh Tran; White, Nicholas J; Michon, Pascal; Siba, Peter; Tavul, Livingstone; Harrison, Gabrielle; Barry, Alyssa; Mueller, Ivo; Ferreira, Marcelo U; Karunaweera, Nadira; Randrianarivelojosia, Milijaona; Gao, Qi; Hubbart, Christina; Hart, Lee; Jeffery, Ben; Drury, Eleanor; Mead, Daniel; Kekre, Mihir; Campino, Susana; Manske, Magnus; Cornelius, Victoria J; MacInnis, Bronwyn; Rockett, Kirk A; Miles, Alistair; Rayner, Julian C; Fairhurst, Rick M; Nosten, Francois; Price, Ric N; Kwiatkowski, Dominic P

2016-01-01

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination. PMID:27348299

Intravascular ultrasound guided wiring re-entry technique for complex chronic total occlusions.

PubMed

Huang, Wei-Chieh; Teng, Hsin-I; Hsueh, Chien-Hung; Lin, Shing-Jong; Chan, Wan-Leong; Lu, Tse-Min

2018-05-03

The successful recanalization rate of chronic total occlusion (CTO) lesions without retrograde collaterals available is always low. Intravascular ultrasound (IVUS) may be useful to guide the subintimal guidewire to re-enter the true lumen. We evaluated the clinical feasibility and efficacy of the IVUS-guided wiring re-entry technique for these complex CTO lesions. Twenty consecutive patients (19 male, mean age: 65.3 ± 12.8 years) with both failed antegrade and retrograde approaches were enrolled. The IVUS catheter was introduced into the subintimal space to identify the entry point into the subintimal space, and guide another stiff wire to re-enter the true lumen with the adjacent side-branch or first wire as markers, or using IVUS-guided parallel wire technique. The entry point into the subintimal space was identified by IVUS in all cases, and the IVUS-guided wiring re-entry technique succeeded in 17 cases (85%). No procedure-related complication was noted except one case of delayed cardiac tamponade due to the wire perforation. During the mean follow-up period of 1.9 ± 1.3 years, there was no adverse cardiac event, except one patient died of the complication of cardiac transplantation. The IVUS-guided wiringre-entry technique might be feasible and safe for the recanalization of complex CTO lesions. © 2018, Wiley Periodicals, Inc.

Usefulness and Safety of a Guide Catheter Extension System for the Percutaneous Treatment of Complex Coronary Lesions by a Transradial Approach

PubMed Central

García-Blas, Sergio; Núñez, Julio; Mainar, Luis; Miñana, Gema; Bonanad, Clara; Racugno, Paolo; Rodríguez, Juan Carlos; Moyano, Patricia; Sanchis, Juan

2015-01-01

Objective The aim of this study was to describe our initial experience with the GuideLiner® catheter (Vascular Solutions Inc.) in the transradial treatment of complex lesions. Materials and Methods The clinical, angiographic and procedural data of percutaneous coronary interventions where GuideLiner was used during 2013 were collected. The transradial approach was used in all cases. The indication for its use, efficacy and periprocedural complications were determined. Sixteen consecutive procedures (in 15 patients; 12 males and 3 females) were evaluated. The indication for the use of GuideLiner was a difficulty to advance and properly position a stent through a tortuous and/or calcified artery despite using high-support guide catheters or other useful techniques. Results Of the 16 angiographic procedures, 14 (87.5s%) were successful (stent deployment in 13 cases and a drug-eluting balloon in 1 case). Unsuccessful cases were a chronic total occlusion and a diffusely diseased left anterior descendant artery. A type B dissection of a proximal left circumflex artery was the only periprocedural complication. Conclusion Use of the GuideLiner was an effective and safe technique for the percutaneous treatment of complex coronary lesions in which the adequate progress of angioplasty devices had failed. GuideLiner was particularly helpful when using the transradial approach. Only one minor complication was recorded. PMID:25531292

Usefulness and safety of a guide catheter extension system for the percutaneous treatment of complex coronary lesions by a transradial approach.

PubMed

García-Blas, Sergio; Núñez, Julio; Mainar, Luis; Miñana, Gema; Bonanad, Clara; Racugno, Paolo; Rodríguez, Juan Carlos; Moyano, Patricia; Sanchis, Juan

2015-01-01

The aim of this study was to describe our initial experience with the GuideLiner® catheter (Vascular Solutions Inc.) in the transradial treatment of complex lesions. The clinical, angiographic and procedural data of percutaneous coronary interventions where GuideLiner was used during 2013 were collected. The transradial approach was used in all cases. The indication for its use, efficacy and periprocedural complications were determined. Sixteen consecutive procedures (in 15 patients; 12 males and 3 females) were evaluated. The indication for the use of GuideLiner was a difficulty to advance and properly position a stent through a tortuous and/or calcified artery despite using high-support guide catheters or other useful techniques. Of the 16 angiographic procedures, 14 (87.5%) were successful (stent deployment in 13 cases and a drug-eluting balloon in 1 case). Unsuccessful cases were a chronic total occlusion and a diffusely diseased left anterior descendant artery. A type B dissection of a proximal left circumflex artery was the only periprocedural complication. Use of the GuideLiner was an effective and safe technique for the percutaneous treatment of complex coronary lesions in which the adequate progress of angioplasty devices had failed. GuideLiner was particularly helpful when using the transradial approach. Only one minor complication was recorded. © 2014 S. Karger AG, Basel.

Gene Editing and Crop Improvement Using CRISPR-Cas9 System

PubMed Central

Arora, Leena; Narula, Alka

2017-01-01

Advancements in Genome editing technologies have revolutionized the fields of functional genomics and crop improvement. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat)-Cas9 is a multipurpose technology for genetic engineering that relies on the complementarity of the guideRNA (gRNA) to a specific sequence and the Cas9 endonuclease activity. It has broadened the agricultural research area, bringing in new opportunities to develop novel plant varieties with deletion of detrimental traits or addition of significant characters. This RNA guided genome editing technology is turning out to be a groundbreaking innovation in distinct branches of plant biology. CRISPR technology is constantly advancing including options for various genetic manipulations like generating knockouts; making precise modifications, multiplex genome engineering, and activation and repression of target genes. The review highlights the progression throughout the CRISPR legacy. We have studied the rapid evolution of CRISPR/Cas9 tools with myriad functionalities, capabilities, and specialized applications. Among varied diligences, plant nutritional improvement, enhancement of plant disease resistance and production of drought tolerant plants are reviewed. The review also includes some information on traditional delivery methods of Cas9-gRNA complexes into plant cells and incorporates the advent of CRISPR ribonucleoproteins (RNPs) that came up as a solution to various limitations that prevailed with plasmid-based CRISPR system. PMID:29167680

Gene Editing and Crop Improvement Using CRISPR-Cas9 System.

PubMed

Arora, Leena; Narula, Alka

2017-01-01

Advancements in Genome editing technologies have revolutionized the fields of functional genomics and crop improvement. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat)-Cas9 is a multipurpose technology for genetic engineering that relies on the complementarity of the guideRNA (gRNA) to a specific sequence and the Cas9 endonuclease activity. It has broadened the agricultural research area, bringing in new opportunities to develop novel plant varieties with deletion of detrimental traits or addition of significant characters. This RNA guided genome editing technology is turning out to be a groundbreaking innovation in distinct branches of plant biology. CRISPR technology is constantly advancing including options for various genetic manipulations like generating knockouts; making precise modifications, multiplex genome engineering, and activation and repression of target genes. The review highlights the progression throughout the CRISPR legacy. We have studied the rapid evolution of CRISPR/Cas9 tools with myriad functionalities, capabilities, and specialized applications. Among varied diligences, plant nutritional improvement, enhancement of plant disease resistance and production of drought tolerant plants are reviewed. The review also includes some information on traditional delivery methods of Cas9-gRNA complexes into plant cells and incorporates the advent of CRISPR ribonucleoproteins (RNPs) that came up as a solution to various limitations that prevailed with plasmid-based CRISPR system.

Analyzing the evolutionary mechanisms of the Air Transportation System-of-Systems using network theory and machine learning algorithms

NASA Astrophysics Data System (ADS)

Kotegawa, Tatsuya

Complexity in the Air Transportation System (ATS) arises from the intermingling of many independent physical resources, operational paradigms, and stakeholder interests, as well as the dynamic variation of these interactions over time. Currently, trade-offs and cost benefit analyses of new ATS concepts are carried out on system-wide evaluation simulations driven by air traffic forecasts that assume fixed airline routes. However, this does not well reflect reality as airlines regularly add and remove routes. A airline service route network evolution model that projects route addition and removal was created and combined with state-of-the-art air traffic forecast methods to better reflect the dynamic properties of the ATS in system-wide simulations. Guided by a system-of-systems framework, network theory metrics and machine learning algorithms were applied to develop the route network evolution models based on patterns extracted from historical data. Constructing the route addition section of the model posed the greatest challenge due to the large pool of new link candidates compared to the actual number of routes historically added to the network. Of the models explored, algorithms based on logistic regression, random forests, and support vector machines showed best route addition and removal forecast accuracies at approximately 20% and 40%, respectively, when validated with historical data. The combination of network evolution models and a system-wide evaluation tool quantified the impact of airline route network evolution on air traffic delay. The expected delay minutes when considering network evolution increased approximately 5% for a forecasted schedule on 3/19/2020. Performance trade-off studies between several airline route network topologies from the perspectives of passenger travel efficiency, fuel burn, and robustness were also conducted to provide bounds that could serve as targets for ATS transformation efforts. The series of analysis revealed that high robustness is achievable only in exchange of lower passenger travel and fuel burn efficiency. However, increase in the network density can mitigate this trade-off.

Specialized Environmental Chamber Test Complex: User Test Planning Guide

NASA Technical Reports Server (NTRS)

Montz, Michael E.

2011-01-01

Test process, milestones and inputs are unknowns to first-time users of the Specialized Environmental Test Complex. The User Test Planning Guide aids in establishing expectations for both NASA and non-NASA facility customers. The potential audience for this guide includes both internal and commercial spaceflight hardware/software developers. It is intended to assist their test engineering personnel in test planning and execution. Material covered includes a roadmap of the test process, roles and responsibilities of facility and user, major milestones, facility capabilities, and inputs required by the facility. Samples of deliverables, test article interfaces, and inputs necessary to define test scope, cost, and schedule are included as an appendix to the guide.

Historical development of world wide guided missiles

NASA Technical Reports Server (NTRS)

Spearman, M. L.

1978-01-01

This paper attempts to put in perspective the development of missiles from early history to present time. The influence of World War II in accelerating the development of guided missiles, particularly through German scientists, is discussed. The dispersion of German scientists to other countries and the coupling of their work with native talent to develop guided missiles is traced. Particular emphasis is placed on the evolution of the missile in the U.S. and the U.S.S.R. Since the Soviets possess what is probably the world's most complete array of dedicated missile system types, their known inventory is reviewed in some detail.

Frameless, image-guided stereotactic radiosurgery.

PubMed

Steffey-Stacy, Emily Cassandra

2006-11-01

To trace the evolution from frame-based to frameless image-guided SRS, to discuss the basic radiobiological principle of fractionation, current clinical trial data, and procedural components of the treatment plan. Nursing and medical literature, neurosurgical textbooks, and select internet sites. The CyberKnife (Accuray, Sunnyvale, CA) is the newest machine added to the technologic armamentarium of patient care. Its capacities are only beginning to be explored and the possibilities are limitless, giving hope to countless persons. Technologic advances have necessitated a diversification of nursing roles. Coordination of patient care services requires nurses to advance their knowledge of frameless, image-guided SRS.

Full-field drift Hamiltonian particle orbits in 3D geometry

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Brunner, S.; Isaev, M. Yu

2011-02-01

A Hamiltonian/Lagrangian theory to describe guiding centre orbit drift motion which is canonical in the Boozer coordinate frame has been extended to include full electromagnetic perturbed fields in anisotropic pressure 3D equilibria with nested magnetic flux surfaces. A redefinition of the guiding centre velocity to eliminate the motion due to finite equilibrium radial magnetic fields and the choice of a gauge condition that sets the radial component of the electromagnetic vector potential to zero are invoked to guarantee that the Boozer angular coordinates retain the canonical structure. The canonical momenta are identified and the guiding centre particle radial drift motion and parallel gyroradius evolution are derived. The particle coordinate position is linearly modified by wave-particle interactions. All the nonlinear wave-wave interactions appear explicitly only in the evolution of the parallel gyroradius. The radial variation of the electrostatic potential is related to the binormal component of the displacement vector for MHD-type perturbations. The electromagnetic vector potential projections can then be determined from the electrostatic potential and the radial component of the MHD displacement vector.

Predicting the evolution of sex on complex fitness landscapes.

PubMed

Misevic, Dusan; Kouyos, Roger D; Bonhoeffer, Sebastian

2009-09-01

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, Delta Var(HD), also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. Delta Var(HD) is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction.

Predicting the Evolution of Sex on Complex Fitness Landscapes

PubMed Central

Misevic, Dusan; Kouyos, Roger D.; Bonhoeffer, Sebastian

2009-01-01

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, ΔVarHD, also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. ΔVarHD is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction. PMID:19763171

Data extraction for complex meta-analysis (DECiMAL) guide.

PubMed

Pedder, Hugo; Sarri, Grammati; Keeney, Edna; Nunes, Vanessa; Dias, Sofia

2016-12-13

As more complex meta-analytical techniques such as network and multivariate meta-analyses become increasingly common, further pressures are placed on reviewers to extract data in a systematic and consistent manner. Failing to do this appropriately wastes time, resources and jeopardises accuracy. This guide (data extraction for complex meta-analysis (DECiMAL)) suggests a number of points to consider when collecting data, primarily aimed at systematic reviewers preparing data for meta-analysis. Network meta-analysis (NMA), multiple outcomes analysis and analysis combining different types of data are considered in a manner that can be useful across a range of data collection programmes. The guide has been shown to be both easy to learn and useful in a small pilot study.

The long story of mitochondrial DNA and respiratory complex I.

PubMed

Degli Esposti, Mauro

2017-01-01

This article examines the long story of the relationship between mitochondrial DNA (mtDNA) and respiratory complex I, NADH:Ubiquinone Oxidoreductase, from its beginning  in the genome of the bacterial endosymbiont which then evolved into the mitochondria of our cells. The story begins with the evolution of ancient forms of bacterial complex I into the Nuo14 complex I that was present in the alpha proteobacterial ancestor of mitochondria. The story then becomes complicated in the diversity of eukaryotic organisms that are currently recognized. Therefore, it does not have a clear end, because currently available information shows different situations of metabolic adaptation and gene loss, indicating cases of de-evolution of the original protonmotive complex into a system that may fundamentally assist [FeFe]-hydrogenases in re-oxidising metabolically produced NADH under anaerobic conditions. The history of complex I is thus a never ending story of molecular and physiological evolution producing new perspectives for studying the enzyme complex that occupies the largest proportion of mitochondrial DNA.

"Synergistic selection": a Darwinian frame for the evolution of complexity.

PubMed

Corning, Peter A; Szathmáry, Eörs

2015-04-21

Non-Darwinian theories about the emergence and evolution of complexity date back at least to Lamarck, and include those of Herbert Spencer and the "emergent evolution" theorists of the later nineteenth and early twentieth centuries. In recent decades, this approach has mostly been espoused by various practitioners in biophysics and complexity theory. However, there is a Darwinian alternative - in essence, an economic theory of complexity - proposing that synergistic effects of various kinds have played an important causal role in the evolution of complexity, especially in the "major transitions". This theory is called the "synergism hypothesis". We posit that otherwise unattainable functional advantages arising from various cooperative phenomena have been favored over time in a dynamic that the late John Maynard Smith characterized and modeled as "synergistic selection". The term highlights the fact that synergistic "wholes" may become interdependent "units" of selection. We provide some historical perspective on this issue, as well as a brief explication of the underlying theory and the concept of synergistic selection, and we describe two relevant models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Highly efficient photocatalytic hydrogen evolution from nickel quinolinethiolate complexes under visible light irradiation

NASA Astrophysics Data System (ADS)

Rao, Heng; Yu, Wen-Qian; Zheng, Hui-Qin; Bonin, Julien; Fan, Yao-Ting; Hou, Hong-Wei

2016-08-01

Earth-abundant metal complexes have emerged as promising surrogates of platinum for catalyzing the hydrogen evolution reaction (HER). In this study, we report the design and synthesis of two novel nickel quinolinethiolate complexes, namely [Ni(Hqt)2(4, 4‧-Z-2, 2‧-bpy)] (Hqt = 8-quinolinethiol, Z = sbnd H [1] or sbnd CH3 [2], bpy = bipyridine). An efficient three-component photocatalytic homogeneous system for hydrogen generation working under visible light irradiation was constructed by using the target complexes as catalysts, triethylamine (TEA) as sacrificial electron donor and xanthene dyes as photosensitizer. We obtain turnover numbers (TON, vs. catalyst) for H2 evolution of 5923/7634 under the optimal conditions with 5.0 × 10-6 M complex 1/2 respectively, 1.0 × 10-3 M fluorescein and 5% (v/v) TEA at pH 12.3 in EtOH/H2O (1:1, v/v) mixture after 8 h irradiation (λ > 420 nm). We discuss the mechanism of H2 evolution in the homogeneous photocatalytic system based on fluorescence spectrum and cyclic voltammetry data.

Detection of timescales in evolving complex systems

PubMed Central

Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

2016-01-01

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

Use of a very flexible guide wire to permit dilation of complex malignant strictures of the esophagus.

PubMed

Vargas-Tank, L; Ovalle, L; Fernández, C; Mella, B; Estay, R; del Solar, M P; Soto, J R

1995-01-01

Risk of perforation is a major impediment to the use of polyvinyl bougies in palliative dilation of cancerous strictures of the esophagus. We encountered 23 patients with complex malignant strictures in whom initial dilation with Savary-Gilliard bougies was thwarted because attempts to pass a conventional Eder-Puestow guide wire were unsuccessful. As a recourse, we probed these strictures with a very flexible guide wire of the type used to implant prostheses in the biliary tract. The purpose was to establish a passage through which a standard guide wire could then be inserted. The procedure was successful in all but 4 of the 23 patients. We conclude that in such cases the preliminary use of the very flexible guide, even though time-consuming, improves the chance of effective dilation with minimal added risk.

Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.

PubMed

Koch, Robin; Kupczok, Anne; Stucken, Karina; Ilhan, Judith; Hammerschmidt, Katrin; Dagan, Tal

2017-08-31

Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that form true-branching filaments exemplify the most complex cyanobacteria. However, the mechanisms underlying the true-branching morphology remain poorly understood despite of several investigations that focused on the identification of novel genes or pathways. An alternative route for the evolution of novel traits is based on existing phenotypic plasticity. According to that scenario - termed genetic assimilation - the fixation of a novel phenotype precedes the fixation of the genotype. Here we show that the evolution of transcriptional regulatory elements constitutes a major mechanism for the evolution of new traits. We found that supplementation with sucrose reconstitutes the ancestral branchless phenotype of two true-branching Fischerella species and compared the transcription start sites (TSSs) between the two phenotypic states. Our analysis uncovers several orthologous TSSs whose transcription level is correlated with the true-branching phenotype. These TSSs are found in genes that encode components of the septosome and elongasome (e.g., fraC and mreB). The concept of genetic assimilation supplies a tenable explanation for the evolution of novel traits but testing its feasibility is hindered by the inability to recreate and study the evolution of present-day traits. We present a novel approach to examine transcription data for the plasticity first route and provide evidence for its occurrence during the evolution of complex colony morphology in true-branching cyanobacteria. Our results reveal a route for evolution of the true-branching phenotype in cyanobacteria via modification of the transcription level of pre-existing genes. Our study supplies evidence for the 'plasticity-first' hypothesis and highlights the importance of transcriptional regulation in the evolution of novel traits.

Complex Homology and the Evolution of Nervous Systems.

PubMed

Liebeskind, Benjamin J; Hillis, David M; Zakon, Harold H; Hofmann, Hans A

2016-02-01

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states. Copyright © 2015. Published by Elsevier Ltd.

Modification of feeding circuits in the evolution of social behavior.

PubMed

Fischer, Eva K; O'Connell, Lauren A

2017-01-01

Adaptive trade-offs between foraging and social behavior intuitively explain many aspects of individual decision-making. Given the intimate connection between social behavior and feeding/foraging at the behavioral level, we propose that social behaviors are linked to foraging on a mechanistic level, and that modifications of feeding circuits are crucial in the evolution of complex social behaviors. In this Review, we first highlight the overlap between mechanisms underlying foraging and parental care and then expand this argument to consider the manipulation of feeding-related pathways in the evolution of other complex social behaviors. We include examples from diverse taxa to highlight that the independent evolution of complex social behaviors is a variation on the theme of feeding circuit modification. © 2017. Published by The Company of Biologists Ltd.

Business Opportunities Guide

DTIC Science & Technology

1987-01-01

Electronic Systems Division Business Opportunities Guide. We remain committed to providing industry the best information possible on pending ESD...Commander Justific ill,):, By_ D.is’ * . ’ . Dist, : :,. ELECTRONIC SYSTEMS DIVISION BUSINESS OPPORTUNITIES GUIDE The complex Command, Control...Communications (C) systems necessary for tomorrow’s Air Foice can only be developed by a stronq’ESD/industry team. Our first Business Opportunities Guide

Cooperation in memory-based prisoner's dilemma game on interdependent networks

NASA Astrophysics Data System (ADS)

Luo, Chao; Zhang, Xiaolin; Liu, Hong; Shao, Rui

2016-05-01

Memory or so-called experience normally plays the important role to guide the human behaviors in real world, that is essential for rational decisions made by individuals. Hence, when the evolutionary behaviors of players with bounded rationality are investigated, it is reasonable to make an assumption that players in system are with limited memory. Besides, in order to unravel the intricate variability of complex systems in real world and make a highly integrative understanding of their dynamics, in recent years, interdependent networks as a comprehensive network structure have obtained more attention in this community. In this article, the evolution of cooperation in memory-based prisoner's dilemma game (PDG) on interdependent networks composed by two coupled square lattices is studied. Herein, all or part of players are endowed with finite memory ability, and we focus on the mutual influence of memory effect and interdependent network reciprocity on cooperation of spatial PDG. We show that the density of cooperation can be significantly promoted within an optimal region of memory length and interdependent strength. Furthermore, distinguished by whether having memory ability/external links or not, each kind of players on networks would have distinct evolutionary behaviors. Our work could be helpful to understand the emergence and maintenance of cooperation under the evolution of memory-based players on interdependent networks.

A Qualitative Study of Secondary School Teachers’ Perception of Social Network Analysis Metrics in the Context of Alcohol Consumption among Adolescents

PubMed Central

Quiroga, Enedina; Benavides, Carmen; Martín, Vicente

2017-01-01

Adolescence is a transitional period during which a number of changes occur. Social relationships established during this period influence adolescent behaviour and affect academic performance or alcohol consumption habits, among other issues. Teachers are very important actors in observing and guiding the evolution of their students, and should therefore have the appropriate knowledge and tools to gain insight into the complex social relationships that exist in their classes. The use of social network analysis (SNA) techniques may be helpful in order to study and monitor the evolution of these social networks. This study tries to understand how teachers perceive SNA metrics from an intuitive point of view. Using this information, useful tools could be created that allow teachers to use SNA techniques to improve their understanding of student relationships. A number of interviews with different teachers were held in secondary schools in Spain, allowing SNA concepts to be related to the everyday terms used by the teachers to characterize their students. Results from the study have an impact on questionnaire design for gathering data from students in order to perform an SNA analysis and on the design of software applications that can help teachers to understand the results of this analysis. PMID:29292718

The Evolution of Biological Complexity in Digital Organisms

NASA Astrophysics Data System (ADS)

Ofria, Charles

2013-03-01

When Darwin first proposed his theory of evolution by natural selection, he realized that it had a problem explaining the origins of traits of ``extreme perfection and complication'' such as the vertebrate eye. Critics of Darwin's theory have latched onto this perceived flaw as a proof that Darwinian evolution is impossible. In anticipation of this issue, Darwin described the perfect data needed to understand this process, but lamented that such data are ``scarcely ever possible'' to obtain. In this talk, I will discuss research where we use populations of digital organisms (self-replicating and evolving computer programs) to elucidate the genetic and evolutionary processes by which new, highly-complex traits arise, drawing inspiration directly from Darwin's wistful thinking and hypotheses. During the process of evolution in these fully-transparent computational environments we can measure the incorporation of new information into the genome, a process akin to a natural Maxwell's Demon, and identify the original source of any such information. We show that, as Darwin predicted, much of the information used to encode a complex trait was already in the genome as part of simpler evolved traits, and that many routes must be possible for a new complex trait to have a high probability of successfully evolving. In even more extreme examples of the evolution of complexity, we are now using these same principles to examine the evolutionary dynamics the drive major transitions in evolution; that is transitions to higher-levels of organization, which are some of the most complex evolutionary events to occur in nature. Finally, I will explore some of the implications of this research to other aspects of evolutionary biology and as well as ways that these evolutionary principles can be applied toward solving computational and engineering problems.

A new dynamic 3D virtual methodology for teaching the mechanics of atrial septation as seen in the human heart

PubMed Central

Schleich, Jean-Marc; Dillenseger, Jean-Louis; Houyel, Lucile; Almange, Claude; Anderson, Robert H.

2009-01-01

Background Learning embryology remains difficult, since it requires understanding of many complex phenomena. The temporal evolution of developmental events has classically been illustrated using cartoons, which create difficulty in linking spatial and temporal aspects, such correlation being the keystone of descriptive embryology. Methods We synthesized the bibliographic data from recent studies of atrial septal development. On the basis of this synthesis, consensus on the stages of atrial septation as seen in the human heart has been reached by a group of experts in cardiac embryology and paediatric cardiology. This has permitted the preparation of three-dimensional (3-D) computer graphic objects for the anatomical components involved in the different stages of normal human atrial septation. Results We have provided a virtual guide to the process of normal atrial septation, the animation providing an appreciation of the temporal and morphologic events necessary to separate the systemic and pulmonary venous returns. Conclusion We have shown that our animations of normal human atrial septation increase significantly the teaching of the complex developmental processes involved, and provide a new dynamic for the process of learning. PMID:19363807

Metal-directed design of supramolecular protein assemblies

PubMed Central

Bailey, Jake B.; Subramanian, Rohit H.; Churchfield, Lewis A.

2016-01-01

Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive non-covalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, Metal-Directed Protein Self-Assembly (MDPSA) and Metal-Templated Interface Redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution. PMID:27586336

The changing nature of life cycle assessment

PubMed Central

McManus, Marcelle C.; Taylor, Caroline M.

2015-01-01

LCA has evolved from its origins in energy analysis in the 1960s and 70s into a wide ranging tool used to determine impacts of products or systems over several environmental and resource issues. The approach has become more prevalent in research, industry and policy. Its use continues to expand as it seeks to encompass impacts as diverse as resource accounting and social well being. Carbon policy for bioenergy has driven many of these changes. Enabling assessment of complex issues over a life cycle basis is beneficial, but the process is sometimes difficult. LCA's use in framing is increasingly complex and more uncertain, and in some cases, irreconcilable. The charged environment surrounding biofuels and bioenergy exacerbates all of these. Reaching its full potential to help guide difficult policy discussions and emerging research involves successfully managing LCA's transition from attributional to consequential and from retrospective to prospective. This paper examines LCA's on-going evolution and its use within bioenergy deployment. The management of methodological growth in the context of the unique challenges associated with bioenergy and biofuels is explored. Changes seen in bioenergy LCA will bleed into other LCA arenas, especially where it is important that a sustainable solution is chosen. PMID:26664146

Remote Sensing of Extraterrestrial life: Complexity as the key characteristicsof living systems

NASA Astrophysics Data System (ADS)

Wolf, Sebastian

2015-07-01

Motivated by the detection of planetary candidates around more than one thousand stars since 1995 and the beginning characterization of their major properties (orbit, mass, physical conditions and chemical composition of their atmosphere), the quest for understanding the origin and evolution of life from the broadest possible perspective comes into reach of scientific exploration. Due to the apparent lack of a better starting point, the search for life outside Earth is strongly influenced and guided by biological and biochemical studies of life on our planet so far. Furthermore, this search is built on the assumption that life - in the sense of animated matter - is qualitatively different from inanimate matter. However, the first constraint might unnecessarily limit our search, while the latter underlying assumption is not justified. In this study, a more general approach to search for life in the universe with astrophysical means is proposed, which is not based on the above constraint and assumption. More specifically, the property of living systems to possess a high degree of complexity in structure and its response to the environment is discussed in view of its potential to be used for remote sensing of extraterrestrial life.

MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

PubMed

Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

2010-04-08

RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

MicroRNA–Directed siRNA Biogenesis in Caenorhabditis elegans

PubMed Central

Corrêa, Régis L.; Steiner, Florian A.; Berezikov, Eugene; Ketting, René F.

2010-01-01

RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi–related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer. PMID:20386745

Assessment Environment for Complex Systems Software Guide

NASA Technical Reports Server (NTRS)

2013-01-01

This Software Guide (SG) describes the software developed to test the Assessment Environment for Complex Systems (AECS) by the West Virginia High Technology Consortium (WVHTC) Foundation's Mission Systems Group (MSG) for the National Aeronautics and Space Administration (NASA) Aeronautics Research Mission Directorate (ARMD). This software is referred to as the AECS Test Project throughout the remainder of this document. AECS provides a framework for developing, simulating, testing, and analyzing modern avionics systems within an Integrated Modular Avionics (IMA) architecture. The purpose of the AECS Test Project is twofold. First, it provides a means to test the AECS hardware and system developed by MSG. Second, it provides an example project upon which future AECS research may be based. This Software Guide fully describes building, installing, and executing the AECS Test Project as well as its architecture and design. The design of the AECS hardware is described in the AECS Hardware Guide. Instructions on how to configure, build and use the AECS are described in the User's Guide. Sample AECS software, developed by the WVHTC Foundation, is presented in the AECS Software Guide. The AECS Hardware Guide, AECS User's Guide, and AECS Software Guide are authored by MSG. The requirements set forth for AECS are presented in the Statement of Work for the Assessment Environment for Complex Systems authored by NASA Dryden Flight Research Center (DFRC). The intended audience for this document includes software engineers, hardware engineers, project managers, and quality assurance personnel from WVHTC Foundation (the suppliers of the software), NASA (the customer), and future researchers (users of the software). Readers are assumed to have general knowledge in the field of real-time, embedded computer software development.

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

PubMed

Kim, Inhae; Lee, Heetak; Han, Seong Kyu; Kim, Sanguk

2014-10-01

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

KRISSY: user's guide to modeling three-dimensional wind flow in complex terrain

Treesearch

Michael A. Fosberg; Michael L. Sestak

1986-01-01

KRISSY is a computer model for generating three-dimensional wind flows in complex terrain from data that were not or perhaps cannot be collected. The model is written in FORTRAN IV This guide describes data requirements, modeling, and output from an applications viewpoint rather than that of programming or theoretical modeling. KRISSY is designed to minimize...

Life history, cognition and the evolution of complex foraging niches.

PubMed

Schuppli, Caroline; Graber, Sereina M; Isler, Karin; van Schaik, Carel P

2016-03-01

Animal species that live in complex foraging niches have, in general, improved access to energy-rich and seasonally stable food sources. Because human food procurement is uniquely complex, we ask here which conditions may have allowed species to evolve into such complex foraging niches, and also how niche complexity is related to relative brain size. To do so, we divided niche complexity into a knowledge-learning and a motor-learning dimension. Using a sample of 78 primate and 65 carnivoran species, we found that two life-history features are consistently correlated with complex niches: slow, conservative development or provisioning of offspring over extended periods of time. Both act to buffer low energy yields during periods of learning, and may thus act as limiting factors for the evolution of complex niches. Our results further showed that the knowledge and motor dimensions of niche complexity were correlated with pace of development in primates only, and with the length of provisioning in only carnivorans. Accordingly, in primates, but not carnivorans, living in a complex foraging niche requires enhanced cognitive abilities, i.e., a large brain. The patterns in these two groups of mammals show that selection favors evolution into complex niches (in either the knowledge or motor dimension) in species that either develop more slowly or provision their young for an extended period of time. These findings help to explain how humans constructed by far the most complex niche: our ancestors managed to combine slow development (as in other primates) with systematic provisioning of immatures and even adults (as in carnivorans). This study also provides strong support for the importance of ecological factors in brain size evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impairment Rating Ambiguity in the United States: The Utah Impairment Guides for Calculating Workers' Compensation Impairments

PubMed Central

Hunter, Bradley; Bunkall, Larry D.; Holmes, Edward B.

2009-01-01

Since the implementation of workers' compensation, accurately and consistently rating impairment has been a concern for the employee and employer, as well as rating physicians. In an attempt to standardize and classify impairments, the American Medical Association (AMA) publishes the AMA Guides ("Guides"), and recently published its 6th edition of the AMA Guides. Common critiques of the AMA Guides 6th edition are that they are too complex, lacking in evidence-based methods, and rarely yield consistent ratings. Many states mandate use of some edition of the AMA Guides, but few states are adopting the current edition due to the increasing difficulty and frustration with their implementation. A clearer, simpler approach is needed. Some states have begun to develop their own supplemental guides to combat problems in complexity and validity. Likewise studies in Korea show that past methods for rating impairment are outdated and inconsistent, and call for measures to adapt current methods to Korea's specific needs. The Utah Supplemental Guides to the AMA Guides have been effective in increasing consistency in rating impairment. It is estimated that litigation of permanent impairment has fallen below 1% and Utah is now one of the least costly states for obtaining workers' compensation insurance, while maintaining a medical fee schedule above the national average. Utah's guides serve as a model for national or international impairment guides. PMID:19503678

Rise and fall of political complexity in island South-East Asia and the Pacific.

PubMed

Currie, Thomas E; Greenhill, Simon J; Gray, Russell D; Hasegawa, Toshikazu; Mace, Ruth

2010-10-14

There is disagreement about whether human political evolution has proceeded through a sequence of incremental increases in complexity, or whether larger, non-sequential increases have occurred. The extent to which societies have decreased in complexity is also unclear. These debates have continued largely in the absence of rigorous, quantitative tests. We evaluated six competing models of political evolution in Austronesian-speaking societies using phylogenetic methods. Here we show that in the best-fitting model political complexity rises and falls in a sequence of small steps. This is closely followed by another model in which increases are sequential but decreases can be either sequential or in bigger drops. The results indicate that large, non-sequential jumps in political complexity have not occurred during the evolutionary history of these societies. This suggests that, despite the numerous contingent pathways of human history, there are regularities in cultural evolution that can be detected using computational phylogenetic methods.

Could Bertrand Russell's barber have bitten his own teeth? A problem of logic and definitions.

PubMed

Aitken, Kenneth John

2014-08-01

Guiding the positive evolution of behavior is an admirable goal. Wilson et al.'s arguments are based largely on studies of problem correction. The methodology is sound, but not the post hoc ergo procter hoc extrapolation. What is required is evidence that it can proactively generate positive change. The evolution of human behavior to date has been affected by many factors that include unmalleable and unpredicted environmental changes.

Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.

PubMed

Villarreal A, Juan Carlos; Crandall-Stotler, Barbara J; Hart, Michelle L; Long, David G; Forrest, Laura L

2016-03-01

We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization. © 2015 Royal Botanic Garden Edinburgh. New Phytologist © 2015 New Phytologist Trust.

Prediction in complex systems: The case of the international trade network

NASA Astrophysics Data System (ADS)

Vidmer, Alexandre; Zeng, An; Medo, Matúš; Zhang, Yi-Cheng

2015-10-01

Predicting the future evolution of complex systems is one of the main challenges in complexity science. Based on a current snapshot of a network, link prediction algorithms aim to predict its future evolution. We apply here link prediction algorithms to data on the international trade between countries. This data can be represented as a complex network where links connect countries with the products that they export. Link prediction techniques based on heat and mass diffusion processes are employed to obtain predictions for products exported in the future. These baseline predictions are improved using a recent metric of country fitness and product similarity. The overall best results are achieved with a newly developed metric of product similarity which takes advantage of causality in the network evolution.

Information-theoretic metamodel of organizational evolution

NASA Astrophysics Data System (ADS)

Sepulveda, Alfredo

2011-12-01

Social organizations are abstractly modeled by holarchies---self-similar connected networks---and intelligent complex adaptive multiagent systems---large networks of autonomous reasoning agents interacting via scaled processes. However, little is known of how information shapes evolution in such organizations, a gap that can lead to misleading analytics. The research problem addressed in this study was the ineffective manner in which classical model-predict-control methods used in business analytics attempt to define organization evolution. The purpose of the study was to construct an effective metamodel for organization evolution based on a proposed complex adaptive structure---the info-holarchy. Theoretical foundations of this study were holarchies, complex adaptive systems, evolutionary theory, and quantum mechanics, among other recently developed physical and information theories. Research questions addressed how information evolution patterns gleamed from the study's inductive metamodel more aptly explained volatility in organization. In this study, a hybrid grounded theory based on abstract inductive extensions of information theories was utilized as the research methodology. An overarching heuristic metamodel was framed from the theoretical analysis of the properties of these extension theories and applied to business, neural, and computational entities. This metamodel resulted in the synthesis of a metaphor for, and generalization of organization evolution, serving as the recommended and appropriate analytical tool to view business dynamics for future applications. This study may manifest positive social change through a fundamental understanding of complexity in business from general information theories, resulting in more effective management.

Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.

PubMed

Koonin, Eugene V

2017-02-10

Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.

Evolution of complexity following a global quench

NASA Astrophysics Data System (ADS)

Moosa, Mudassir

2018-03-01

The rate of complexification of a quantum state is conjectured to be bounded from above by the average energy of the state. A different conjecture relates the complexity of a holographic CFT state to the on-shell gravitational action of a certain bulk region. We use `complexity equals action' conjecture to study the time evolution of the complexity of the CFT state after a global quench. We find that the rate of growth of complexity is not only consistent with the conjectured bound, but it also saturates the bound soon after the system has achieved local equilibrium.

[How to make your own custom cutting guides for both mandibular and fibular stair step osteotomies?

PubMed

Rem, K; Bosc, R; De Kermadec, H; Hersant, B; Meningaud, J-P

2017-12-01

Using tailored cutting guides for osteocutaneous free fibula flap in complex mandibular reconstruction after cancer resection surgery constitutes a substantial improvement. Autonomously conceiving and manufacturing the cutting guides within a plastic surgery department with computer-aided design (CAD) and three-dimensional (3D) printing allows planning more complex osteotomies, such as stair-step osteotomies, in order to achieve more stable internal fixations. For the past three years, we have been producing by ourselves patient-tailored cutting guides using CAD and 3D printing. Osteotomies were virtually planned, making the cutting lines more complex in order to optimize the internal fixation stability. We also printed reconstructed mandible templates and shaped the reconstruction plates on them. We recorded data including manufacturing techniques and surgical outcomes. Eleven consecutive patients were operated on for an oral cavity cancer. For each patient, we planned the fibular and mandibular stair-step osteotomies and we produced tailored cutting guides. In all patients, we achieved to get immediately stable internal fixations and in 10 patients, a complete bone consolidation after 6 months. Autonomously manufacturing surgical cutting guides for mandibular reconstruction by free fibula flap is a significant improvement, regarding ergonomics and precision. Planning stair-step osteotomies to perform complementary internal fixation increases contact surface and congruence between the bone segments, thus improving the reconstructed mandible stability. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Extended use of the GuideLiner in complex coronary interventions.

PubMed

Chan, Pak Hei; Alegria-Barrero, Eduardo; Foin, Nicholas; Paulo, Manuel; Lindsay, Alistair C; Viceconte, Nicola; Di Mario, Carlo

2015-07-01

Challenging coronary anatomies including chronic total occlusions (CTO), extreme vessel tortuosity, diseased bypass grafts, and anomalous coronary arteries pose difficulties in coronary interventions. The GuideLiner is a monorail catheter originally developed to facilitate delivery of stents to target lesions in tortuous vessels. We conducted a study on the feasibility and safety of utilising this catheter in a wider array of complex coronary interventions. Consecutive patients undergoing coronary or peripheral interventions where a GuideLiner was used were recruited into this study. Patient demographics, lesion and vessel characteristics, procedural details and outcomes were prospectively entered into our database and analysed. From September 2009 to October 2011, 54 consecutive patients underwent coronary intervention in our institution using a GuideLiner; 21 out of 54 coronary applications were motivated by the need to increase support to cross CTOs, predominantly of the RCA. Anomalous or angulated take-off of the treatment vessels (31%), previously deployed proximal stents (15%), heavy proximal calcification (9%) and tortuosity (7%) accounted for the remaining reasons. One patient had successful renal denervation with the aid of a GuideLiner catheter. Procedural success was 98% in our series with no device-related periprocedural complications such as ostial dissection or myocardial necrosis. The use of a GuideLiner facilitates the approach to complex coronary interventions including chronic total occlusion and saphenous vein graft intervention by providing greater back-up support and easier engagement of coronary ostia.

The spatiotemporal system dynamics of acquired resistance in an engineered microecology.

PubMed

Datla, Udaya Sree; Mather, William H; Chen, Sheng; Shoultz, Isaac W; Täuber, Uwe C; Jones, Caroline N; Butzin, Nicholas C

2017-11-22

Great strides have been made in the understanding of complex networks; however, our understanding of natural microecologies is limited. Modelling of complex natural ecological systems has allowed for new findings, but these models typically ignore the constant evolution of species. Due to the complexity of natural systems, unanticipated interactions may lead to erroneous conclusions concerning the role of specific molecular components. To address this, we use a synthetic system to understand the spatiotemporal dynamics of growth and to study acquired resistance in vivo. Our system differs from earlier synthetic systems in that it focuses on the evolution of a microecology from a killer-prey relationship to coexistence using two different non-motile Escherichia coli strains. Using empirical data, we developed the first ecological model emphasising the concept of the constant evolution of species, where the survival of the prey species is dependent on location (distance from the killer) or the evolution of resistance. Our simple model, when expanded to complex microecological association studies under varied spatial and nutrient backgrounds may help to understand the complex relationships between multiple species in intricate natural ecological networks. This type of microecological study has become increasingly important, especially with the emergence of antibiotic-resistant pathogens.

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits.

PubMed

Wang, Yaqiong; Ma, Hong

2015-09-01

Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Mapping the Evolution of Scientific Fields

PubMed Central

Herrera, Mark; Roberts, David C.; Gulbahce, Natali

2010-01-01

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985–2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development. PMID:20463949

Mapping the evolution of scientific fields.

PubMed

Herrera, Mark; Roberts, David C; Gulbahce, Natali

2010-05-04

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985-2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development.

A Guided Inquiry Activity for Teaching Ligand Field Theory

ERIC Educational Resources Information Center

Johnson, Brian J.; Graham, Kate J.

2015-01-01

This paper will describe a guided inquiry activity for teaching ligand field theory. Previous research suggests the guided inquiry approach is highly effective for student learning. This activity familiarizes students with the key concepts of molecular orbital theory applied to coordination complexes. Students will learn to identify factors that…

41 CFR 101-5.303 - Guiding principles.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Guiding principles. 101-5... COMPLEXES 5.3-Federal Employee Health Services § 101-5.303 Guiding principles. The following principles will..., the compensation of the employees of the health unit, and other factors of medical economics prevalent...

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

PubMed

Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Particle-in-cell simulations of collisionless magnetic reconnection with a non-uniform guide field

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

Wilson, F., E-mail: fw237@st-andrews.ac.uk; Neukirch, T., E-mail: tn3@st-andrews.ac.uk; Harrison, M. G.

Results are presented of a first study of collisionless magnetic reconnection starting from a recently found exact nonlinear force-free Vlasov–Maxwell equilibrium. The initial state has a Harris sheet magnetic field profile in one direction and a non-uniform guide field in a second direction, resulting in a spatially constant magnetic field strength as well as a constant initial plasma density and plasma pressure. It is found that the reconnection process initially resembles guide field reconnection, but that a gradual transition to anti-parallel reconnection happens as the system evolves. The time evolution of a number of plasma parameters is investigated, and themore » results are compared with simulations starting from a Harris sheet equilibrium and a Harris sheet plus constant guide field equilibrium.« less

Modified unified kinetic scheme for all flow regimes.

PubMed

Liu, Sha; Zhong, Chengwen

2012-06-01

A modified unified kinetic scheme for the prediction of fluid flow behaviors in all flow regimes is described. The time evolution of macrovariables at the cell interface is calculated with the idea that both free transport and collision mechanisms should be considered. The time evolution of macrovariables is obtained through the conservation constraints. The time evolution of local Maxwellian distribution is obtained directly through the one-to-one mapping from the evolution of macrovariables. These improvements provide more physical realities in flow behaviors and more accurate numerical results in all flow regimes especially in the complex transition flow regime. In addition, the improvement steps introduce no extra computational complexity.

Analyzing complex networks evolution through Information Theory quantifiers

NASA Astrophysics Data System (ADS)

Carpi, Laura C.; Rosso, Osvaldo A.; Saco, Patricia M.; Ravetti, Martín Gómez

2011-01-01

A methodology to analyze dynamical changes in complex networks based on Information Theory quantifiers is proposed. The square root of the Jensen-Shannon divergence, a measure of dissimilarity between two probability distributions, and the MPR Statistical Complexity are used to quantify states in the network evolution process. Three cases are analyzed, the Watts-Strogatz model, a gene network during the progression of Alzheimer's disease and a climate network for the Tropical Pacific region to study the El Niño/Southern Oscillation (ENSO) dynamic. We find that the proposed quantifiers are able not only to capture changes in the dynamics of the processes but also to quantify and compare states in their evolution.

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

PubMed

Pallen, M J; Gophna, U

2007-01-01

Bacterial flagella at first sight appear uniquely sophisticated in structure, so much so that they have even been considered 'irreducibly complex' by the intelligent design movement. However, a more detailed analysis reveals that these remarkable pieces of molecular machinery are the product of processes that are fully compatible with Darwinian evolution. In this chapter we present evidence for such processes, based on a review of experimental studies, molecular phylogeny and microbial genomics. Several processes have played important roles in flagellar evolution: self-assembly of simple repeating subunits, gene duplication with subsequent divergence, recruitment of elements from other systems ('molecular bricolage'), and recombination. We also discuss additional tentative new assignments of homology (FliG with MgtE, FliO with YscJ). In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components.

Preventing a Cyber Dresden: How the Evolution of Air Power can Guide the Evolution of Cyber

DTIC Science & Technology

2011-06-01

24 Paul Cornish, On Cyber Warfare, (London: RUSI, 2010), 1. 25 CNN‟s footage of Project Aurora, the staged demonstration of SCADA vulnerabilities... Paul McHugh, “Striving for Coherence: Psychiatry‟s Efforts Over Classification”, The Journal of American Medical Association, no.293 (2005):2526-2528...Randall Wakelam, The Science of Bombing: Operational Research in RAF Bomber Command (Toronto: University of Toronto Press, 2009), 157-182 and Dana

Experiences and practices of evolution instructors at Christian universities that can inform culturally competent evolution education

PubMed Central

Barnes, M. Elizabeth

2017-01-01

Abstract Students’ religious beliefs and religious cultures have been shown to be the main factors predicting whether they will accept evolution, yet college biology instructors teaching evolution at public institutions often have religious beliefs and cultures that are different from their religious students. This difference in religious beliefs and cultures may be a barrier to effective evolution education. To explore when evolution instructors have similar religious cultures and beliefs as their students, we interviewed 32 evolution instructors at Christian universities nationwide about their practices and experiences teaching evolution. Christian university instructors emphasized teaching for acceptance of evolution while holding an inclusive teaching philosophy that they perceived led to a safe environment for students. Additionally, almost all instructors reported using practices that have been shown to increase student acceptance of evolution and reduce student conflict between evolution and religion. Further, we found that these instructors perceived that their own religious backgrounds have guided their decisions to teach evolution to their students in a culturally competent way. We discuss how these data, combined with past research literature on public college instructors, indicate that cultural competence could be a useful new framework for promoting effective evolution education in higher education institutions. PMID:29398727

[The motive force of evolution based on the principle of organismal adjustment evolution.].

PubMed

Cao, Jia-Shu

2010-08-01

From the analysis of the existing problems of the prevalent theories of evolution, this paper discussed the motive force of evolution based on the knowledge of the principle of organismal adjustment evolution to get a new understanding of the evolution mechanism. In the guide of Schrodinger's theory - "life feeds on negative entropy", the author proposed that "negative entropy flow" actually includes material flow, energy flow and information flow, and the "negative entropy flow" is the motive force for living and development. By modifying my own theory of principle of organismal adjustment evolution (not adaptation evolution), a new theory of "regulation system of organismal adjustment evolution involved in DNA, RNA and protein interacting with environment" is proposed. According to the view that phylogenetic development is the "integral" of individual development, the difference of negative entropy flow between organisms and environment is considered to be a motive force for evolution, which is a new understanding of the mechanism of evolution. Based on such understanding, evolution is regarded as "a changing process that one subsystem passes all or part of its genetic information to the next generation in a larger system, and during the adaptation process produces some new elements, stops some old ones, and thereby lasts in the larger system". Some other controversial questions related to evolution are also discussed.

Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

PubMed

Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

2016-01-01

This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms

PubMed Central

Grabowski, Laura M.; Bryson, David M.; Dyer, Fred C.; Pennock, Robert T.; Ofria, Charles

2013-01-01

Investigating the evolution of animal behavior is difficult. The fossil record leaves few clues that would allow us to recapitulate the path that evolution took to build a complex behavior, and the large population sizes and long time scales required prevent us from re-evolving such behaviors in a laboratory setting. We present results of a study in which digital organisms–self-replicating computer programs that are subject to mutations and selection–evolved in different environments that required information about past experience for fitness-enhancing behavioral decisions. One population evolved a mechanism for step-counting, a surprisingly complex odometric behavior that was only indirectly related to enhancing fitness. We examine in detail the operation of the evolved mechanism and the evolutionary transitions that produced this striking example of a complex behavior. PMID:23577113

Progress on Complex Langevin simulations of a finite density matrix model for QCD

NASA Astrophysics Data System (ADS)

Bloch, Jacques; Glesaaen, Jonas; Verbaarschot, Jacobus; Zafeiropoulos, Savvas

2018-03-01

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplemented with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.

Convergent evolution: floral guides, stingless bee nest entrances, and insectivorous pitchers

NASA Astrophysics Data System (ADS)

Biesmeijer, Jacobus C.; Giurfa, Martin; Koedam, Dirk; Potts, Simon G.; Joel, Daniel M.; Dafni, Amots

2005-09-01

Several recent hypotheses, including sensory drive and sensory exploitation, suggest that receiver biases may drive selection of biological signals in the context of sexual selection. Here we suggest that a similar mechanism may have led to convergence of patterns in flowers, stingless bee nest entrances, and pitchers of insectivorous plants. A survey of these non-related visual stimuli shows that they share features such as stripes, dark centre, and peripheral dots. Next, we experimentally show that in stingless bees the close-up approach to a flower is guided by dark centre preference. Moreover, in the approach towards their nest entrance, they have a spontaneous preference for entrance patterns containing a dark centre and disrupted ornamentation. Together with existing empirical evidence on the honeybee's and other insects’ orientation to flowers, this suggests that the signal receivers of the natural patterns we examined, mainly Hymenoptera, have spontaneous preferences for radiating stripes, dark centres, and peripheral dots. These receiver biases may have evolved in other behavioural contexts in the ancestors of Hymenoptera, but our findings suggest that they have triggered the convergent evolution of visual stimuli in floral guides, stingless bee nest entrances, and insectivorous pitchers.

Convergent evolution: floral guides, stingless bee nest entrances, and insectivorous pitchers.

PubMed

Biesmeijer, Jacobus C; Giurfa, Martin; Koedam, Dirk; Potts, Simon G; Joel, Daniel M; Dafni, Amots

2005-09-01

Several recent hypotheses, including sensory drive and sensory exploitation, suggest that receiver biases may drive selection of biological signals in the context of sexual selection. Here we suggest that a similar mechanism may have led to convergence of patterns in flowers, stingless bee nest entrances, and pitchers of insectivorous plants. A survey of these non-related visual stimuli shows that they share features such as stripes, dark centre, and peripheral dots. Next, we experimentally show that in stingless bees the close-up approach to a flower is guided by dark centre preference. Moreover, in the approach towards their nest entrance, they have a spontaneous preference for entrance patterns containing a dark centre and disrupted ornamentation. Together with existing empirical evidence on the honeybee's and other insects' orientation to flowers, this suggests that the signal receivers of the natural patterns we examined, mainly Hymenoptera, have spontaneous preferences for radiating stripes, dark centres, and peripheral dots. These receiver biases may have evolved in other behavioural contexts in the ancestors of Hymenoptera, but our findings suggest that they have triggered the convergent evolution of visual stimuli in floral guides, stingless bee nest entrances, and insectivorous pitchers.

Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach.

PubMed

Otey, Christopher R; Silberg, Jonathan J; Voigt, Christopher A; Endelman, Jeffrey B; Bandara, Geethani; Arnold, Frances H

2004-03-01

Recombination generates chimeric proteins whose ability to fold depends on minimizing structural perturbations that result when portions of the sequence are inherited from different parents. These chimeric sequences can display functional properties characteristic of the parents or acquire entirely new functions. Seventeen chimeras were generated from two CYP102 members of the functionally diverse cytochrome p450 family. Chimeras predicted to have limited structural disruption, as defined by the SCHEMA algorithm, displayed CO binding spectra characteristic of folded p450s. Even this small population exhibited significant functional diversity: chimeras displayed altered substrate specificities, a wide range in thermostabilities, up to a 40-fold increase in peroxidase activity, and ability to hydroxylate a substrate toward which neither parent heme domain shows detectable activity. These results suggest that SCHEMA-guided recombination can be used to generate diverse p450s for exploring function evolution within the p450 structural framework.

General visual robot controller networks via artificial evolution

NASA Astrophysics Data System (ADS)

Cliff, David; Harvey, Inman; Husbands, Philip

1993-08-01

We discuss recent results from our ongoing research concerning the application of artificial evolution techniques (i.e., an extended form of genetic algorithm) to the problem of developing `neural' network controllers for visually guided robots. The robot is a small autonomous vehicle with extremely low-resolution vision, employing visual sensors which could readily be constructed from discrete analog components. In addition to visual sensing, the robot is equipped with a small number of mechanical tactile sensors. Activity from the sensors is fed to a recurrent dynamical artificial `neural' network, which acts as the robot controller, providing signals to motors governing the robot's motion. Prior to presentation of new results, this paper summarizes our rationale and past work, which has demonstrated that visually guided control networks can arise without any explicit specification that visual processing should be employed: the evolutionary process opportunistically makes use of visual information if it is available.

Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes.

PubMed

Li, Guangyue; Wang, Jian-Bo; Reetz, Manfred T

2018-04-01

Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Receiver discriminability drives the evolution of complex sexual signals by sexual selection.

PubMed

Cui, Jianguo; Song, Xiaowei; Zhu, Bicheng; Fang, Guangzhan; Tang, Yezhong; Ryan, Michael J

2016-04-01

A hallmark of sexual selection by mate choice is the evolution of exaggerated traits, such as longer tails in birds and more acoustic components in the calls of birds and frogs. Trait elaboration can be opposed by costs such as increased metabolism and greater predation risk, but cognitive processes of the receiver can also put a brake on trait elaboration. For example, according to Weber's Law traits of a fixed absolute difference will be more difficult to discriminate as the absolute magnitude increases. Here, we show that in the Emei music frog (Babina daunchina) increases in the fundamental frequency between successive notes in the male advertisement call, which increases the spectral complexity of the call, facilitates the female's ability to compare the number of notes between calls. These results suggest that female's discriminability provides the impetus to switch from enhancement of signaling magnitude (i.e., adding more notes into calls) to employing a new signal feature (i.e., increasing frequency among notes) to increase complexity. We suggest that increasing the spectral complexity of notes ameliorates some of the effects of Weber's Law, and highlights how perceptual and cognitive biases of choosers can have important influences on the evolution of courtship signals. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Evolution of weighted complex bus transit networks with flow

NASA Astrophysics Data System (ADS)

Huang, Ailing; Xiong, Jie; Shen, Jinsheng; Guan, Wei

2016-02-01

Study on the intrinsic properties and evolutional mechanism of urban public transit networks (PTNs) has great significance for transit planning and control, particularly considering passengers’ dynamic behaviors. This paper presents an empirical analysis for exploring the complex properties of Beijing’s weighted bus transit network (BTN) based on passenger flow in L-space, and proposes a bi-level evolution model to simulate the development of transit routes from the view of complex network. The model is an iterative process that is driven by passengers’ travel demands and dual-controlled interest mechanism, which is composed of passengers’ spatio-temporal requirements and cost constraint of transit agencies. Also, the flow’s dynamic behaviors, including the evolutions of travel demand, sectional flow attracted by a new link and flow perturbation triggered in nearby routes, are taken into consideration in the evolutional process. We present the numerical experiment to validate the model, where the main parameters are estimated by using distribution functions that are deduced from real-world data. The results obtained have proven that our model can generate a BTN with complex properties, such as the scale-free behavior or small-world phenomenon, which shows an agreement with our empirical results. Our study’s results can be exploited to optimize the real BTN’s structure and improve the network’s robustness.

Carbon in the Universe

NASA Technical Reports Server (NTRS)

Allamandola, Louis J.

2013-01-01

Over the past few decades, NASA missions have revealed that we live in a Universe that is not a hydrogen-dominated, physicist's paradise, but in a molecular Universe with complex molecules directly interwoven into its fabric. These missions have shown that molecules are an abundant and important component of astronomical objects at all stages of their evolution and that they play a key role in many processes that dominate the structure and evolution of galaxies. Closer to home in our galaxy, the Milky Way, they have revealed a unique and complex organic inventory of regions of star and planet formation that may well represent some of the prebiotic roots to life. Astrobiology emerges from the great interest in understanding astrochemical evolution from simple to complex molecules, especially those with biogenic potential and the roles they may play as primordial seeds in the origin of life on habitable worlds. The first part of this talk will highlight how infrared spectroscopic studies of interstellar space, combined with dedicated laboratory simulations, have revealed the widespread presence of complex organics across deep space. The remainder of the presentation will focus on the evolution of these materials and astrobiology.

Beverton-Holt discrete pest management models with pulsed chemical control and evolution of pesticide resistance

NASA Astrophysics Data System (ADS)

Liang, Juhua; Tang, Sanyi; Cheke, Robert A.

2016-07-01

Pest resistance to pesticides is usually managed by switching between different types of pesticides. The optimal switching time, which depends on the dynamics of the pest population and on the evolution of the pesticide resistance, is critical. Here we address how the dynamic complexity of the pest population, the development of resistance and the spraying frequency of pulsed chemical control affect optimal switching strategies given different control aims. To do this, we developed novel discrete pest population growth models with both impulsive chemical control and the evolution of pesticide resistance. Strong and weak threshold conditions which guarantee the extinction of the pest population, based on the threshold values of the analytical formula for the optimal switching time, were derived. Further, we addressed switching strategies in the light of chosen economic injury levels. Moreover, the effects of the complex dynamical behaviour of the pest population on the pesticide switching times were also studied. The pesticide application period, the evolution of pesticide resistance and the dynamic complexity of the pest population may result in complex outbreak patterns, with consequent effects on the pesticide switching strategies.

The systematics and independent evolution of cave ecomorphology in distantly related clades of Bent-toed Geckos (Genus Cyrtodactylus Gray, 1827) from the Mekong Delta and islands in the Gulf of Thailand.

PubMed

Grismer, L Lee; Wood, P L Jr; Tri, Ngo Van; Murdoch, Matthew L

2015-06-26

An integrative taxonomic analysis of the distantly related Cyrtodactylus condorensis and intermedius species complexes of the Mekong Delta revealed that C. paradoxus is a junior synonym of C. condorensis and that C. thochuensis is a junior synonym of C. leegrismeri. Additionally, the analysis revealed that a cave-dwelling ecomorpholgy has evolved independently early on in the evolution of both complexes (represented by C. hontreensis in the intermedius complex and C. grismeri and C. eisenmani in the condorensis complex) and cave ecomorphs exist in sympatry-but not syntopy-with general scansorial ecomorphs. Multiple, recent, cyclical, glacioeustatic driven changes in sea levels across the Sunda Shelf are hypothesized to account for the evolution and distribution of the widely separated, conspecific insular populations of C. condorensis and C. leegrismeri. The independent evolution of cave ecomorphology is proposed to have been driven by competition avoidance. Habitat islands across the Mekong Delta are an important source of endemism and in need of protection.

Qureshi-5 Catheter for Complex Supra- and Abdominal-Aortic Catheterization

PubMed Central

Qureshi, Adnan I.; Xiao, WeiGang; Liu, HongLiang

2015-01-01

Background The use of previously described catheter technique was expanded to complex supra- and abdominal- aortic catheterizations. Methods A new (Qureshi 5) catheter with curved shape at the distal end that has two lumens was used. One of lumens can accommodate a 0.035-inch guide wire and the second lumen can accommodate a 0.018-inch guide wire and terminates at the beginning of the distal curve of the first lumen. The manipulation and engagement of the curved distal end catheter was facilitated by rotation and movement of the J-shaped 0.018-inch guide wire extended coaxial and beyond the distal end of catheter. Subsequently, either contrast was injected or a 0.035-inch guide wire advanced into the target artery. Results The catheters were used in one patient to perform diagnostic cerebral and abdominal angiography through a 6F introducer sheath placed in the right common femoral artery. The catheterization was complex because of severe tortuosity of arch and descending aorta secondary to kyphosis. The left and right internal carotid arteries and left and right vertebral arteries, left renal artery, and superior mesenteric artery were catheterized in patient (fluoroscopy time 19:46 min). No complications were observed in the patient. Conclusions The Qureshi-5 catheter was successful in complex supra- and abdominal-aortic catheterizations. PMID:26600925

Qureshi-5 Catheter for Complex Supra- and Abdominal-Aortic Catheterization.

PubMed

Qureshi, Adnan I; Xiao, WeiGang; Liu, HongLiang

2015-10-01

The use of previously described catheter technique was expanded to complex supra- and abdominal- aortic catheterizations. A new (Qureshi 5) catheter with curved shape at the distal end that has two lumens was used. One of lumens can accommodate a 0.035-inch guide wire and the second lumen can accommodate a 0.018-inch guide wire and terminates at the beginning of the distal curve of the first lumen. The manipulation and engagement of the curved distal end catheter was facilitated by rotation and movement of the J-shaped 0.018-inch guide wire extended coaxial and beyond the distal end of catheter. Subsequently, either contrast was injected or a 0.035-inch guide wire advanced into the target artery. The catheters were used in one patient to perform diagnostic cerebral and abdominal angiography through a 6F introducer sheath placed in the right common femoral artery. The catheterization was complex because of severe tortuosity of arch and descending aorta secondary to kyphosis. The left and right internal carotid arteries and left and right vertebral arteries, left renal artery, and superior mesenteric artery were catheterized in patient (fluoroscopy time 19:46 min). No complications were observed in the patient. The Qureshi-5 catheter was successful in complex supra- and abdominal-aortic catheterizations.

Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Beyond complexity measures, sometimes it is worthwhile in addition to investigate how complexity changes structurally, especially in artificial systems where we have complete knowledge about the evolutionary process. Hierarchical decomposition is a useful way of assessing structural complexity changes of organisms modeled as automata, and we show how recently developed computational tools can be used for this purpose, by computing holonomy decompositions and holonomy complexity. To gain insight into the evolution of complexity, we investigate the smoothness of the landscape structure of complexity under minimal transitions. As a proof of concept, we illustrate how the hierarchical complexity analysis reveals symmetries and irreversible structure in biological networks by applying the methods to the lac operon mechanism in the genetic regulatory network of Escherichia coli.

The evolution of complex and higher organisms

NASA Technical Reports Server (NTRS)

Milne, D. (Editor); Raup, D. (Editor); Billingham, J. (Editor); Niklaus, K. (Editor); Padian, K. (Editor)

1985-01-01

The evolution of Phanerozoic life has probably been influenced by extraterrestrial events and properties of the Earth-Moon system that have not, until now, been widely recognized. Tide range, gravitational strength, the Earth's axial tilt, and other planetary properties provide background conditions whose effects on evolution may be difficult to distinguish. Solar flares, asteroid impacts, supernovae, and passage of the solar system through galactic clouds can provide catastrophic changes on the Earth with consequent characteristic extinctions. Study of the fossil record and the evolution of complex Phanerozoic life can reveal evidence of past disturbances in space near the Earth. Conversely, better understanding of environmental influences caused by extraterrestrial factors and properties of the solar system can clarify aspects of evolution, and may aid in visualizing life on other planets with different properties.

Complexities’ day-to-day dynamic evolution analysis and prediction for a Didi taxi trip network based on complex network theory

NASA Astrophysics Data System (ADS)

Zhang, Lin; Lu, Jian; Zhou, Jialin; Zhu, Jinqing; Li, Yunxuan; Wan, Qian

2018-03-01

Didi Dache is the most popular taxi order mobile app in China, which provides online taxi-hailing service. The obtained big database from this app could be used to analyze the complexities’ day-to-day dynamic evolution of Didi taxi trip network (DTTN) from the level of complex network dynamics. First, this paper proposes the data cleaning and modeling methods for expressing Nanjing’s DTTN as a complex network. Second, the three consecutive weeks’ data are cleaned to establish 21 DTTNs based on the proposed big data processing technology. Then, multiple topology measures that characterize the complexities’ day-to-day dynamic evolution of these networks are provided. Third, these measures of 21 DTTNs are calculated and subsequently explained with actual implications. They are used as a training set for modeling the BP neural network which is designed for predicting DTTN complexities evolution. Finally, the reliability of the designed BP neural network is verified by comparing with the actual data and the results obtained from ARIMA method simultaneously. Because network complexities are the basis for modeling cascading failures and conducting link prediction in complex system, this proposed research framework not only provides a novel perspective for analyzing DTTN from the level of system aggregated behavior, but can also be used to improve the DTTN management level.

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

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

Zhou, Xiaofan; Peris, David; Kominek, Jacek

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

DOE PAGES

Zhou, Xiaofan; Peris, David; Kominek, Jacek; ...

2016-09-16

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage.

PubMed

Dayeh, Daniel M; Kruithoff, Bradley C; Nakanishi, Kotaro

2018-04-27

Some gene transcripts have cellular functions as regulatory noncoding RNAs. For example, ∼23-nucleotide (nt)-long siRNAs are loaded into Argonaute proteins. The resultant ribonucleoprotein assembly, the RNA-induced silencing complex (RISC), cleaves RNAs that are extensively base-paired with the loaded siRNA. To date, base complementarity is recognized as the major determinant of specific target cleavage (or slicing), but little is known about how Argonaute inspects base pairing before cleavage. A hallmark of Argonaute proteins is their bilobal structure, but despite the significance of this structure for curtailing slicing activity against mismatched targets, the molecular mechanism remains elusive. Here, our structural and functional studies of a bilobed yeast Argonaute protein and its isolated catalytic C-terminal lobe (C-lobe) revealed that the C-lobe alone retains almost all properties of bilobed Argonaute: siRNA-duplex loading, passenger cleavage/ejection, and siRNA-dependent RNA cleavage. A 2.1 Å-resolution crystal structure revealed that the catalytic C-lobe mirrors the bilobed Argonaute in terms of guide-RNA recognition and that all requirements for transitioning to the catalytically active conformation reside in the C-lobe. Nevertheless, we found that in the absence of the N-terminal lobe (N-lobe), target RNAs are scanned for complementarity only at positions 5-14 on a 23-nt guide RNA before endonucleolytic cleavage, thereby allowing for some off-target cleavage. Of note, acquisition of an N-lobe expanded the range of the guide RNA strand used for inspecting target complementarity to positions 2-23. These findings offer clues to the evolution of the bilobal structure of catalytically active Argonaute proteins. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

A Signal Processing Approach with a Smooth Empirical Mode Decomposition to Reveal Hidden Trace of Corrosion in Highly Contaminated Guided Wave Signals for Concrete-Covered Pipes

PubMed Central

Rostami, Javad; Chen, Jingming; Tse, Peter W.

2017-01-01

Ultrasonic guided waves have been extensively applied for non-destructive testing of plate-like structures particularly pipes in past two decades. In this regard, if a structure has a simple geometry, obtained guided waves’ signals are easy to explain. However, any small degree of complexity in the geometry such as contacting with other materials may cause an extra amount of complication in the interpretation of guided wave signals. The problem deepens if defects have irregular shapes such as natural corrosion. Signal processing techniques that have been proposed for guided wave signals’ analysis are generally good for simple signals obtained in a highly controlled experimental environment. In fact, guided wave signals in a real situation such as the existence of natural corrosion in wall-covered pipes are much more complicated. Considering pipes in residential buildings that pass through concrete walls, in this paper we introduced Smooth Empirical Mode Decomposition (SEMD) to efficiently separate overlapped guided waves. As empirical mode decomposition (EMD) which is a good candidate for analyzing non-stationary signals, suffers from some shortcomings, wavelet transform was adopted in the sifting stage of EMD to improve its outcome in SEMD. However, selection of mother wavelet that suits best for our purpose plays an important role. Since in guided wave inspection, the incident waves are well known and are usually tone-burst signals, we tailored a complex tone-burst signal to be used as our mother wavelet. In the sifting stage of EMD, wavelet de-noising was applied to eliminate unwanted frequency components from each IMF. SEMD greatly enhances the performance of EMD in guided wave analysis for highly contaminated signals. In our experiment on concrete covered pipes with natural corrosion, this method not only separates the concrete wall indication clearly in time domain signal, a natural corrosion with complex geometry that was hidden and located inside the concrete section was successfully exposed. PMID:28178220

A Signal Processing Approach with a Smooth Empirical Mode Decomposition to Reveal Hidden Trace of Corrosion in Highly Contaminated Guided Wave Signals for Concrete-Covered Pipes.

PubMed

Rostami, Javad; Chen, Jingming; Tse, Peter W

2017-02-07

Ultrasonic guided waves have been extensively applied for non-destructive testing of plate-like structures particularly pipes in past two decades. In this regard, if a structure has a simple geometry, obtained guided waves' signals are easy to explain. However, any small degree of complexity in the geometry such as contacting with other materials may cause an extra amount of complication in the interpretation of guided wave signals. The problem deepens if defects have irregular shapes such as natural corrosion. Signal processing techniques that have been proposed for guided wave signals' analysis are generally good for simple signals obtained in a highly controlled experimental environment. In fact, guided wave signals in a real situation such as the existence of natural corrosion in wall-covered pipes are much more complicated. Considering pipes in residential buildings that pass through concrete walls, in this paper we introduced Smooth Empirical Mode Decomposition (SEMD) to efficiently separate overlapped guided waves. As empirical mode decomposition (EMD) which is a good candidate for analyzing non-stationary signals, suffers from some shortcomings, wavelet transform was adopted in the sifting stage of EMD to improve its outcome in SEMD. However, selection of mother wavelet that suits best for our purpose plays an important role. Since in guided wave inspection, the incident waves are well known and are usually tone-burst signals, we tailored a complex tone-burst signal to be used as our mother wavelet. In the sifting stage of EMD, wavelet de-noising was applied to eliminate unwanted frequency components from each IMF. SEMD greatly enhances the performance of EMD in guided wave analysis for highly contaminated signals. In our experiment on concrete covered pipes with natural corrosion, this method not only separates the concrete wall indication clearly in time domain signal, a natural corrosion with complex geometry that was hidden and located inside the concrete section was successfully exposed.

Exploring the Scopes "Monkey" Trial in Dayton, Tennessee: A Guide to People & Places

ERIC Educational Resources Information Center

Cameron, Jacquelyn; Moore, Randy

2015-01-01

Many biology teachers visit Dayton, Tennessee, to experience "ground zero" of the evolution-creationism controversy. This article provides concise descriptions, addresses, and GPS coordinates for the trial-related sites in and around Dayton.

High school biology evolution learning experiences in a rural context: a case of and for cultural border crossing

NASA Astrophysics Data System (ADS)

Borgerding, Lisa A.

2017-03-01

Although the concept of "rural" is difficult to define, rural science education provides the possibility for learning centered upon a strong connection to the local community. Rural American adolescents tend to be more religious than their urban counterparts and less accepting of evolution than their non-rural peers. Because the status and perception of evolutionary theory may be very different within the students' lifeworlds and the subcultures of the science classroom and science itself, a cultural border crossing metaphor can be applied to evolution teaching and learning. This study examines how a teacher may serve as a cultural border crossing tour guide for students at a rural high school as they explore the concept of biological evolution in their high school biology class. Data collection entailed two formal teacher interviews, field note observations of two biology class periods each day for 16 days during the Evolution unit, individual interviews with 14 students, student evolution acceptance surveys, student evolution content tests, and classroom artifacts. The major findings center upon three themes regarding how this teacher and these students had largely positive evolution learning experiences even as some students continued to reject evolution. First, the teacher strategically positioned himself in two ways: using his unique "local" trusted position in the community and school and taking a position in which he did not personally represent science by instead consistently teaching evolution "according to scientists." Second, his instruction honored local "rural" funds of knowledge with respect to local knowledge of nature and by treating students' religious knowledge as a form of local expertise about one set of answers to questions also addressed by evolution. Third, the teacher served as a border crossing "tour guide" by helping students identify how the culture of science and the culture of their lifeworlds may differ with respect to evolutionary theory. Students negotiated the cultural borders for learning evolution in several ways, and different types of border crossings are described. The students respected the teacher's apparent neutrality, sensitivity toward multiple positions, explicit attention to religion/evolution, and transparency of purposes for teaching evolution. These findings add to the current literature on rural science education by highlighting local funds of knowledge for evolution learning and how rural teachers may help students navigate seemingly hazardous scientific topics. The study's findings also add to the current evolution education literature by examining how students' religious perspectives may be respected as a form of expertise about questions of origins by allowing students to examine similarities and differences between scientific and religious approaches to questions of biological origins and change.

Historical development of worldwide guided missiles

NASA Technical Reports Server (NTRS)

Spearman, M. L.

1983-01-01

The development of missiles from early history to present time is put in perspective. The influence of World War II in accelerating the development of guided missiles, particularly through German scientists, is discussed. The dispersion of German scientists to other countries and the coupling of their work with native talent to develop guide missiles is traced. Particular emphasis is placed on the evolution of the missile in the U.S. and the U.S.S.R. Since the Soviets possess what is probably the world's most complete array of dedicated missile system types, their known inventory is reviewed. Some philosophical observations of missile design trends and missile purposes are made as related to the interests of various countries.

SWITCH user's manual

NASA Technical Reports Server (NTRS)

1987-01-01

The planning program, SWITCH, and its surrounding changed-goal-replanning program, Runaround, are described. The evolution of SWITCH and Runaround from an earlier planner, DEVISER, is recounted. SWITCH's plan representation, and its process of building a plan by backward chaining with strict chronological backtracking, are described. A guide for writing knowledge base files is provided, as are narrative guides for installing the program, running it, and interacting with it while it is running. Some utility functions are documented. For the sake of completeness, a narrative guide to the experimental discrepancy-replanning feature is provided. Appendices contain knowledge base files for a blocksworld domain, and a DRIBBLE file illustrating the output from, and user interaction with, the program in that domain.

Cope's Rule and the Universal Scaling Law of Ornament Complexity.

PubMed

Raia, Pasquale; Passaro, Federico; Carotenuto, Francesco; Maiorino, Leonardo; Piras, Paolo; Teresi, Luciano; Meiri, Shai; Itescu, Yuval; Novosolov, Maria; Baiano, Mattia Antonio; Martínez, Ricard; Fortelius, Mikael

2015-08-01

Luxuriant, bushy antlers, bizarre crests, and huge, twisting horns and tusks are conventionally understood as products of sexual selection. This view stems from both direct observation and from the empirical finding that the size of these structures grows faster than body size (i.e., ornament size shows positive allometry). We contend that the familiar evolutionary increase in the complexity of ornaments over time in many animal clades is decoupled from ornament size evolution. Increased body size comes with extended growth. Since growth scales to the quarter power of body size, we predicted that ornament complexity should scale according to the quarter power law as well, irrespective of the role of sexual selection in the evolution and function of the ornament. To test this hypothesis, we selected three clades (ammonites, deer, and ceratopsian dinosaurs) whose species bore ornaments that differ in terms of the importance of sexual selection to their evolution. We found that the exponent of the regression of ornament complexity to body size is the same for the three groups and is statistically indistinguishable from 0.25. We suggest that the evolution of ornament complexity is a by-product of Cope's rule. We argue that although sexual selection may control size in most ornaments, it does not influence their shape.

Evolution of Brain and Language

ERIC Educational Resources Information Center

Schoenemann, P. Thomas

2009-01-01

The evolution of language and the evolution of the brain are tightly interlinked. Language evolution represents a special kind of adaptation, in part because language is a complex behavior (as opposed to a physical feature) but also because changes are adaptive only to the extent that they increase either one's understanding of others, or one's…

Lower bound on the time complexity of local adiabatic evolution

NASA Astrophysics Data System (ADS)

Chen, Zhenghao; Koh, Pang Wei; Zhao, Yan

2006-11-01

The adiabatic theorem of quantum physics has been, in recent times, utilized in the design of local search quantum algorithms, and has been proven to be equivalent to standard quantum computation, that is, the use of unitary operators [D. Aharonov in Proceedings of the 45th Annual Symposium on the Foundations of Computer Science, 2004, Rome, Italy (IEEE Computer Society Press, New York, 2004), pp. 42-51]. Hence, the study of the time complexity of adiabatic evolution algorithms gives insight into the computational power of quantum algorithms. In this paper, we present two different approaches of evaluating the time complexity for local adiabatic evolution using time-independent parameters, thus providing effective tests (not requiring the evaluation of the entire time-dependent gap function) for the time complexity of newly developed algorithms. We further illustrate our tests by displaying results from the numerical simulation of some problems, viz. specially modified instances of the Hamming weight problem.

Progress on Complex Langevin simulations of a finite density matrix model for QCD

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

Bloch, Jacques; Glesaan, Jonas; Verbaarschot, Jacobus

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplementedmore » with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.« less

Evolution of an ancient protein function involved in organized multicellularity in animals.

PubMed

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-07

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which - the evolution of GKPID's capacity to bind the cortical marker protein - can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.

The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean

USDA-ARS?s Scientific Manuscript database

A comparative genomics approach was used to investigate the evolution of a complex NB-LRR gene cluster found in soybean (Glycine max), common bean (Phaseolus vulgaris), and other legumes. In soybean, the cluster is associated with several disease resistance (R) genes of known function including Rpg1...

Handbook of Techniques and Guides for the Study of the San Francisco Bay-Delta-Estuary Complex, Part 2. Key to the Phytoplankton Phyla and Genera.

ERIC Educational Resources Information Center

Helrich, Jane

Project MER (Marine Ecology Research) is aimed at improving environmental education in the San Francisco Bay Area schools. This document is the second of a series of guides designed to help students and teachers gather data concerning the San Francisco Bay-Delta-Estuary Complex and to organize these data to make a contribution to the literature of…

Guiding principles for peptide nanotechnology through directed discovery.

PubMed

Lampel, A; Ulijn, R V; Tuttle, T

2018-05-21

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

Multiple subclasses of Purkinje cells in the primate floccular complex provide similar signals to guide learning in the vestibulo-ocular reflex

NASA Technical Reports Server (NTRS)

Raymond, J. L.; Lisberger, S. G.

1997-01-01

The neural "learning rules" governing the induction of plasticity in the cerebellum were analyzed by recording the patterns of neural activity in awake, behaving animals during stimuli that induce a form of cerebellum-dependent learning. We recorded the simple- and complex-spike responses of a broad sample of Purkinje cells in the floccular complex during a number of stimulus conditions that induce motor learning in the vestibulo-ocular reflex (VOR). Each subclass of Purkinje cells carried essentially the same information about required changes in the gain of the VOR. The correlation of simple-spike activity in Purkinje cells with activity in vestibular pathways could guide learning during low-frequency but not high-frequency stimuli. Climbing fiber activity could guide learning during all stimuli tested but only if compared with the activity present approximately 100 msec earlier in either vestibular pathways or Purkinje cells.

Guided and magnetic self-assembly of tunable magnetoceptive gels

NASA Astrophysics Data System (ADS)

Tasoglu, S.; Yu, C. H.; Gungordu, H. I.; Guven, S.; Vural, T.; Demirci, U.

2014-09-01

Self-assembly of components into complex functional patterns at microscale is common in nature, and used increasingly in numerous disciplines such as optoelectronics, microfabrication, sensors, tissue engineering and computation. Here, we describe the use of stable radicals to guide the self-assembly of magnetically tunable gels, which we call ‘magnetoceptive’ materials at the scale of hundreds of microns to a millimeter, each can be programmed by shape and composition, into heterogeneous complex structures. Using paramagnetism of free radicals as a driving mechanism, complex heterogeneous structures are built in the magnetic field generated by permanent magnets. The overall magnetic signature of final structure is erased via an antioxidant vitamin E, subsequent to guided self-assembly. We demonstrate unique capabilities of radicals and antioxidants in fabrication of soft systems with heterogeneity in material properties, such as porosity, elastic modulus and mass density; then in bottom-up tissue engineering and finally, levitational and selective assembly of microcomponents.

Guided and magnetic self-assembly of tunable magnetoceptive gels

PubMed Central

Tasoglu, S.; Yu, C.H.; Gungordu, H.I.; Guven, S.; Vural, T.; Demirci, U.

2014-01-01

Self-assembly of components into complex functional patterns at microscale is common in nature, and used increasingly in numerous disciplines such as optoelectronics, microfabrication, sensors, tissue engineering and computation. Here, we describe the use of stable radicals to guide the self-assembly of magnetically tunable gels, which we call ‘magnetoceptive’ materials at the scale of hundreds of microns to a millimeter, each can be programmed by shape and composition, into heterogeneous complex structures. Using paramagnetism of free radicals as a driving mechanism, complex heterogeneous structures are built in the magnetic field generated by permanent magnets. The overall magnetic signature of final structure is erased via an antioxidant vitamin E, subsequent to guided self-assembly. We demonstrate unique capabilities of radicals and antioxidants in fabrication of soft systems with heterogeneity in material properties, such as porosity, elastic modulus and mass density; then in bottom-up tissue engineering and finally, levitational and selective assembly of microcomponents. PMID:25175148

Complex facial deformity reconstruction with a surgical guide incorporating a built-in occlusal stent as the positioning reference.

PubMed

Fang, Jing-Jing; Liu, Jia-Kuang; Wu, Tzu-Chieh; Lee, Jing-Wei; Kuo, Tai-Hong

2013-05-01

Computer-aided design has gained increasing popularity in clinical practice, and the advent of rapid prototyping technology has further enhanced the quality and predictability of surgical outcomes. It provides target guides for complex bony reconstruction during surgery. Therefore, surgeons can efficiently and precisely target fracture restorations. Based on three-dimensional models generated from a computed tomographic scan, precise preoperative planning simulation on a computer is possible. Combining the interdisciplinary knowledge of surgeons and engineers, this study proposes a novel surgical guidance method that incorporates a built-in occlusal wafer that serves as the positioning reference.Two patients with complex facial deformity suffering from severe facial asymmetry problems were recruited. In vitro facial reconstruction was first rehearsed on physical models, where a customized surgical guide incorporating a built-in occlusal stent as the positioning reference was designed to implement the surgery plan. This study is intended to present the authors' preliminary experience in a complex facial reconstruction procedure. It suggests that in regions with less information, where intraoperative computed tomographic scans or navigation systems are not available, our approach could be an effective, expedient, straightforward aid to enhance surgical outcome in a complex facial repair.

Malcolm X in Context: A Study Guide to the Man and His Times.

ERIC Educational Resources Information Center

Murphy, Don, Ed.; Radtke, Jennifer, Ed.

This study guide is designed for those with varying levels of understanding to open possible contexts to consider Malcolm X and develop some of the critical thinking skills necessary to make sense out of any complex historical phenomena and to suggest to students some directions for further research. The guide uses the "Autobiography of…

A Citizen's Guide to U.S. Foreign Policy: Election '88. Nonpartisan Briefs on 18 Key Issues.

ERIC Educational Resources Information Center

Hoepli, Nancy, Ed.; And Others

In order to make informed voting decisions citizens need background information on complex foreign policy issues facing the United States. This guide presents current issues and provides information to help citizens cast a thoughtful vote. The guide is divided into six main headings: Leadership; Security; Economic and Social Issues; Critical…

Guiding Students to Develop an Understanding of Scientific Inquiry: A Science Skills Approach to Instruction and Assessment

ERIC Educational Resources Information Center

Stone, Elisa M.

2014-01-01

New approaches for teaching and assessing scientific inquiry and practices are essential for guiding students to make the informed decisions required of an increasingly complex and global society. The Science Skills approach described here guides students to develop an understanding of the experimental skills required to perform a scientific…

World Cultures: A Theme Guide to K-12 Curricular Resources, Activities, and Processes.

ERIC Educational Resources Information Center

Stanford Univ., CA. Stanford Program on International and Cross Cultural Education.

This guide is for educators who wish to improve existing curricular frameworks for teaching about world cultures. The guide is anchored by six goal statements for student learning: (1) to begin to understand that cultures are complex and are made up of many components (values, behavior, habitat, aesthetics, etc.); (2) to recognize the part…

Personal Finance Education Guide for Planning Secondary School Programs. Second Edition.

ERIC Educational Resources Information Center

Oregon State Dept. of Education, Salem.

This guide has been developed to help teachers plan programs that meet both individual and common needs of all students in personal finance education. It defines the skills and knowledge necessary to function as an intelligent consumer in our complex and rapidly changing economic order. The guide has been developed around five basic concepts:…

Evolution and the complexity of bacteriophages.

PubMed

Serwer, Philip

2007-03-13

The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution. This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages.

Predicting the resilience and recovery of aquatic systems: a framework for model evolution within environmental observatories

USGS Publications Warehouse

Hipsey, Matthew R.; Hamilton, David P.; Hanson, Paul C.; Carey, Cayelan C.; Coletti, Janaine Z; Read, Jordan S.; Ibelings, Bas W; Valensini, Fiona J; Brookes, Justin D

2015-01-01

Maintaining the health of aquatic systems is an essential component of sustainable catchmentmanagement, however, degradation of water quality and aquatic habitat continues to challenge scientistsand policy-makers. To support management and restoration efforts aquatic system models are requiredthat are able to capture the often complex trajectories that these systems display in response to multiplestressors. This paper explores the abilities and limitations of current model approaches in meeting this chal-lenge, and outlines a strategy based on integration of flexible model libraries and data from observationnetworks, within a learning framework, as a means to improve the accuracy and scope of model predictions.The framework is comprised of a data assimilation component that utilizes diverse data streams from sensornetworks, and a second component whereby model structural evolution can occur once the model isassessed against theoretically relevant metrics of system function. Given the scale and transdisciplinarynature of the prediction challenge, network science initiatives are identified as a means to develop and inte-grate diverse model libraries and workflows, and to obtain consensus on diagnostic approaches to modelassessment that can guide model adaptation. We outline how such a framework can help us explore thetheory of how aquatic systems respond to change by bridging bottom-up and top-down lines of enquiry,and, in doing so, also advance the role of prediction in aquatic ecosystem management.

Predicting the resilience and recovery of aquatic systems: A framework for model evolution within environmental observatories

NASA Astrophysics Data System (ADS)

Hipsey, Matthew R.; Hamilton, David P.; Hanson, Paul C.; Carey, Cayelan C.; Coletti, Janaine Z.; Read, Jordan S.; Ibelings, Bas W.; Valesini, Fiona J.; Brookes, Justin D.

2015-09-01

Maintaining the health of aquatic systems is an essential component of sustainable catchment management, however, degradation of water quality and aquatic habitat continues to challenge scientists and policy-makers. To support management and restoration efforts aquatic system models are required that are able to capture the often complex trajectories that these systems display in response to multiple stressors. This paper explores the abilities and limitations of current model approaches in meeting this challenge, and outlines a strategy based on integration of flexible model libraries and data from observation networks, within a learning framework, as a means to improve the accuracy and scope of model predictions. The framework is comprised of a data assimilation component that utilizes diverse data streams from sensor networks, and a second component whereby model structural evolution can occur once the model is assessed against theoretically relevant metrics of system function. Given the scale and transdisciplinary nature of the prediction challenge, network science initiatives are identified as a means to develop and integrate diverse model libraries and workflows, and to obtain consensus on diagnostic approaches to model assessment that can guide model adaptation. We outline how such a framework can help us explore the theory of how aquatic systems respond to change by bridging bottom-up and top-down lines of enquiry, and, in doing so, also advance the role of prediction in aquatic ecosystem management.

Intracontinental Rifts As Glorious Failures

NASA Astrophysics Data System (ADS)

Burke, K.

2012-12-01

Rifts: "Elongate depressions overlying places where the lithosphere has ruptured in extension" develop in many environments because rocks are weak in extension (Sengor 2nd edn. Springer Encycl. Solid Earth Geophys.). I focus on intra-continental rifts in which the Wilson Cycle failed to develop but in which that failure has led to glory because rocks and structures in those rifts throw exceptional light on how Earth's complex continental evolution can operate: The best studied record of human evolution is in the East African Rift; The Ventersdorp rifts (2.7 Ga) have yielded superb crustal-scale rift seismic reflection records; "Upside-down drainage" (Sleep 1997) has guided supra-plume-head partial melt into older continental rifts leading Deccan basalt of ~66Ma to erupt into a Late Paleozoic (~ 300Ma) rift and the CAMP basalts of ~201 Ma into Ladinian, ~230 Ma, rifts. Nepheline syenites and carbonatites, which are abundant in rifts that overlie sutures in the underlying mantle lithosphere, form by decompression melting of deformed nepheline syenites and carbonatites ornamenting those sutures (Burke et al.2003). Folding, faulting and igneous episodes involving decompression melting in old rifts can relate to collision at a remote plate margin (Guiraud and Bosworth 1997, Dewey and Burke 1974) or to passage of the rift over a plume generation zone (PGZ Burke et al.2008) on the Core Mantle Boundary (e.g.Lake Ellen MI kimberlites at ~206 Ma).

Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes.

PubMed

Price, Samantha A; Tavera, Jose J; Near, Thomas J; Wainwright, Peter C

2013-02-01

The relationship between habitat complexity and species richness is well established but comparatively little is known about the evolution of morphological diversity in complex habitats. Reefs are structurally complex, highly productive shallow-water marine ecosystems found in tropical (coral reefs) and temperate zones (rocky reefs) that harbor exceptional levels of biodiversity. We investigated whether reef habitats promote the evolution of morphological diversity in the feeding and locomotion systems of grunts (Haemulidae), a group of predominantly nocturnal fishes that live on both temperate and tropical reefs. Using phylogenetic comparative methods and statistical analyses that take into account uncertainty in phylogeny and the evolutionary history of reef living, we demonstrate that rates of morphological evolution are faster in reef-dwelling haemulids. The magnitude of this effect depends on the type of trait; on average, traits involved in the functional systems for prey capture and processing evolve twice as fast on reefs as locomotor traits. This result, along with the observation that haemulids do not exploit unique feeding niches on reefs, suggests that fine-scale trophic niche partitioning and character displacement may be driving higher rates of morphological evolution. Whatever the cause, there is growing evidence that reef habitats stimulate morphological and functional diversification in teleost fishes. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Modeling process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Yu, Cheng; Liu, Zeliang; Lian, Yanping; Wolff, Sarah; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-02-01

This paper presents our latest work on comprehensive modeling of process-structure-property relationships for additive manufacturing (AM) materials, including using data-mining techniques to close the cycle of design-predict-optimize. To illustrate the processstructure relationship, the multi-scale multi-physics process modeling starts from the micro-scale to establish a mechanistic heat source model, to the meso-scale models of individual powder particle evolution, and finally to the macro-scale model to simulate the fabrication process of a complex product. To link structure and properties, a highefficiency mechanistic model, self-consistent clustering analyses, is developed to capture a variety of material response. The model incorporates factors such as voids, phase composition, inclusions, and grain structures, which are the differentiating features of AM metals. Furthermore, we propose data-mining as an effective solution for novel rapid design and optimization, which is motivated by the numerous influencing factors in the AM process. We believe this paper will provide a roadmap to advance AM fundamental understanding and guide the monitoring and advanced diagnostics of AM processing.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Degradation Mechanisms of an Advanced Jet Engine Service-Retired TBC Component

NASA Astrophysics Data System (ADS)

Wu, Rudder T.; Osawa, Makoto; Yokokawa, Tadaharu; Kawagishi, Kyoko; Harada, Hiroshi

Current use of TBCs is subjected to premature spallation failure mainly due to the formation of thermally grown oxides (TGOs). Although extensive research has been carried out to gain better understanding of the thermo - mechanical and -chemical characteristics of TBCs, laboratory-scale studies and simulation tests are often carried out in conditions significantly differed from the complex and extreme environment typically of a modern gas-turbine engine, thus, failed to truly model service conditions. In particular, the difference in oxygen partial pressure and the effects of contaminants present in the engine compartment have often been neglected. In this respect, an investigation is carried out to study the in-service degradation of an EB-PVD TBC coated nozzle-guide vane. Several modes of degradation were observed due to three factors: 1) presence of residual stresses induced by the thermal-expansion mismatches, 2) evolution of bond coat microstructure and subsequent formation of oxide spinels, 3) deposition of CMAS on the surface of TBC.

A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases.

PubMed

Cahn, Jackson K B; Werlang, Caroline A; Baumschlager, Armin; Brinkmann-Chen, Sabine; Mayo, Stephen L; Arnold, Frances H

2017-02-17

The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal-Structural Analysis and Library Design (CSR-SALAD).

Energy boost in laser wakefield accelerators using sharp density transitions

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

Döpp, A.; Guillaume, E.; Thaury, C.

The energy gain in laser wakefield accelerators is limited by dephasing between the driving laser pulse and the highly relativistic electrons in its wake. Since this phase depends on both the driver and the cavity length, the effects of dephasing can be mitigated with appropriate tailoring of the plasma density along propagation. Preceding studies have discussed the prospects of continuous phase-locking in the linear wakefield regime. However, most experiments are performed in the highly non-linear regime and rely on self-guiding of the laser pulse. Due to the complexity of the driver evolution in this regime, it is much more difficultmore » to achieve phase locking. As an alternative, we study the scenario of rapid rephasing in sharp density transitions, as was recently demonstrated experimentally. Starting from a phenomenological model, we deduce expressions for the electron energy gain in such density profiles. The results are in accordance with particle-in-cell simulations, and we present gain estimations for single and multiple stages of rephasing.« less

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.

Smartphones in ecology and evolution: a guide for the app-rehensive.

PubMed

Teacher, Amber G F; Griffiths, David J; Hodgson, David J; Inger, Richard

2013-12-01

Smartphones and their apps (application software) are now used by millions of people worldwide and represent a powerful combination of sensors, information transfer, and computing power that deserves better exploitation by ecological and evolutionary researchers. We outline the development process for research apps, provide contrasting case studies for two new research apps, and scan the research horizon to suggest how apps can contribute to the rapid collection, interpretation, and dissemination of data in ecology and evolutionary biology. We emphasize that the usefulness of an app relies heavily on the development process, recommend that app developers are engaged with the process at the earliest possible stage, and commend efforts to create open-source software scaffolds on which customized apps can be built by nonexperts. We conclude that smartphones and their apps could replace many traditional handheld sensors, calculators, and data storage devices in ecological and evolutionary research. We identify their potential use in the high-throughput collection, analysis, and storage of complex ecological information.

ClonEvol: clonal ordering and visualization in cancer sequencing.

PubMed

Dang, H X; White, B S; Foltz, S M; Miller, C A; Luo, J; Fields, R C; Maher, C A

2017-12-01

Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones throughout metastatic progression observed in the tumors of a published breast cancer patient. ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine. ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

PubMed Central

Rockenbach, Kate; Havird, Justin C.; Monroe, J. Grey; Triant, Deborah A.; Taylor, Douglas R.; Sloan, Daniel B.

2016-01-01

Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastid–nuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid–nuclear conflict as a novel cause of accelerated evolution. PMID:27707788

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: a path for the optimization of low-energy many-body bases.

PubMed

Reboredo, Fernando A; Kim, Jeongnim

2014-02-21

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

NASA Astrophysics Data System (ADS)

Reboredo, Fernando A.; Kim, Jeongnim

2014-02-01

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

A morphospace for synthetic organs and organoids: the possible and the actual.

PubMed

Ollé-Vila, Aina; Duran-Nebreda, Salva; Conde-Pueyo, Núria; Montañez, Raúl; Solé, Ricard

2016-04-18

Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.

Nonlinear gyrotropic motion of skyrmion in a magnetic nanodisk

NASA Astrophysics Data System (ADS)

Chen, Yi-fu; Li, Zhi-xiong; Zhou, Zhen-wei; Xia, Qing-lin; Nie, Yao-zhuang; Guo, Guang-hua

2018-07-01

We study the nonlinear gyrotropic motion of a magnetic skyrmion in a nanodisk by means of micromagnetic simulations. The skyrmion is driven by a linearly polarized harmonic field with the frequency of counterclockwise gyrotropic mode. It is found that the motion of the skyrmion displays different patterns with increasing field amplitude. In the linear regime of weak driving field, the skyrmion performs a single counterclockwise gyrotropic motion. The guiding center of the skyrmion moves along a helical line from the centre of the nanodisk to a stable circular orbit. The stable orbital radius increases linearly with the field amplitude. When the driving field is larger than a critical value, the skyrmion exhibits complex nonlinear motion. With the advance of time, the motion trajectory of the skyrmion goes through a series of evolution process, from a single circular motion to a bird nest-like and a flower-like trajectory and finally, to a gear-like steady-state motion. The frequency spectra show that except the counterclockwise gyrotropic mode, the clockwise gyrotropic mode is also nonlinearly excited and its amplitude increases with time. The complex motion trajectory of the skyrmion is the result of superposition of the two gyrotropic motions with changing amplitude. Both the linear and nonlinear gyrotropic motions of the skyrmion can be well described by a generalized Thiele's equation of motion.

saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription.

PubMed

Portnoy, Victoria; Lin, Szu Hua Sharon; Li, Kathy H; Burlingame, Alma; Hu, Zheng-Hui; Li, Hao; Li, Long-Cheng

2016-03-01

Small activating RNAs (saRNAs) targeting specific promoter regions are able to stimulate gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). It is known that RNAa depends on Ago2 and is associated with epigenetic changes at the target promoters. However, the precise molecular mechanism of RNAa remains elusive. Using human CDKN1A (p21) as a model gene, we characterized the molecular nature of RNAa. We show that saRNAs guide Ago2 to and associate with target promoters. saRNA-loaded Ago2 facilitates the assembly of an RNA-induced transcriptional activation (RITA) complex, which, in addition to saRNA-Ago2 complex, includes RHA and CTR9, the latter being a component of the PAF1 complex. RITA interacts with RNA polymerase II to stimulate transcription initiation and productive elongation, accompanied by monoubiquitination of histone 2B. Our results establish the existence of a cellular RNA-guided genome-targeting and transcriptional activation mechanism and provide important new mechanistic insights into the RNAa process.

Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait.

PubMed

Maurer, Matthew J; Sutardja, Lawrence; Pinel, Dominic; Bauer, Stefan; Muehlbauer, Amanda L; Ames, Tyler D; Skerker, Jeffrey M; Arkin, Adam P

2017-03-17

Engineering complex phenotypes for industrial and synthetic biology applications is difficult and often confounds rational design. Bioethanol production from lignocellulosic feedstocks is a complex trait that requires multiple host systems to utilize, detoxify, and metabolize a mixture of sugars and inhibitors present in plant hydrolysates. Here, we demonstrate an integrated approach to discovering and optimizing host factors that impact fitness of Saccharomyces cerevisiae during fermentation of a Miscanthus x giganteus plant hydrolysate. We first used high-resolution Quantitative Trait Loci (QTL) mapping and systematic bulk Reciprocal Hemizygosity Analysis (bRHA) to discover 17 loci that differentiate hydrolysate tolerance between an industrially related (JAY291) and a laboratory (S288C) strain. We then used this data to identify a subset of favorable allelic loci that were most amenable for strain engineering. Guided by this "genetic blueprint", and using a dual-guide Cas9-based method to efficiently perform multikilobase locus replacements, we engineered an S288C-derived strain with superior hydrolysate tolerance than JAY291. Our methods should be generalizable to engineering any complex trait in S. cerevisiae, as well as other organisms.

A Novel Approach of Groupwise fMRI-Guided Tractography Allowing to Characterize the Clinical Evolution of Alzheimer's Disease

PubMed Central

Preti, Maria Giulia; Makris, Nikos; Papadimitriou, George; Laganà, Maria Marcella; Griffanti, Ludovica; Clerici, Mario; Nemni, Raffaello; Westin, Carl-Fredrik; Baselli, Giuseppe; Baglio, Francesca

2014-01-01

Guiding diffusion tract-based anatomy by functional magnetic resonance imaging (fMRI), we aim to investigate the relationship between structural connectivity and functional activity in the human brain. To this purpose, we introduced a novel groupwise fMRI-guided tractographic approach, that was applied on a population ranging between prodromic and moderate stages of Alzheimer's disease (AD). The study comprised of 15 subjects affected by amnestic mild cognitive impairment (aMCI), 14 diagnosed with AD and 14 elderly healthy adults who were used as controls. By creating representative (ensemble) functionally guided tracts within each group of participants, our methodology highlighted the white matter fiber connections involved in verbal fluency functions for a specific population, and hypothesized on brain compensation mechanisms that potentially counteract or reduce cognitive impairment symptoms in prodromic AD. Our hope is that this fMRI-guided tractographic approach could have potential impact in various clinical studies, while investigating white/gray matter connectivity, in both health and disease. PMID:24637718

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

PubMed Central

Dibrova, Daria V.; Cherepanov, Dmitry A.; Galperin, Michael Y.; Skulachev, Vladimir P.; Mulkidjanian, Armen Y.

2013-01-01

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. PMID:23871937

A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

PubMed Central

Castillo, Andreina I; Nelson, Andrew D L; Haug-Baltzell, Asher K; Lyons, Eric

2018-01-01

Abstract Integrated platforms for storage, management, analysis and sharing of large quantities of omics data have become fundamental to comparative genomics. CoGe (https://genomevolution.org/coge/) is an online platform designed to manage and study genomic data, enabling both data- and hypothesis-driven comparative genomics. CoGe’s tools and resources can be used to organize and analyse both publicly available and private genomic data from any species. Here, we demonstrate the capabilities of CoGe through three example workflows using 17 Plasmodium genomes as a model. Plasmodium genomes present unique challenges for comparative genomics due to their rapidly evolving and highly variable genomic AT/GC content. These example workflows are intended to serve as templates to help guide researchers who would like to use CoGe to examine diverse aspects of genome evolution. In the first workflow, trends in genome composition and amino acid usage are explored. In the second, changes in genome structure and the distribution of synonymous (Ks) and non-synonymous (Kn) substitution values are evaluated across species with different levels of evolutionary relatedness. In the third workflow, microsyntenic analyses of multigene families’ genomic organization are conducted using two Plasmodium-specific gene families—serine repeat antigen, and cytoadherence-linked asexual gene—as models. In general, these example workflows show how to achieve quick, reproducible and shareable results using the CoGe platform. We were able to replicate previously published results, as well as leverage CoGe’s tools and resources to gain additional insight into various aspects of Plasmodium genome evolution. Our results highlight the usefulness of the CoGe platform, particularly in understanding complex features of genome evolution. Database URL: https://genomevolution.org/coge/

Rethinking programme evaluation in health professions education: beyond 'did it work?'.

PubMed

Haji, Faizal; Morin, Marie-Paule; Parker, Kathryn

2013-04-01

For nearly 40 years, outcome-based models have dominated programme evaluation in health professions education. However, there is increasing recognition that these models cannot address the complexities of the health professions context and studies employing alternative evaluation approaches that are appearing in the literature. A similar paradigm shift occurred over 50 years ago in the broader discipline of programme evaluation. Understanding the development of contemporary paradigms within this field provides important insights to support the evolution of programme evaluation in the health professions. In this discussion paper, we review the historical roots of programme evaluation as a discipline, demonstrating parallels with the dominant approach to evaluation in the health professions. In tracing the evolution of contemporary paradigms within this field, we demonstrate how their aim is not only to judge a programme's merit or worth, but also to generate information for curriculum designers seeking to adapt programmes to evolving contexts, and researchers seeking to generate knowledge to inform the work of others. From this evolution, we distil seven essential elements of educational programmes that should be evaluated to achieve the stated goals. Our formulation is not a prescriptive method for conducting programme evaluation; rather, we use these elements as a guide for the development of a holistic 'programme of evaluation' that involves multiple stakeholders, uses a combination of available models and methods, and occurs throughout the life of a programme. Thus, these elements provide a roadmap for the programme evaluation process, which allows evaluators to move beyond asking whether a programme worked, to establishing how it worked, why it worked and what else happened. By engaging in this process, evaluators will generate a sound understanding of the relationships among programmes, the contexts in which they operate, and the outcomes that result from them. © Blackwell Publishing Ltd 2013.

Evolution of allosteric regulation in chorismate mutases from early plants

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

Kroll, Kourtney; Holland, Cynthia K.; Starks, Courtney M.

Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plants; however, no biochemical information on these enzymes is available. To understand the evolution of allosteric regulation in plantmore » chorismate mutases, we analyzed a basal lineage of plant enzymes homologous to AtCM1 based on sequence similarity. The chorismate mutases from the moss/bryophyte Physcomitrella patens (PpCM1 and PpCM2), the lycophyte Selaginella moellendorffii (SmCM), and the basal angiosperm Amborella trichopoda (AmtCM1 and AmtCM2) were characterized biochemically. Tryptophan was a positive effector for each of the five enzymes examined. Histidine was a weak positive effector for PpCM1 and AmtCM1. Neither tyrosine nor phenylalanine altered the activity of SmCM; however, tyrosine was a negative regulator of the other four enzymes. Phenylalanine down-regulates both moss enzymes and AmtCM2. The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides our understanding of the evolution of allosteric regulation in these enzymes.« less

The Evolution and Increasing Complexity of the Resident Assistant Role in the United States from Colonial to Modern Times

ERIC Educational Resources Information Center

Boone, Katherine B.; Davidson, Denise L.; Bauman, Mark

2016-01-01

The evolution of the resident assistant position and its history are important to understanding its increasing complexities. In this article we examine how court cases and federal legislation, along with changes in popular culture, have altered and shaped the role of the resident assistant. Our premise is that this role, originally relatively…

Geometry of Quantum Computation with Qudits

PubMed Central

Luo, Ming-Xing; Chen, Xiu-Bo; Yang, Yi-Xian; Wang, Xiaojun

2014-01-01

The circuit complexity of quantum qubit system evolution as a primitive problem in quantum computation has been discussed widely. We investigate this problem in terms of qudit system. Using the Riemannian geometry the optimal quantum circuits are equivalent to the geodetic evolutions in specially curved parametrization of SU(dn). And the quantum circuit complexity is explicitly dependent of controllable approximation error bound. PMID:24509710

Design and performance of optimal detectors for guided wave structural health monitoring

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

Dib, G.; Udpa, L.

2016-01-01

Ultrasonic guided wave measurements in a long term structural health monitoring system are affected by measurement noise, environmental conditions, transducer aging and malfunction. This results in measurement variability which affects detection performance, especially in complex structures where baseline data comparison is required. This paper derives the optimal detector structure, within the framework of detection theory, where a guided wave signal at the sensor is represented by a single feature value that can be used for comparison with a threshold. Three different types of detectors are derived depending on the underlying structure’s complexity: (i) Simple structures where defect reflections can bemore » identified without the need for baseline data; (ii) Simple structures that require baseline data due to overlap of defect scatter with scatter from structural features; (iii) Complex structure with dense structural features that require baseline data. The detectors are derived by modeling the effects of variabilities and uncertainties as random processes. Analytical solutions for the performance of detectors in terms of the probability of detection and false alarm are derived. A finite element model is used to generate guided wave signals and the performance results of a Monte-Carlo simulation are compared with the theoretical performance. initial results demonstrate that the problems of signal complexity and environmental variability can in fact be exploited to improve detection performance.« less

A governor's guide to emergency management. Volume two : homeland security

DOT National Transportation Integrated Search

2002-09-19

Homeland security is a complex challenge that demands significant investment; collaboration among local, state, and federal governments; and integration with the private sector. The purpose of A Governor's Guide to Emergency Management Volume Two: Ho...

Kentucky Consumer & Homemaking Education. Clothing and Textiles. Curriculum Guide, Comprehensive Courses.

ERIC Educational Resources Information Center

Harris, Dianne

Intended for use by teachers on the junior high and high school levels, this curriculum guide, which is one in a series of guides for consumer and homemaking education in Kentucky, outlines four courses in the clothing and textile areas. Starting at the seventh grade level in Unit 1, the topics and instruction increase in complexity from one unit…

Finite element analysis of electromagnetic propagation in an absorbing wave guide

NASA Technical Reports Server (NTRS)

Baumeister, Kenneth J.

1986-01-01

Wave guides play a significant role in microwave space communication systems. The attenuation per unit length of the guide depends on its construction and design frequency range. A finite element Galerkin formulation has been developed to study TM electromagnetic propagation in complex two-dimensional absorbing wave guides. The analysis models the electromagnetic absorptive characteristics of a general wave guide which could be used to determine wall losses or simulate resistive terminations fitted into the ends of a guide. It is believed that the general conclusions drawn by using this simpler two-dimensional geometry will be fundamentally the same for other geometries.

Effects of guided breath exercise on complex behaviour of heart rate dynamics.

PubMed

Tavares, Bruna S; de Paula Vidigal, Giovanna; Garner, David M; Raimundo, Rodrigo D; de Abreu, Luiz Carlos; Valenti, Vitor E

2017-11-01

Cardiac autonomic regulation is influenced by changes in respiratory rate, which has been demonstrated by linear analysis of heart rate variability (HRV). Conversely, the complex behaviour is not well defined for HRV during this physiological state. In this sense, Higuchi Fractal Dimension is applied directly to the time series. It analyses the fractal dimension of discrete time sequences and is simpler and faster than correlation dimension and many other classical measures derived from chaos theory. We investigated chaotic behaviour of heart rate dynamics during guided breath exercises. We investigated 21 healthy male volunteers aged between 18 and 30 years. HRV was analysed 10 min before and 10 min during guided breath exercises. HRV was analysed in the time and frequency domain for linear analysis and through HFD for non-linear analysis. Linear analysis indicated that SDNN, pNN50, RMSSD, LF, HF and LF/HF increased during guided breath exercises. HFD analysis illustrated that between K max 20 to K max 120 intervals, was enhanced during guided breath exercises. Guided breath exercises acutely increased chaotic behaviour of HRV measured by HFD. © 2016 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

Advances for studying clonal evolution in cancer.

PubMed

Ding, Li; Raphael, Benjamin J; Chen, Feng; Wendl, Michael C

2013-11-01

The "clonal evolution" model of cancer emerged and "evolved" amid ongoing advances in technology, especially in recent years during which next generation sequencing instruments have provided ever higher resolution pictures of the genetic changes in cancer cells and heterogeneity in tumors. It has become increasingly clear that clonal evolution is not a single sequential process, but instead frequently involves simultaneous evolution of multiple subclones that co-exist because they are of similar fitness or are spatially separated. Co-evolution of subclones also occurs when they complement each other's survival advantages. Recent studies have also shown that clonal evolution is highly heterogeneous: different individual tumors of the same type may undergo very different paths of clonal evolution. New methodological advancements, including deep digital sequencing of a mixed tumor population, single cell sequencing, and the development of more sophisticated computational tools, will continue to shape and reshape the models of clonal evolution. In turn, these will provide both an improved framework for the understanding of cancer progression and a guide for treatment strategies aimed at the elimination of all, rather than just some, of the cancer cells within a patient. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Evolution of mixing width induced by general Rayleigh-Taylor instability.

PubMed

Zhang, You-Sheng; He, Zhi-Wei; Gao, Fu-Jie; Li, Xin-Liang; Tian, Bao-Lin

2016-06-01

Turbulent mixing induced by Rayleigh-Taylor (RT) instability occurs ubiquitously in many natural phenomena and engineering applications. As the simplest and primary descriptor of the mixing process, the evolution of mixing width of the mixing zone plays a notable role in the flows. The flows generally involve complex varying acceleration histories and widely varying density ratios, two dominant factors affecting the evolution of mixing width. However, no satisfactory theory for predicting the evolution has yet been established. Here a theory determining the evolution of mixing width in general RT flows is established to reproduce, first, all of the documented experiments conducted for diverse (i.e., constant, impulsive, oscillating, decreasing, increasing, and complex) acceleration histories and all density ratios. The theory is established in terms of the conservation principle, with special consideration given to the asymmetry of the volume-averaged density fields occurring in actual flows. The results reveal the sensitivity or insensitivity of the evolution of a mixing front of a neighboring light or heavy fluid to the degree of asymmetry and thus explain the distinct evolutions in two experiments with the same configurations.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

PubMed

Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

2018-05-22

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

Introduction

USGS Publications Warehouse

Friend, Milton; Franson, J. Christian; Friend, Milton; Gibbs, Samantha E.J.; Wild, Margaret A.

2015-01-01

This is the third iteration of the National Wildlife Health Center's (NWHC) field guide developed primarily to assist field managers and biologists address diseases they encounter. By itself, the first iteration, “Field Guide of Wildlife Diseases: General Field Procedures and Diseases of Migratory Birds,” was simply another addition to an increasing array of North American field guides and other publications focusing on disease in free-ranging wildlife populations. Collectively, those publications were reflecting the ongoing transition in the convergence of wildlife management and wildlife disease as foundational components within the structure of wildlife conservation as a social enterprise serving the stewardship of our wildlife resources. For context, it is useful to consider those publications relative to a timeline of milestones involving the evolution of wildlife conservation in North America.

Teacher Modeling Using Complex Informational Texts

ERIC Educational Resources Information Center

Fisher, Douglas; Frey, Nancy

2015-01-01

Modeling in complex texts requires that teachers analyze the text for factors of qualitative complexity and then design lessons that introduce students to that complexity. In addition, teachers can model the disciplinary nature of content area texts as well as word solving and comprehension strategies. Included is a planning guide for think aloud.

The Evolution of the Brain, the Human Nature of Cortical Circuits, and Intellectual Creativity

PubMed Central

DeFelipe, Javier

2011-01-01

The tremendous expansion and the differentiation of the neocortex constitute two major events in the evolution of the mammalian brain. The increase in size and complexity of our brains opened the way to a spectacular development of cognitive and mental skills. This expansion during evolution facilitated the addition of microcircuits with a similar basic structure, which increased the complexity of the human brain and contributed to its uniqueness. However, fundamental differences even exist between distinct mammalian species. Here, we shall discuss the issue of our humanity from a neurobiological and historical perspective. PMID:21647212

The evolution of the neocortex in mammals: intrinsic and extrinsic contributions to the cortical phenotype.

PubMed

Karlen, Sarah J; Krubitzer, Leah

2006-01-01

The neocortex is that portion of the brain that is involved in volitional motor control, perception, cognition and a number of other complex behaviours exhibited by mammals, including humans. Indeed, the increase in the size of the cortical sheet and cortical field number is one of the hallmarks of human brain evolution. Fossil records and comparative studies of the neocortex indicate that early mammalian neocortices were composed of only a few parts or cortical fields, and that in some lineages such as primates, the neocortex expanded dramatically. More significantly, the number of cortical fields increased and the connectivity between cortical fields became more complex. While we do not know the exact transformation between this type of increase in cortical field number and connectivity; and the emergence of complex behaviours like those mentioned above, we know that species that have large neocorticies with multiple parts generally have more complex behaviours, both overt and covert. Although a number of inroads have been made into understanding how neurons in the neocortex respond to a variety of stimuli, the micro and macro circuitry of particular neocortical fields, and the molecular developmental events that construct current organization, very little is known about how more cortical fields are added in evolution. In particular, we do not know the rules of change, nor the constraints imposed on evolving nervous systems that dictate the particular phenotype that will ultimately emerge. One reason why these issues are unresolved is that the brain is a compromise between existing genetic constraints and the need to adapt. Thus, the functions that the brain generates are absolutely imperfect, although functionally optimized. This makes it very difficult to determine the rules of construction, to generate viable computational models of brain evolution, and to predict the direction of changes that may occur over time. Despite these obstacles, it is still possible to study the evolution of the neocortex. One way is to study the products of the evolutionary process--extant mammal brains-and to make inferences about the process. The second way to study brain evolution is to examine the developmental mechanisms that give rise to complex brains. We have begun to test our theories regarding cortical evolution, generated from comparative studies, by 'tweaking' in a developing nervous system what we believe is naturally being modified in evolution. Our goals are to identify the constraints imposed on the evolving neocortex, to disentangle the genetic and activity dependent mechanisms that give rise to complex brains, and ultimately to produce a cortical phenotype that is consistent with what would naturally occur in evolution.

Traffic and data preparation for AASHTO MEPDG analysis and designs.

DOT National Transportation Integrated Search

2011-10-01

"The Mechanistic Empirical Pavement Design Guide (MEPDG) and the : subsequent AASHTO product DARWin-ME are signifi cant advancements in : pavement design. However, they are substantially more complex than the : 1993 AASHTO Guide, which is currently u...

Synergy from reproductive division of labor and genetic complexity drive the evolution of sex.

PubMed

Jaffe, Klaus

2018-04-16

Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating. Looking at the evolution of sex as a complex system through individual-based simulations explains better the diversity of sexual strategies known to exist in nature, compared to classical analytical models.

Evolution of the social network of scientific collaborations

NASA Astrophysics Data System (ADS)

Barabasi, Albert-Laszlo; Jeong, Hawoong; Neda, Zoltan; Ravasz, Erzsebet; Schubert, Andras; Vicsek, Tamas

2002-03-01

The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer the dynamic and the structural mechanisms that govern the evolution and topology of this complex system. First, empirical measurements allow us to uncover the topological measures that characterize the network at a given moment, as well as the time evolution of these quantities. The results indicate that the network is scale-free, and that the network evolution is governed by preferential attachment, affecting both internal and external links. However, in contrast with most model predictions the average degree increases in time, and the node separation decreases. Second, we propose a simple model that captures the network's time evolution. Third, numerical simulations are used to uncover the behavior of quantities that could not be predicted analytically.

The (De-)Evolution of Evolution Games: A Content Analysis of the Representation of Evolution through Natural Selection in Digital Games

ERIC Educational Resources Information Center

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-01-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a…

A Pragmatic Approach to Guide Implementation Evaluation Research: Strategy Mapping for Complex Interventions.

PubMed

Huynh, Alexis K; Hamilton, Alison B; Farmer, Melissa M; Bean-Mayberry, Bevanne; Stirman, Shannon Wiltsey; Moin, Tannaz; Finley, Erin P

2018-01-01

Greater specification of implementation strategies is a challenge for implementation science, but there is little guidance for delineating the use of multiple strategies involved in complex interventions. The Cardiovascular (CV) Toolkit project entails implementation of a toolkit designed to reduce CV risk by increasing women's engagement in appropriate services. The CV Toolkit project follows an enhanced version of Replicating Effective Programs (REP), an evidence-based implementation strategy, to implement the CV Toolkit across four phases: pre-conditions, pre-implementation, implementation, and maintenance and evolution. Our current objective is to describe a method for mapping implementation strategies used in real time as part of the CV Toolkit project. This method supports description of the timing and content of bundled strategies and provides a structured process for developing a plan for implementation evaluation. We conducted a process of strategy mapping to apply Proctor and colleagues' rubric for specification of implementation strategies, constructing a matrix in which we identified each implementation strategy, its conceptual group, and the corresponding REP phase(s) in which it occurs. For each strategy, we also specified the actors involved, actions undertaken, action targets, dose of the implementation strategy, and anticipated outcome addressed. We iteratively refined the matrix with the implementation team, including use of simulation to provide initial validation. Mapping revealed patterns in the timing of implementation strategies within REP phases. Most implementation strategies involving the development of stakeholder interrelationships and training and educating stakeholders were introduced during the pre-conditions or pre-implementation phases. Strategies introduced in the maintenance and evolution phase emphasized communication, re-examination, and audit and feedback. In addition to its value for producing valid and reliable process evaluation data, mapping implementation strategies has informed development of a pragmatic blueprint for implementation and longitudinal analyses and evaluation activities. We update recent recommendations on specification of implementation strategies by considering the implications for multi-strategy frameworks and propose an approach for mapping the use of implementation strategies within complex, multi-level interventions, in support of rigorous evaluation. Developing pragmatic tools to aid in operationalizing the conduct of implementation and evaluation activities is essential to enacting sound implementation research.

Emergence of life: Physical chemistry changes the paradigm.

PubMed

Spitzer, Jan; Pielak, Gary J; Poolman, Bert

2015-06-10

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Family feuds: social competition and sexual conflict in complex societies

PubMed Central

Rubenstein, Dustin R.

2012-01-01

Darwin was initially puzzled by the processes that led to ornamentation in males—what he termed sexual selection—and those that led to extreme cooperation and altruism in complex animal societies—what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities—particularly in females—and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females. PMID:22777018

Family feuds: social competition and sexual conflict in complex societies.

PubMed

Rubenstein, Dustin R

2012-08-19

Darwin was initially puzzled by the processes that led to ornamentation in males-what he termed sexual selection-and those that led to extreme cooperation and altruism in complex animal societies-what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities-particularly in females-and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females.

Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

PubMed

Austerlitz, Frédéric; Heyer, Evelyne

2018-06-01

Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

Towards Complex Abiotic Systems for Chemical and Biological Sensing

DTIC Science & Technology

2009-11-01

such as phage display, cell surface display, and Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Other processes necessary to...Directed evolution by in vitro compartmentalization. Nat Methods 2006, 3, 561-570. l7Chelliserrykattil, J.; Ellington, A.D. Evolution of a T7 RNA

Propagating modes in gain-guided optical fibers.

PubMed

Siegman, A E

2003-08-01

Optical fibers in which gain-guiding effects are significant or even dominant compared with conventional index guiding may become of practical interest for future high-power single-mode fiber lasers. I derive the propagation characteristics of symmetrical slab waveguides and cylindrical optical fibers having arbitrary amounts of mixed gain and index guiding, assuming a single uniform transverse profile for both the gain and the refractive-index steps. Optical fibers of this type are best characterized by using a complex-valued v-squared parameter in place of the real-valued v parameter commonly used to describe conventional index-guided optical fibers.

Solutions to Peto's paradox revealed by mathematical modelling and cross-species cancer gene analysis

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

Caulin, Aleah F.; Graham, Trevor A.; Wang, Li-San

Whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. This observation is known as Peto's paradox. How much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? Analysis of previously published models of colorectal cancer suggests that a two- to three-fold decrease in the mutation rate or stem cell division rate is enough to reduce a whale's cancer riskmore » to that of a human. Similarly, the addition of one to two required tumour-suppressor gene mutations would also be sufficient. Also, we surveyed mammalian genomes and did not find a positive correlation of tumour-suppressor genes with increasing body mass and longevity. However, we found evidence of the amplification of TP53 in elephants, MAL in horses and FBXO31 in microbats, which might explain Peto's paradox in those species. Lastly, exploring parameters that evolution may have fine-tuned in large, long-lived organisms will help guide future experiments to reveal the underlying biology responsible for Peto's paradox and guide cancer prevention in humans.« less

Solutions to Peto's paradox revealed by mathematical modelling and cross-species cancer gene analysis

DOE PAGES

Caulin, Aleah F.; Graham, Trevor A.; Wang, Li-San; ...

2015-06-08

Whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. This observation is known as Peto's paradox. How much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? Analysis of previously published models of colorectal cancer suggests that a two- to three-fold decrease in the mutation rate or stem cell division rate is enough to reduce a whale's cancer riskmore » to that of a human. Similarly, the addition of one to two required tumour-suppressor gene mutations would also be sufficient. Also, we surveyed mammalian genomes and did not find a positive correlation of tumour-suppressor genes with increasing body mass and longevity. However, we found evidence of the amplification of TP53 in elephants, MAL in horses and FBXO31 in microbats, which might explain Peto's paradox in those species. Lastly, exploring parameters that evolution may have fine-tuned in large, long-lived organisms will help guide future experiments to reveal the underlying biology responsible for Peto's paradox and guide cancer prevention in humans.« less

An evolutionary perspective on the systems of adaptive immunity.

PubMed

Müller, Viktor; de Boer, Rob J; Bonhoeffer, Sebastian; Szathmáry, Eörs

2018-02-01

We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Openers for Biology Classes.

ERIC Educational Resources Information Center

Gridley, C. Robert R.

This teaching guide contains 200 activities that are suitable for openers and demonstrations in biology classes. Details are provided regarding the use of these activities. Some of the broad topics under which the activities are organized include algae, amphibians, bacteria, biologists, crustaceans, dinosaurs, ecology, evolution, flowering plants,…

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

Larson, Natalie M.; Zok, Frank W.

One route for producing fiber-reinforced ceramic-matrix composites entails repeated impregnation and pyrolysis of a preceramic polymer in a fiber preform. The process relies crucially on the development of networks of contiguous cracks during pyrolysis, thereby allowing further impregnation to attain nearly-full densification. The present study employs in-situ x-ray computed tomography (XCT) to reveal in three dimensions the evolution of matrix structure during pyrolysis of a SiC-based preceramic polymer to 1200 °C. Observations are used to guide the development of a taxonomy of crack geometries and crack structures and to identify the temporal sequence of their formation. A quantitative analysis ismore » employed to characterize effects of local microstructural dimensions on the conditions required to form cracks of various types. Complementary measurements of gas evolution and mass loss of the preceramic polymer during pyrolysis as well as changes in mass density and Young's modulus provide context for the physical changes revealed by XCT. Furthermore, the findings provide a foundation for future development of physics-based models to guide composite fabrication processes.« less

Evolution of cognitive-behavioral therapy for eating disorders.

PubMed

Agras, W Stewart; Fitzsimmons-Craft, Ellen E; Wilfley, Denise E

2017-01-01

The evolution of cognitive-behavioral therapy (CBT) for the treatment of bulimic disorders is described in this review. The impacts of successive attempts to enhance CBT such as the addition of exposure and response prevention; the development of enhanced CBT; and broadening the treatment from bulimia nervosa to binge eating disorder are considered. In addition to developing advanced forms of CBT, shortening treatment to guided self-help was the first step in broadening access to treatment. The use of technology such as computer-based therapy and more recently the Internet, promises further broadening of access to self-help and to therapist guided treatment. Controlled studies in this area are reviewed, and the balance of risks and benefits that accompany the use of technology and lessened therapist input are considered. Looking into the future, more sophisticated forms of treatment delivered as mobile applications ("apps") may lead to more personalized and efficacious treatments for bulimic disorders, thus enhancing the delivery of treatments for eating disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiple secondary islands formation in nonlinear evolution of double tearing mode simulations

NASA Astrophysics Data System (ADS)

Guo, W.; Ma, J.; Yu, Z.

2017-03-01

A new numerical code solving the conservative perturbed resistive magnetohydrodynamic (MHD) model is developed. Numerical tests of the ideal Kelvin-Helmholtz instability and the resistive double tearing mode (DTM) show its capability in solving linear and nonlinear MHD instabilities. The nonlinear DTM evolution in 2D geometry is numerically investigated with low guiding field B z 0 , short half-distance y 0 between the equilibrium current sheets, and small resistivity η. The interaction of islands on the two initial current sheets may generate an unstable flow driven current sheet with a high length-to-thickness aspect ratio (α), and multiple secondary islands can form. In general, the length-to-thickness aspect ratio α and the number of secondary islands increase with decreasing guide field B z 0 , decreasing half-distance y 0 , and increasing Lundquist number of the flow driven current sheet S L although the dependence may be non-monotonic. The reconnection rate dependence on S L , B z 0 , and y 0 is also investigated.

Influence of chemical disorder on energy dissipation and defect evolution in concentrated solid solution alloys

DOE PAGES

Zhang, Yanwen; Stocks, George Malcolm; Jin, Ke; ...

2015-10-28

A long-standing objective in materials research is to understand how energy is dissipated in both the electronic and atomic subsystems in irradiated materials, and how related non-equilibrium processes may affect defect dynamics and microstructure evolution. Here we show that alloy complexity in concentrated solid solution alloys having both an increasing number of principal elements and altered concentrations of specific elements can lead to substantial reduction in the electron mean free path and thermal conductivity, which has a significant impact on energy dissipation and consequentially on defect evolution during ion irradiation. Enhanced radiation resistance with increasing complexity from pure nickel tomore » binary and to more complex quaternary solid solutions is observed under ion irradiation up to an average damage level of 1 displacement per atom. Understanding how materials properties can be tailored by alloy complexity and their influence on defect dynamics may pave the way for new principles for the design of radiation tolerant structural alloys.« less

Big cats as a model system for the study of the evolution of intelligence.

PubMed

Borrego, Natalia

2017-08-01

Currently, carnivores, and felids in particular, are vastly underrepresented in cognitive literature, despite being an ideal model system for tests of social and ecological intelligence hypotheses. Within Felidae, big cats (Panthera) are uniquely suited to studies investigating the evolutionary links between social, ecological, and cognitive complexity. Intelligence likely did not evolve in a unitary way but instead evolved as the result of mutually reinforcing feedback loops within the physical and social environments. The domain-specific social intelligence hypothesis proposes that social complexity drives only the evolution of cognitive abilities adapted only to social domains. The domain-general hypothesis proposes that the unique demands of social life serve as a bootstrap for the evolution of superior general cognition. Big cats are one of the few systems in which we can directly address conflicting predictions of the domain-general and domain-specific hypothesis by comparing cognition among closely related species that face roughly equivalent ecological complexity but vary considerably in social complexity. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of an ancient protein function involved in organized multicellularity in animals

PubMed Central

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-01

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals. DOI: http://dx.doi.org/10.7554/eLife.10147.001 PMID:26740169

Predicting protein complexes using a supervised learning method combined with local structural information.

PubMed

Dong, Yadong; Sun, Yongqi; Qin, Chao

2018-01-01

The existing protein complex detection methods can be broadly divided into two categories: unsupervised and supervised learning methods. Most of the unsupervised learning methods assume that protein complexes are in dense regions of protein-protein interaction (PPI) networks even though many true complexes are not dense subgraphs. Supervised learning methods utilize the informative properties of known complexes; they often extract features from existing complexes and then use the features to train a classification model. The trained model is used to guide the search process for new complexes. However, insufficient extracted features, noise in the PPI data and the incompleteness of complex data make the classification model imprecise. Consequently, the classification model is not sufficient for guiding the detection of complexes. Therefore, we propose a new robust score function that combines the classification model with local structural information. Based on the score function, we provide a search method that works both forwards and backwards. The results from experiments on six benchmark PPI datasets and three protein complex datasets show that our approach can achieve better performance compared with the state-of-the-art supervised, semi-supervised and unsupervised methods for protein complex detection, occasionally significantly outperforming such methods.

The Effects of Guided Careful Online Planning on Complexity, Accuracy and Fluency in Intermediate EFL Learners' Oral Production: The Case of English Articles

ERIC Educational Resources Information Center

Ahmadian, Mohammad Javad

2012-01-01

The purpose of the study reported in this article was twofold: First, to see whether guided careful online planning assists intermediate learners of English as a foreign language (EFL) in accurate oral production of English articles ("an/a" and "the"); and, second, to see whether guided careful online planning has any effects…

Mariner's guide for hurricane awareness in the North Atlantic basin.

DOT National Transportation Integrated Search

2000-08-01

This guide will hopefully aid the Mariner in understanding the complex structure and behavior of : tropical cyclones in the North Atlantic Ocean. Once armed with this knowledge, and the information : on where to acquire forecasts and guidance for cur...

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

2016-01-01

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.

Evolution for Young Victorians

ERIC Educational Resources Information Center

Lightman, Bernard

2012-01-01

Evolution was a difficult topic to tackle when writing books for the young in the wake of the controversies over Darwin's "Origin of Species." Authors who wrote about evolution for the young experimented with different ways of making the complex concepts of evolutionary theory accessible and less controversial. Many authors depicted presented…

Thermodynamical Arguments against Evolution

ERIC Educational Resources Information Center

Rosenhouse, Jason

2017-01-01

The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be…

Extensive video-game experience alters cortical networks for complex visuomotor transformations.

PubMed

Granek, Joshua A; Gorbet, Diana J; Sergio, Lauren E

2010-10-01

Using event-related functional magnetic resonance imaging (fMRI), we examined the effect of video-game experience on the neural control of increasingly complex visuomotor tasks. Previously, skilled individuals have demonstrated the use of a more efficient movement control brain network, including the prefrontal, premotor, primary sensorimotor and parietal cortices. Our results extend and generalize this finding by documenting additional prefrontal cortex activity in experienced video gamers planning for complex eye-hand coordination tasks that are distinct from actual video-game play. These changes in activation between non-gamers and extensive gamers are putatively related to the increased online control and spatial attention required for complex visually guided reaching. These data suggest that the basic cortical network for processing complex visually guided reaching is altered by extensive video-game play. Crown Copyright © 2009. Published by Elsevier Srl. All rights reserved.

Voids and the Cosmic Web: cosmic depression & spatial complexity

NASA Astrophysics Data System (ADS)

van de Weygaert, Rien

2016-10-01

Voids form a prominent aspect of the Megaparsec distribution of galaxies and matter. Not only do theyrepresent a key constituent of the Cosmic Web, they also are one of the cleanest probesand measures of global cosmological parameters. The shape and evolution of voids are highly sensitive tothe nature of dark energy, while their substructure and galaxy population provides a direct key to thenature of dark matter. Also, the pristine environment of void interiors is an important testing groundfor our understanding of environmental influences on galaxy formation and evolution. In this paper, we reviewthe key aspects of the structure and dynamics ofvoids, with a particular focus on the hierarchical evolution of the void population. We demonstratehow the rich structural pattern of the Cosmic Web is related to the complex evolution and buildupof voids.

Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

PubMed

Remington, David L

2015-12-01

Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Man-made Boards Technology Trends based on TRIZ Evolution Theory

NASA Astrophysics Data System (ADS)

Yu, Huiling; Fan, Delin

China is one of the world's largest manufacturers and consumers of man-made board applications. A systematic and efficient method of foreseeing future technology trends and their evolutionary potentials is a key task that can help companies guide their planning and allocate their resources. Application of the law of evolution with a S-shaped curve could contribute essentially to the accuracy of the long-term forecast. This research seeks to determine the current stage and the position on the S-curve of man-made board technology in China on the TRIZ evolution theo ryand introduce a methodology which combines patent analysis and technology life cycle forecasting to find a niche space of man-made technology development in China.

Computed tomography image-guided surgery in complex acetabular fractures.

PubMed

Brown, G A; Willis, M C; Firoozbakhsh, K; Barmada, A; Tessman, C L; Montgomery, A

2000-01-01

Eleven complex acetabular fractures in 10 patients were treated by open reduction with internal fixation incorporating computed tomography image guided software intraoperatively. Each of the implants placed under image guidance was found to be accurate and without penetration of the pelvis or joint space. The setup time for the system was minimal. Accuracy in the range of 1 mm was found when registration was precise (eight cases) and was in the range of 3.5 mm when registration was only approximate (three cases). Added benefits included reduced intraoperative fluoroscopic time, less need for more extensive dissection, and obviation of additional surgical approaches in some cases. Compared with a series of similar fractures treated before this image guided series, the reduction in operative time was significant. For patients with complex anterior and posterior combined fractures, the average operation times with and without application of three-dimensional imaging technique were, respectively, 5 hours 15 minutes and 6 hours 14 minutes, revealing 16% less operative time for those who had surgery using image guidance. In the single column fracture group, the operation time for those with three-dimensional imaging application, was 2 hours 58 minutes and for those with traditional surgery, 3 hours 42 minutes, indicating 20% less operative time for those with imaging modality. Intraoperative computed tomography guided imagery was found to be an accurate and suitable method for use in the operative treatment of complex acetabular fractures with substantial displacement.

Time-evolution of quantum systems via a complex nonlinear Riccati equation. I. Conservative systems with time-independent Hamiltonian

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

Cruz, Hans, E-mail: hans@ciencias.unam.mx; Schuch, Dieter; Castaños, Octavio, E-mail: ocasta@nucleares.unam.mx

2015-09-15

The sensitivity of the evolution of quantum uncertainties to the choice of the initial conditions is shown via a complex nonlinear Riccati equation leading to a reformulation of quantum dynamics. This sensitivity is demonstrated for systems with exact analytic solutions with the form of Gaussian wave packets. In particular, one-dimensional conservative systems with at most quadratic Hamiltonians are studied.

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

PubMed Central

Andreani, Jessica; Faure, Guilhem; Guerois, Raphaël

2012-01-01

Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into protein-protein interaction prediction. Using a database of 1,024 couples of close and remote heteromeric structural interologs, we studied protein-protein interactions from a structural and evolutionary point of view. We systematically and quantitatively analyzed the conservation of different types of interface contacts. Our study highlights astonishing plasticity regarding polar contacts at complex interfaces. It also reveals that up to a quarter of the residues switch out of the interface when comparing two homologous complexes. Despite such versatility, we identify two important interface descriptors which correlate with an increased conservation in the evolution of interfaces: apolar patches and contacts surrounding anchor residues. These observations hold true even when restricting the dataset to transiently formed complexes. We show that a combination of six features related either to sequence or to geometric properties of interfaces can be used to rank positions likely to share similar contacts between two interologs. Altogether, our analysis provides important tracks for extracting meaningful information from multiple sequence alignments of conserved binding partners and for discriminating near-native interfaces using evolutionary information. PMID:22952442

Biogeography predicts macro-evolutionary patterning of gestural display complexity in a passerine family.

PubMed

Miles, Meredith C; Cheng, Samantha; Fuxjager, Matthew J

2017-05-01

Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species' geographical distribution and social mating system predict macro-evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The physics of evolution

NASA Astrophysics Data System (ADS)

Eigen, Manfred

1988-12-01

The Darwinian concept of evolution through natural selection has been revised and put on a solid physical basis, in a form which applies to self-replicable macromolecules. Two new concepts are introduced: sequence space and quasi-species. Evolutionary change in the DNA- or RNA-sequence of a gene can be mapped as a trajectory in a sequence space of dimension ν, where ν corresponds to the number of changeable positions in the genomic sequence. Emphasis, however, is shifted from the single surviving wildtype, a single point in the sequence space, to the complex structure of the mutant distribution that constitutes the quasi-species. Selection is equivalent to an establishment of the quasi-species in a localized region of sequence space, subject to threshold conditions for the error rate and sequence length. Arrival of a new mutant may violate the local threshold condition and thereby lead to a displacement of the quasi-species into a different region of sequence space. This transformation is similar to a phase transition; the dynamical equations that describe the quase-species have been shown to be analogous to those of the two-dimensional Ising model of ferromagnetism. The occurrence of a selectively advantageous mutant is biased by the particulars of the quasi-species distribution, whose mutants are populated according to their fitness relative to that of the wild-type. Inasmuch as fitness regions are connected (like mountain ridges) the evolutionary trajectory is guided to regions of optimal fitness. Evolution experiments in test tubes confirm this modification of the simple chance and law nature of the Darwinian concept. The results of the theory can also be applied to the construction of a machine that provides optimal conditions for a rapid evolution of functionally active macromolecules. An introduction to the physics of molecular evolution by the author has appeared recently.1 Detailed studies of the kinetics and mechanisms of replication of RNA, the most likely candidate for early evolution2,3, and of the implications on natural selection have been given in Refs. 4 and 5. The quasi-species model has been constructed in Refs. 6 and 7 using the concept of sequence space. Subsequently various methods have been invented to elucidate this concept and to relate it to the theory of critical phenomena 8-19. The instability of the quasi-species at the error threshold is discussed in Ref. 10. Evolution experiments with RNA strands in test tubes are described in Refs. 21 and 22.

Evolutionary Theory as a Guide to Socioscientific Decision-Making

ERIC Educational Resources Information Center

Sadler, Troy D.

2005-01-01

Evolutionary theory serves as the fundamental cornerstone to all life science; yet students frequently possess misconceptions regarding evolution or resist learning the idea altogether. This study, which emerged from a larger project focused on informal reasoning, explores how college students' conceptions of evolutionary theory affect their…

Best practices for modifying transportation design, planning, and project evaluation in Texas.

DOT National Transportation Integrated Search

2017-03-01

This guidebook is a desktop guide for TxDOT staff to facilitate an understanding of CAV technologies and the current trends in development and deployment. The overview should aid in anticipating the evolution of the Texas fleet and its use under vari...

Olympic Values Education: Evolution of a Pedagogy

ERIC Educational Resources Information Center

Binder, Deanna L.

2012-01-01

Guided by the twentieth century hermeneutic idea that application co-determines understanding, this paper explores the conversations between theory and application that evolved during the implementation of three Olympic-related curriculum projects. Each of these projects was informed by specific fields of then-current educational theory, and…

Building Whales in Sand and Mind.

ERIC Educational Resources Information Center

Warner, Carolyn

1980-01-01

Describes two-week summer workshops on evolution, adaptation, and behavior of whales, conducted for children by Cold Spring Harbor Whaling Museum (New York), and culminating in creation of life-size sand sculptures of whales. Provides selected list of periodicals, teaching materials, identification guides, records, and societies devoted to whales…

Complex networks generated by the Penna bit-string model: Emergence of small-world and assortative mixing

NASA Astrophysics Data System (ADS)

Li, Chunguang; Maini, Philip K.

2005-10-01

The Penna bit-string model successfully encompasses many phenomena of population evolution, including inheritance, mutation, evolution, and aging. If we consider social interactions among individuals in the Penna model, the population will form a complex network. In this paper, we first modify the Verhulst factor to control only the birth rate, and introduce activity-based preferential reproduction of offspring in the Penna model. The social interactions among individuals are generated by both inheritance and activity-based preferential increase. Then we study the properties of the complex network generated by the modified Penna model. We find that the resulting complex network has a small-world effect and the assortative mixing property.

Advances for Studying Clonal Evolution in Cancer

PubMed Central

Raphael, Benjamin J.; Chen, Feng; Wendl, Michael C.

2013-01-01

The “clonal evolution” model of cancer emerged and “evolved” amid ongoing advances in technology, especially in recent years during which next generation sequencing instruments have provided ever higher resolution pictures of the genetic changes in cancer cells and heterogeneity in tumors. It has become increasingly clear that clonal evolution is not a single sequential process, but instead frequently involves simultaneous evolution of multiple subclones that co-exist because they are of similar fitness or are spatially separated. Co-evolution of subclones also occurs when they complement each other’s survival advantages. Recent studies have also shown that clonal evolution is highly heterogeneous: different individual tumors of the same type may undergo very different paths of clonal evolution. New methodological advancements, including deep digital sequencing of a mixed tumor population, single cell sequencing, and the development of more sophisticated computational tools, will continue to shape and reshape the models of clonal evolution. In turn, these will provide both an improved framework for the understanding of cancer progression and a guide for treatment strategies aimed at the elimination of all, rather than just some, of the cancer cells within a patient. PMID:23353056

Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway.

PubMed

Hagey, Lee R; Møller, Peter R; Hofmann, Alan F; Krasowski, Matthew D

2010-01-01

Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates.

Self-determined mechanisms in complex networks

NASA Astrophysics Data System (ADS)

Liu, Yang; Yuan, Jian; Shan, Xiuming; Ren, Yong; Ma, Zhengxin

2008-03-01

Self-organized networks are pervasive in communication systems such as the Internet, overlay networks, peer-to-peer networks, and cluster-based services. These networks evolve into complex topologies, under specific driving forces, i.e. user demands, technological innovations, design objectives and so on. Our study focuses on the driving forces behind individual evolutions of network components, and their stimulation and domination to the self-organized networks which are defined as self-determined mechanisms in this paper. Understanding forces underlying the evolution of networks should enable informed design decisions and help to avoid unwanted surprises, such as congestion collapse. A case study on the macroscopic evolution of the Internet topology of autonomous systems under a specific driving force is then presented. Using computer simulations, it is found that the power-law degree distribution can originate from a connection preference to larger numbers of users, and that the small-world property can be caused by rapid growth in the number of users. Our results provide a new feasible perspective to understand intrinsic fundamentals in the topological evolution of complex networks.

The influence of AVPR1A genotype on individual differences in behaviors during a mirror self-recognition task in chimpanzees (Pan troglodytes).

PubMed

Mahovetz, L M; Young, L J; Hopkins, W D

2016-06-01

The mark/rouge test has been used to assess mirror self-recognition (MSR) in many species. Despite consistent evidence of MSR in great apes, genetic or non-genetic factors may account for the individual differences in behavioral responses that have been reported. We examined whether vasopressin receptor gene (AVPR1A) polymorphisms are associated with MSR-related behaviors in chimpanzees since vasopressin has been implicated in the development and evolution of complex social relations and cognition and chimpanzees are polymorphic for the presence of the RS3-containing DupB region. We compared a sample of DupB+/- and DupB-/- chimpanzees on a mark test to assess its role on social behavior toward a mirror. Chimpanzees were administered two, 10-min sessions where frequencies of mirror-guided self-directed behaviors, contingent actions and other social behaviors were recorded. Approximately one-third showed evidence of MSR and these individuals exhibited more mirror-guided self-exploratory behaviors and mouth contingent actions than chimpanzees not classified as passers. Moreover, DupB+/- males exhibited more scratching and agonistic behaviors than other male and female cohorts. Our findings support previous studies demonstrating individual differences in MSR abilities in chimpanzees and suggest that AVPR1A partly explains individual differences in MSR by influencing the behavioral reactions of chimpanzees in front of a mirror. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Documentation and Cultural Heritage Inventories - Case of the Historic City of Ahmadabad

NASA Astrophysics Data System (ADS)

Shah, K.

2015-08-01

Located in the western Indian state of Gujarat, the historic city of Ahmadabad is renowned for the unparalleled richness of its monumental architecture, traditional house form, community based settlement patterns, city structure, crafts and mercantile culture. This paper describes the process followed for documentation and development of comprehensive Heritage Inventories for the historic city with an aim of illustrating the Outstanding Universal Values of its Architectural and Urban Heritage. The exercise undertaken between 2011 & 2014 as part of the preparation of world heritage nomination dossier included thorough archival research, field surveys, mapping and preparation of inventories using a combination of traditional data procurement and presentation tools as well as creation of advanced digital database using GIS. The major challenges encountered were: need to adapt documentation methodology and survey formats to field conditions, changing and ever widening scope of work, corresponding changes in time frame, management of large quantities of data generated during the process along with difficulties in correlating existing databases procured from the local authority in varying formats. While the end result satisfied the primary aim, the full potential of Heritage Inventory as a protection and management tool will only be realised after its acceptance as the statutory list and its integration within the larger urban development plan to guide conservation, development and management strategy for the city. The rather detailed description of evolution of documentation process and the complexities involved is presented to understand the relevance of methods used in Ahmadabad and guide similar future efforts in the field.

Evolution of the transcription complex during sporulation of Bacillus subtilis.

PubMed

Brevet, J

1976-01-01

Ribonucleic acid polymerase activity in partially purified extract of cells of Bacillus subtilis harvested at different times (t-1, to, t1, and t2) was studied by zone centrifugation. During the course of sporulation, vegetative sigma-factor activity decreased and the transcription complex lost some of its affinity for active sigma factor. The complex underwent a two-stage change in sedimentation value, from 14.5S in vegetative growth phase to a 13S species very early in sporulation to a 16S species at later times. Two SpoO mutants have been studied by zone centrifugation. One strain, a rifampin-resistant (RfmR) mutant, failed to show any modification of the transcription complex, whereas the other, a Rfms strain, underwent a partial evolution of the transcription complex after to.

The protein-protein interface evolution acts in a similar way to antibody affinity maturation.

PubMed

Li, Bohua; Zhao, Lei; Wang, Chong; Guo, Huaizu; Wu, Lan; Zhang, Xunming; Qian, Weizhu; Wang, Hao; Guo, Yajun

2010-02-05

Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniques to evaluate prediction success rates of the computational method in affinity improvement in four different systems: antibody-receptor, antibody-peptide, receptor-membrane ligand, and receptor-soluble ligand. It was interesting to find that the same evolutionary information could improve the prediction success rates in all the four protein-protein complexes with an exceptional high accuracy (>57%). One of the most striking findings in our present study is that not only in the antibody-combining site but in other protein-protein interfaces almost all of the affinity-enhancing mutations are located at the germline hotspot sequences (RGYW or WA), indicating that DNA hot spot mechanisms may be widely used in the evolution of protein-protein interfaces. Our data suggest that the evolution of distinct protein-protein interfaces may use the same basic strategy under selection pressure to maintain interactions. Additionally, our data indicate that classical simulation techniques incorporating the evolutionary information derived from in vivo antibody affinity maturation can be utilized as a powerful tool to improve the binding affinity of protein-protein complex with a high accuracy.

Complex Pattern Formation from Current-Driven Dynamics of Single-Layer Homoepitaxial Islands on Crystalline Conducting Substrates

NASA Astrophysics Data System (ADS)

Kumar, Ashish; Dasgupta, Dwaipayan; Maroudas, Dimitrios

2017-07-01

We report a systematic study of complex pattern formation resulting from the driven dynamics of single-layer homoepitaxial islands on surfaces of face-centered-cubic (fcc) crystalline conducting substrates under the action of an externally applied electric field. The analysis is based on an experimentally validated nonlinear model of mass transport via island edge atomic diffusion, which also accounts for edge diffusional anisotropy. We analyze the morphological stability and simulate the field-driven evolution of rounded islands for an electric field oriented along the fast edge diffusion direction. For larger-than-critical island sizes on {110 } and {100 } fcc substrates, we show that multiple necking instabilities generate complex island patterns, including not-simply-connected void-containing islands mediated by sequences of breakup and coalescence events and distributed symmetrically with respect to the electric field direction. We analyze the dependence of the formed patterns on the original island size and on the duration of application of the external field. Starting from a single large rounded island, we characterize the evolution of the number of daughter islands and their average size and uniformity. The evolution of the average island size follows a universal power-law scaling relation, and the evolution of the total edge length of the islands in the complex pattern follows Kolmogorov-Johnson-Mehl-Avrami kinetics. Our study makes a strong case for the use of electric fields, as precisely controlled macroscopic forcing, toward surface patterning involving complex nanoscale features.

Knowledge-guided mutation in classification rules for autism treatment efficacy.

PubMed

Engle, Kelley; Rada, Roy

2017-03-01

Data mining methods in biomedical research might benefit by combining genetic algorithms with domain-specific knowledge. The objective of this research is to show how the evolution of treatment rules for autism might be guided. The semantic distance between two concepts in the taxonomy is measured by the number of relationships separating the concepts in the taxonomy. The hypothesis is that replacing a concept in a treatment rule will change the accuracy of the rule in direct proportion to the semantic distance between the concepts. The method uses a patient database and autism taxonomies. Treatment rules are developed with an algorithm that exploits the taxonomies. The results support the hypothesis. This research should both advance the understanding of autism data mining in particular and of knowledge-guided evolutionary search in biomedicine in general.

Management of Retained Intervention Guide-wire: A Literature Review

PubMed Central

Al-Moghairi, Abdulrahman M; Al-Amri, Hussein S

2013-01-01

Percutaneous coronary angioplasty is increasingly employed in the treatment of patients with complex coronary artery disease. Different steerable guide wires used to open occluded vessel and facilitate balloon and stent deployment. However, the guide-wire itself is not without hazard: it may perforate or dissect the vessel, but fracture or entrapment is uncommon. Its management depends on the clinical situation of the patient, as well as the position and length of the remnant. In this review we discuss the angioplasty guide-wire fracture and entrapment risk factors, potential risks and management. PMID:23116055

Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor.

PubMed

Mitra, Avik; Ghosh, Arindam; Das, Ranabir; Patel, Apoorva; Kumar, Anil

2005-12-01

Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover's search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, using the local adiabatic evolution, the algorithms given by J. Roland and N.J. Cerf for Grover's search [J. Roland, N.J. Cerf, Quantum search by local adiabatic evolution, Phys. Rev. A 65 (2002) 042308] and by Saurya Das, Randy Kobes, and Gabor Kunstatter for the Deutsch-Jozsa algorithm [S. Das, R. Kobes, G. Kunstatter, Adiabatic quantum computation and Deutsh's algorithm, Phys. Rev. A 65 (2002) 062301], yield a complexity of order N (where N=2(n) and n is the number of qubits). In this paper, we report the experimental implementation of these local adiabatic evolution algorithms on a 2-qubit quantum information processor, by Nuclear Magnetic Resonance.

Assembly and function of the major histocompatibility complex (MHC) I peptide-loading complex are conserved across higher vertebrates.

PubMed

Hinz, Andreas; Jedamzick, Johanna; Herbring, Valentina; Fischbach, Hanna; Hartmann, Jessica; Parcej, David; Koch, Joachim; Tampé, Robert

2014-11-28

Antigen presentation to cytotoxic T lymphocytes via major histocompatibility complex class I (MHC I) molecules depends on the heterodimeric transporter associated with antigen processing (TAP). For efficient antigen supply to MHC I molecules in the ER, TAP assembles a macromolecular peptide-loading complex (PLC) by recruiting tapasin. In evolution, TAP appeared together with effector cells of adaptive immunity at the transition from jawless to jawed vertebrates and diversified further within the jawed vertebrates. Here, we compared TAP function and interaction with tapasin of a range of species within two classes of jawed vertebrates. We found that avian and mammalian TAP1 and TAP2 form heterodimeric complexes across taxa. Moreover, the extra N-terminal domain TMD0 of mammalian TAP1 and TAP2 as well as avian TAP2 recruits tapasin. Strikingly, however, only TAP1 and TAP2 from the same taxon can form a functional heterodimeric translocation complex. These data demonstrate that the dimerization interface between TAP1 and TAP2 and the tapasin docking sites for PLC assembly are conserved in evolution, whereas elements of antigen translocation diverged later in evolution and are thus taxon specific. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure of yeast Argonaute with guide RNA

PubMed Central

Nakanishi, Kotaro; Weinberg, David E.; Bartel, David P.; Patel, Dinshaw J.

2012-01-01

The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded and processed by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1–8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2′-hydroxyl groups pre-organizing the backbone of nucleotides 2–8 in a near–A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide–target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to Ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage. PMID:22722195

Modelling the evolution of complex conductivity during calcite precipitation on glass beads

NASA Astrophysics Data System (ADS)

Leroy, Philippe; Li, Shuai; Jougnot, Damien; Revil, André; Wu, Yuxin

2017-04-01

When pH and alkalinity increase, calcite frequently precipitates and hence modifies the petrophysical properties of porous media. The complex conductivity method can be used to directly monitor calcite precipitation in porous media because it is sensitive to the evolution of the mineralogy, pore structure and its connectivity. We have developed a mechanistic grain polarization model considering the electrochemical polarization of the Stern and diffuse layers surrounding calcite particles. Our complex conductivity model depends on the surface charge density of the Stern layer and on the electrical potential at the onset of the diffuse layer, which are computed using a basic Stern model of the calcite/water interface. The complex conductivity measurements of Wu et al. on a column packed with glass beads where calcite precipitation occurs are reproduced by our surface complexation and complex conductivity models. The evolution of the size and shape of calcite particles during the calcite precipitation experiment is estimated by our complex conductivity model. At the early stage of the calcite precipitation experiment, modelled particles sizes increase and calcite particles flatten with time because calcite crystals nucleate at the surface of glass beads and grow into larger calcite grains. At the later stage of the calcite precipitation experiment, modelled sizes and cementation exponents of calcite particles decrease with time because large calcite grains aggregate over multiple glass beads and only small calcite crystals polarize.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

PubMed Central

2015-01-01

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water. PMID:26574442

Socio-economic and Climate Factors Associated with Dengue Fever Spatial Heterogeneity: A Worked Example in New Caledonia.

PubMed

Teurlai, Magali; Menkès, Christophe Eugène; Cavarero, Virgil; Degallier, Nicolas; Descloux, Elodie; Grangeon, Jean-Paul; Guillaumot, Laurent; Libourel, Thérèse; Lucio, Paulo Sergio; Mathieu-Daudé, Françoise; Mangeas, Morgan

2015-12-01

Understanding the factors underlying the spatio-temporal distribution of infectious diseases provides useful information regarding their prevention and control. Dengue fever spatio-temporal patterns result from complex interactions between the virus, the host, and the vector. These interactions can be influenced by environmental conditions. Our objectives were to analyse dengue fever spatial distribution over New Caledonia during epidemic years, to identify some of the main underlying factors, and to predict the spatial evolution of dengue fever under changing climatic conditions, at the 2100 horizon. We used principal component analysis and support vector machines to analyse and model the influence of climate and socio-economic variables on the mean spatial distribution of 24,272 dengue cases reported from 1995 to 2012 in thirty-three communes of New Caledonia. We then modelled and estimated the future evolution of dengue incidence rates using a regional downscaling of future climate projections. The spatial distribution of dengue fever cases is highly heterogeneous. The variables most associated with this observed heterogeneity are the mean temperature, the mean number of people per premise, and the mean percentage of unemployed people, a variable highly correlated with people's way of life. Rainfall does not seem to play an important role in the spatial distribution of dengue cases during epidemics. By the end of the 21st century, if temperature increases by approximately 3 °C, mean incidence rates during epidemics could double. In New Caledonia, a subtropical insular environment, both temperature and socio-economic conditions are influencing the spatial spread of dengue fever. Extension of this study to other countries worldwide should improve the knowledge about climate influence on dengue burden and about the complex interplay between different factors. This study presents a methodology that can be used as a step by step guide to model dengue spatial heterogeneity in other countries.

Socio-economic and Climate Factors Associated with Dengue Fever Spatial Heterogeneity: A Worked Example in New Caledonia

PubMed Central

Teurlai, Magali; Menkès, Christophe Eugène; Cavarero, Virgil; Degallier, Nicolas; Descloux, Elodie; Grangeon, Jean-Paul; Guillaumot, Laurent; Libourel, Thérèse; Lucio, Paulo Sergio; Mathieu-Daudé, Françoise; Mangeas, Morgan

2015-01-01

Background/Objectives Understanding the factors underlying the spatio-temporal distribution of infectious diseases provides useful information regarding their prevention and control. Dengue fever spatio-temporal patterns result from complex interactions between the virus, the host, and the vector. These interactions can be influenced by environmental conditions. Our objectives were to analyse dengue fever spatial distribution over New Caledonia during epidemic years, to identify some of the main underlying factors, and to predict the spatial evolution of dengue fever under changing climatic conditions, at the 2100 horizon. Methods We used principal component analysis and support vector machines to analyse and model the influence of climate and socio-economic variables on the mean spatial distribution of 24,272 dengue cases reported from 1995 to 2012 in thirty-three communes of New Caledonia. We then modelled and estimated the future evolution of dengue incidence rates using a regional downscaling of future climate projections. Results The spatial distribution of dengue fever cases is highly heterogeneous. The variables most associated with this observed heterogeneity are the mean temperature, the mean number of people per premise, and the mean percentage of unemployed people, a variable highly correlated with people's way of life. Rainfall does not seem to play an important role in the spatial distribution of dengue cases during epidemics. By the end of the 21st century, if temperature increases by approximately 3°C, mean incidence rates during epidemics could double. Conclusion In New Caledonia, a subtropical insular environment, both temperature and socio-economic conditions are influencing the spatial spread of dengue fever. Extension of this study to other countries worldwide should improve the knowledge about climate influence on dengue burden and about the complex interplay between different factors. This study presents a methodology that can be used as a step by step guide to model dengue spatial heterogeneity in other countries. PMID:26624008

A hymenopterist’s guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

USDA-ARS?s Scientific Manuscript database

Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These...

Negotiating a Seat at the Table: Questions to Guide Institutional Involvement

ERIC Educational Resources Information Center

Siering, Gregory J.; Tapp, Suzanne; Lohe, Debra Rudder; Logan, Micah Meixner

2015-01-01

In addition to traditional roles, educational developers increasingly find themselves considering their involvement in issues of institutional change. However, this evolution leads to new challenges as educational developers attempt to discern whether and how to be involved in particular organizational change efforts. This chapter provides a…

Evolution of a Rapidly Learned Representation for Speech.

ERIC Educational Resources Information Center

Nakisa, Ramin Charles; Plunkett, Kim

1998-01-01

Describes a connectionist model accounting for newborn infants' ability to finely discriminate almost all human speech contrasts and the fact that their phonemic category boundaries are identical, even for phonemes outside their target language. The model posits an innately guided learning in which an artificial neural network is stored in a…

Educational Psychology and the Internet

ERIC Educational Resources Information Center

Glassman, Michael

2016-01-01

The first comprehensive, research-based textbook on Internet-infused education, "Educational Psychology and the Internet" offers students an accessible guide to important issues in the field. Michael Glassman begins with an overview of the history that traces the evolution of the Internet and its significance for education. He outlines…

The Role of Teachers' Guided Reflection in Effecting Positive Program Change.

ERIC Educational Resources Information Center

Vogt, Lynn Allington; Au, Kathryn H. P.

1995-01-01

Examines the evolution of teacher support and development in the Kamehameha Elementary Education Program (KEEP) and Rough Rock Community School collaboration. Ongoing teacher development featured regular classroom observation and feedback with mentors and peers and self-reflection through videotaping and journal writing. (two references) (MDM)

Development Aid: A Guide to Facts and Issues.

ERIC Educational Resources Information Center

de Silva, Leelananda

This eight-chapter book provides information on Official Development Assistance (ODA), its importance in relation to developed and developing countries, and its prospects and limitations. Major areas discussed include: (1) the institutional evolution of development aid; (2) forms of ODA, including project aid, program aid, bilateral aid,…

Structural Evolutions of STOCK Markets Controlled by Generalized Entropy Principles of Complex Systems

NASA Astrophysics Data System (ADS)

Wang, Yi Jiao; Feng, Qing Yi; Chai, Li He

As one of the most important financial markets and one of the main parts of economic system, the stock market has become the research focus in economics. The stock market is a typical complex open system far from equilibrium. Many available models that make huge contribution to researches on market are strong in describing the market however, ignoring strong nonlinear interactions among active agents and weak in reveal underlying dynamic mechanisms of structural evolutions of market. From econophysical perspectives, this paper analyzes the complex interactions among agents and defines the generalized entropy in stock markets. Nonlinear evolutionary dynamic equation for the stock markets is then derived from Maximum Generalized Entropy Principle. Simulations are accordingly conducted for a typical case with the given data, by which the structural evolution of the stock market system is demonstrated. Some discussions and implications are finally provided.

Evolution and development of brain networks: from Caenorhabditis elegans to Homo sapiens.

PubMed

Kaiser, Marcus; Varier, Sreedevi

2011-01-01

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. 'Small-world' topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms. In conclusion, evolutionary divergence leads to greater complexity while following essential developmental constraints.

From Evolutionary Allometry to Sexual Display: (A Reply to Holman and Bro-Jørgensen).

PubMed

Raia, Pasquale; Passaro, Federico; Carotenuto, Francesco; Meiri, Shai; Piras, Paolo

2016-08-01

Conventional wisdom holds that the complex shapes of deer antlers are produced under the sole influence of sexual selection. We questioned this view by demonstrating that trends for increased body size evolution passively yield more-complex ornaments, even in organisms where no effect of sexual selection is possible, with similar allometric slopes. Recent investigations suggest that sexual selection on antlers of larger deer species is stronger than that in smaller species; hence, the use of conspicuous antlers for display in large male deer is a secondary function driven by especially intense sexual selection on these large-bodied species. Since ancestral deer were small and had very simple antlers, such an intense selection on antlers shape was probably absent in early deer. Therefore, the evolution of complex ornaments is coupled with body size evolution, even in deer.

Linguistics: evolution and language change.

PubMed

Bowern, Claire

2015-01-05

Linguists have long identified sound changes that occur in parallel. Now novel research shows how Bayesian modeling can capture complex concerted changes, revealing how evolution of sounds proceeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

PubMed Central

Garvin, Michael R.; Bielawski, Joseph P.; Gharrett, Anthony J.

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm. PMID:21969854

Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon.

PubMed

Garvin, Michael R; Bielawski, Joseph P; Gharrett, Anthony J

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm.

T Cell Adaptive Immunity Proceeds through Environment-Induced Adaptation from the Exposure of Cryptic Genetic Variation

PubMed Central

Whitacre, James M.; Lin, Joseph; Harding, Angus

2011-01-01

Evolution is often characterized as a process involving incremental genetic changes that are slowly discovered and fixed in a population through genetic drift and selection. However, a growing body of evidence is finding that changes in the environment frequently induce adaptations that are much too rapid to occur by an incremental genetic search process. Rapid evolution is hypothesized to be facilitated by mutations present within the population that are silent or “cryptic” within the first environment but are co-opted or “exapted” to the new environment, providing a selective advantage once revealed. Although cryptic mutations have recently been shown to facilitate evolution in RNA enzymes, their role in the evolution of complex phenotypes has not been proven. In support of this wider role, this paper describes an unambiguous relationship between cryptic genetic variation and complex phenotypic responses within the immune system. By reviewing the biology of the adaptive immune system through the lens of evolution, we show that T cell adaptive immunity constitutes an exemplary model system where cryptic alleles drive rapid adaptation of complex traits. In naive T cells, normally cryptic differences in T cell receptor reveal diversity in activation responses when the cellular population is presented with a novel environment during infection. We summarize how the adaptive immune response presents a well studied and appropriate experimental system that can be used to confirm and expand upon theoretical evolutionary models describing how seemingly small and innocuous mutations can drive rapid cellular evolution. PMID:22363338

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems

PubMed Central

Yoshida, M. A.; Ogura, A.; Ikeo, K.; Shigeno, S.; Moritaki, T.; Winters, G. C.; Kohn, A. B.; Moroz, L. L.

2015-01-01

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called “evolutionary tinkering” or “co-option”, and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the “camera” eye from nautilus’ “pinhole” eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids’ opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. PMID:26002349

Netgram: Visualizing Communities in Evolving Networks

PubMed Central

Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

2015-01-01

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy

PubMed Central

Sheehan, Oliver; Gray, Russell D.; Atkinson, Quentin D.

2018-01-01

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification—the development of landesque capital intensive agriculture—with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the “prime mover” in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. PMID:29555760

Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

PubMed

Beck, Emily A; Llopart, Ana

2015-11-25

Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

Divide and conquer: intermediate levels of population fragmentation maximize cultural accumulation.

PubMed

Derex, Maxime; Perreault, Charles; Boyd, Robert

2018-04-05

Identifying the determinants of cumulative cultural evolution is a key issue in the interdisciplinary field of cultural evolution. A widely held view is that large and well-connected social networks facilitate cumulative cultural evolution because they promote the spread of useful cultural traits and prevent the loss of cultural knowledge through factors such as drift. This view stems from models that focus on the transmission of cultural information, without considering how new cultural traits actually arise. In this paper, we review the literature from various fields that suggest that, under some circumstances, increased connectedness can decrease cultural diversity and reduce innovation rates. Incorporating this idea into an agent-based model, we explore the effect of population fragmentation on cumulative culture and show that, for a given population size, there exists an intermediate level of population fragmentation that maximizes the rate of cumulative cultural evolution. This result is explained by the fact that fully connected, non-fragmented populations are able to maintain complex cultural traits but produce insufficient variation and so lack the cultural diversity required to produce highly complex cultural traits. Conversely, highly fragmented populations produce a variety of cultural traits but cannot maintain complex ones. In populations with intermediate levels of fragmentation, cultural loss and cultural diversity are balanced in a way that maximizes cultural complexity. Our results suggest that population structure needs to be taken into account when investigating the relationship between demography and cumulative culture.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Spectropolarimetry of SN 2011dh in M51: geometric insights on a Type IIb supernova progenitor and explosion

NASA Astrophysics Data System (ADS)

Mauerhan, Jon C.; Williams, G. Grant; Leonard, Douglas C.; Smith, Paul S.; Filippenko, Alexei V.; Smith, Nathan; Hoffman, Jennifer L.; Huk, Leah; Clubb, Kelsey I.; Silverman, Jeffrey M.; Cenko, S. Bradley; Milne, Peter; Gal-Yam, Avishay; Ben-Ami, Sagi

2015-11-01

We present seven epochs of spectropolarimetry of the Type IIb supernova (SN IIb) 2011dh in M51, spanning 86 d of its evolution. The first epoch was obtained 9 d after the explosion, when the photosphere was still in the depleted hydrogen layer of the stripped-envelope progenitor. Continuum polarization is securely detected at the level of P ≈ 0.5 per cent through day 14 and appears to diminish by day 30, which is different from the prevailing trends suggested by studies of other core-collapse SNe. Time-variable modulations in P and position angle are detected across P-Cygni line features. H α and He I polarization peak after 30 d and exhibit position angles roughly aligned with the earlier continuum, while O I and Ca II appear to be geometrically distinct. We discuss several possibilities to explain the evolution of the continuum and line polarization, including the potential effects of a tidally deformed progenitor star, aspherical radioactive heating by fast-rising plumes of 56Ni from the core, oblique shock breakout, or scattering by circumstellar material. While these possibilities are plausible and guided by theoretical expectations, they are not unique solutions to the data. The construction of more detailed hydrodynamic and radiative-transfer models that incorporate complex aspherical geometries will be required to further elucidate the nature of the polarized radiation from SN 2011dh and other SNe IIb.

Spectroscopic Ellipsometry Studies of n-i-p Hydrogenated Amorphous Silicon Based Photovoltaic Devices

PubMed Central

Karki Gautam, Laxmi; Junda, Maxwell M.; Haneef, Hamna F.; Collins, Robert W.; Podraza, Nikolas J.

2016-01-01

Optimization of thin film photovoltaics (PV) relies on characterizing the optoelectronic and structural properties of each layer and correlating these properties with device performance. Growth evolution diagrams have been used to guide production of materials with good optoelectronic properties in the full hydrogenated amorphous silicon (a-Si:H) PV device configuration. The nucleation and evolution of crystallites forming from the amorphous phase were studied using in situ near-infrared to ultraviolet spectroscopic ellipsometry during growth of films prepared as a function of hydrogen to reactive gas flow ratio R = [H2]/[SiH4]. In conjunction with higher photon energy measurements, the presence and relative absorption strength of silicon-hydrogen infrared modes were measured by infrared extended ellipsometry measurements to gain insight into chemical bonding. Structural and optical models have been developed for the back reflector (BR) structure consisting of sputtered undoped zinc oxide (ZnO) on top of silver (Ag) coated glass substrates. Characterization of the free-carrier absorption properties in Ag and the ZnO + Ag interface as well as phonon modes in ZnO were also studied by spectroscopic ellipsometry. Measurements ranging from 0.04 to 5 eV were used to extract layer thicknesses, composition, and optical response in the form of complex dielectric function spectra (ε = ε1 + iε2) for Ag, ZnO, the ZnO + Ag interface, and undoped a-Si:H layer in a substrate n-i-p a-Si:H based PV device structure. PMID:28773255

Using Evolution to Guide Protein Engineering: The Devil IS in the Details.

PubMed

Swint-Kruse, Liskin

2016-07-12

For decades, protein engineers have endeavored to reengineer existing proteins for novel applications. Overall, protein folds and gross functions can be readily transferred from one protein to another by transplanting large blocks of sequence (i.e., domain recombination). However, predictably fine-tuning function (e.g., by adjusting ligand affinity, specificity, catalysis, and/or allosteric regulation) remains a challenge. One approach has been to use the sequences of protein families to identify amino acid positions that change during the evolution of functional variation. The rationale is that these nonconserved positions could be mutated to predictably fine-tune function. Evolutionary approaches to protein design have had some success, but the engineered proteins seldom replicate the functional performances of natural proteins. This Biophysical Perspective reviews several complexities that have been revealed by evolutionary and experimental studies of protein function. These include 1) challenges in defining computational and biological thresholds that define important amino acids; 2) the co-occurrence of many different patterns of amino acid changes in evolutionary data; 3) difficulties in mapping the patterns of amino acid changes to discrete functional parameters; 4) the nonconventional mutational outcomes that occur for a particular group of functionally important, nonconserved positions; 5) epistasis (nonadditivity) among multiple mutations; and 6) the fact that a large fraction of a protein's amino acids contribute to its overall function. To overcome these challenges, new goals are identified for future studies. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Evolution of electrical properties and domain configuration of Mn modified Pb(In1/2Nb1/2)O3-PbTiO3 single crystals

NASA Astrophysics Data System (ADS)

Qiao, Huimin; He, Chao; Yuan, Feifei; Wang, Zujian; Li, Xiuzhi; Liu, Ying; Guo, Haiyan; Long, Xifa

2018-04-01

The acceptor doped relaxor-based ferroelectric materials are useful for high power applications such as probes in ultrasound-guided high intensity focused ultrasound therapy. In addition, a high Curie temperature is desired because of wider temperature usage and improved temperature stability. Previous investigations have focused on Pb(Mg1/3Nb2/3)O3-PbTiO3 and Pb(Zn1/3Nb2/3)O3-PbTiO3 systems, which have a ultrahigh piezoelectric coefficient and dielectric constant, but a relatively low Curie temperature. It is desirable to study the binary relaxor-based system with a high Curie temperature. Therefore, Pb(In1/2Nb1/2)O3-PbTiO3 (PINT) single crystals were chosen to study the Mn-doped influence on their electrical properties and domain configuration. The evolution of ferroelectric hysteresis loops for doped and virgin samples exhibit the pinning effect in Mn-doped PINT crystals. The relaxation behaviors of doped and virgin samples are studied by fit of the modified Curie-Weiss law and Volgel-Fucher relation. In addition, a short-range correlation length was fitted to study the behavior of polar nanoregions based on the domain configuration obtained by piezoresponse force microscopy. Complex domain structures and smaller short-range correlation lengths (100-150 nm for Mn-doped PINT and >400 nm for pure PINT) were obtained in the Mn-doped PINT single crystals.

Evidence for soft bounds in Ubuntu package sizes and mammalian body masses.

PubMed

Gherardi, Marco; Mandrà, Salvatore; Bassetti, Bruno; Cosentino Lagomarsino, Marco

2013-12-24

The development of a complex system depends on the self-coordinated action of a large number of agents, often determining unexpected global behavior. The case of software evolution has great practical importance: knowledge of what is to be considered atypical can guide developers in recognizing and reacting to abnormal behavior. Although the initial framework of a theory of software exists, the current theoretical achievements do not fully capture existing quantitative data or predict future trends. Here we show that two elementary laws describe the evolution of package sizes in a Linux-based operating system: first, relative changes in size follow a random walk with non-Gaussian jumps; second, each size change is bounded by a limit that is dependent on the starting size, an intriguing behavior that we call "soft bound." Our approach is based on data analysis and on a simple theoretical model, which is able to reproduce empirical details without relying on any adjustable parameter and generates definite predictions. The same analysis allows us to formulate and support the hypothesis that a similar mechanism is shaping the distribution of mammalian body sizes, via size-dependent constraints during cladogenesis. Whereas generally accepted approaches struggle to reproduce the large-mass shoulder displayed by the distribution of extant mammalian species, this is a natural consequence of the softly bounded nature of the process. Additionally, the hypothesis that this model is valid has the relevant implication that, contrary to a common assumption, mammalian masses are still evolving, albeit very slowly.

Structural evolution of Cenozoic basins in northeastern Tunisia, in response to sinistral strike-slip movement on the El Alia-Teboursouk Fault

NASA Astrophysics Data System (ADS)

Bejaoui, Hamida; Aïfa, Tahar; Melki, Fetheddine; Zargouni, Fouad

2017-10-01

This paper resolves the structural complexity of Cenozoic sedimentary basins in northeastern Tunisia. These basins trend NE-SW to ∼ E-W, and are bordered by old fracture networks. Detailed descriptions of the structural features in outcrop and in subsurface data suggest that the El Alia-Teboursouk Fault zone in the Bizerte area evolved through a series of tectonic events. Cross sections, lithostratigraphic correlations, and interpretation of seismic profiles through the basins show evidence for: (i) a Triassic until Jurassic-Early Cretaceous rifting phase that induced lateral variations of facies and strata thicknesses; (ii) a set of faults oriented NE-SW, NW-SE, N-S, and E-W that guided sediment accumulation in pull-apart basins, which were subject to compressive and transpressive deformation during Eocene (Lutetian-Priabonian), Miocene (Tortonian), and Pliocene-Quaternary; and (iii) NNW-SSE to NS contractional events that occurred during the Late Pliocene. Part of the latest phase has been the formation of different synsedimentary folded structures with significant subsidence inversion. Such events have been responsible for the reactivation of inherited faults, and the intrusion of Triassic evaporites, ensuring the role of a slip layer. The combined effects of the different paleoconstraints and halokinetic movements are at the origin of the evolution of these pull-apart basins. The subsurface data suggest that an important fault displacement occurred during the Mesozoic-Cenozoic. The patterns of sediment accumulation in the different basins reflect a high activity of deep ancient faults.

Prebiotic coordination chemistry: The potential role of transition-metal complexes in the chemical evolution

NASA Technical Reports Server (NTRS)

Beck, M.

1979-01-01

In approaching the extremely involved and complex problem of the origin of life, consideration of the coordination chemistry appeared not only as a possibility but as a necessity. The first model experiments appear to be promising because of prebiotic-type synthesis by means of transition-metal complexes. It is especially significant that in some instances various types of vitally important substances (nucleic bases, amino acids) are formed simultaneously. There is ground to hope that systematic studies in this field will clarify the role of transition-metal complexes in the organizatorial phase of chemical evolution. It is obvious that researchers working in the fields of the chemistry of cyano and carbonyl complexes, and of the catalytic effect of transition-metal complexes are best suited to study these aspects of the attractive and interesting problem of the origin of life.

Applying Weick's model of organizing to health care and health promotion: highlighting the central role of health communication.

PubMed

Kreps, Gary L

2009-03-01

Communication is a crucial process in the effective delivery of health care services and the promotion of public health. However, there are often tremendous complexities in using communication effectively to provide the best health care, direct the adoption of health promoting behaviors, and implement evidence-based public health policies and practices. This article describes Weick's model of organizing as a powerful theory of social organizing that can help increase understanding of the communication demands of health care and health promotion. The article identifies relevant applications from the model for health communication research and practice. Weick's model of organizing is a relevant and heuristic theoretical perspective for guiding health communication research and practice. There are many potential applications of this model illustrating the complexities of effective communication in health care and health promotion. Weick's model of organizing can be used as a template for guiding both research and practice in health care and health promotion. The model illustrates the important roles that communication performs in enabling health care consumers and providers to make sense of the complexities of modern health care and health promotion, select the best strategies for responding effectively to complex health care and health promotion situations, and retain relevant information (develop organizational intelligence) for guiding future responses to complex health care and health promotion challenges.

Leveraging Guided Pathways to Improve Financial Aid Design and Delivery

ERIC Educational Resources Information Center

Luna-Torres, Maria; Leafgreen, Melet; McKinney, Lyle

2017-01-01

To address low completion rates, postsecondary leaders are championing a "guided pathways" approach that puts students on a prescribed route towards graduation. Designing solutions to address low completion rates is complex; in addition to academic roadblocks, insufficient financial resources coupled with a complicated financial aid…

41 CFR 101-5.303 - Guiding principles.

Code of Federal Regulations, 2011 CFR

2011-07-01

... System FEDERAL PROPERTY MANAGEMENT REGULATIONS GENERAL 5-CENTRALIZED SERVICES IN FEDERAL BUILDINGS AND COMPLEXES 5.3-Federal Employee Health Services § 101-5.303 Guiding principles. The following principles will control the scope of the health services to be provided in keeping with the objective: (a) Employees who...

41 CFR 101-5.303 - Guiding principles.

Code of Federal Regulations, 2014 CFR

2014-07-01

... System FEDERAL PROPERTY MANAGEMENT REGULATIONS GENERAL 5-CENTRALIZED SERVICES IN FEDERAL BUILDINGS AND COMPLEXES 5.3-Federal Employee Health Services § 101-5.303 Guiding principles. The following principles will control the scope of the health services to be provided in keeping with the objective: (a) Employees who...

41 CFR 101-5.303 - Guiding principles.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Regulations System FEDERAL PROPERTY MANAGEMENT REGULATIONS GENERAL 5-CENTRALIZED SERVICES IN FEDERAL BUILDINGS AND COMPLEXES 5.3-Federal Employee Health Services § 101-5.303 Guiding principles. The following principles will control the scope of the health services to be provided in keeping with the objective: (a...

Laboratory reconnection experiments

NASA Astrophysics Data System (ADS)

Grulke, Olaf

Laboratory experiments dedicated for the study of magnetic reconnection have been contributed considerably to a more detailed understanding of the involved processes. Their strength is to disentangle parameter dependencies, to diagnose in detail the plasma and field response, and to form an excellent testbed for the validation of numerical simulations. In the present paper recent results obtained from the new cylindrical reconnection experiment VINETA II are presented. The experimental setup allows to independently vary plasma parameters, reconnection drive strength/timescale, and current sheet amplitude. Current research objectives focus on two major scientific issues: Guide field effects on magnetic reconnection and the evolution of electromagnetic fluctuations. The superimposed homogeneous magnetic guide field has a strong influence on the spatiotemporal evolution of the current sheet, predominantly due to magnetic pitch angle effects, which leads to a strong elongation of the sheet along the separatrices and results in axial gradients of the reconnection rates. Within the current sheet, incoherent electromagnetic fluctuations are observed. Their magnetic signature is characterized by a broad spectrum somewhat centered around the lower-hybrid frequency and extremely short spatial correlation lengths being typically smaller than the local ion sound radius. The fluctuation amplitude correlates with the local current density and, thus, for low guide fields, displays also axial gradients. Despite the quantitatively different parameter regime and geometry the basic fluctuation properties are in good agreement with studies conducted at the MRX experiment (PPPL).

Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9.

PubMed

Raper, Austin T; Stephenson, Anthony A; Suo, Zucai

2018-02-28

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.

Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes.

PubMed

Jacobi, Ashley M; Rettig, Garrett R; Turk, Rolf; Collingwood, Michael A; Zeiner, Sarah A; Quadros, Rolen M; Harms, Donald W; Bonthuis, Paul J; Gregg, Christopher; Ohtsuka, Masato; Gurumurthy, Channabasavaiah B; Behlke, Mark A

2017-05-15

Genome editing using the CRISPR/Cas9 system requires the presence of guide RNAs bound to the Cas9 endonuclease as a ribonucleoprotein (RNP) complex in cells, which cleaves the host cell genome at sites specified by the guide RNAs. New genetic material may be introduced during repair of the double-stranded break via homology dependent repair (HDR) if suitable DNA templates are delivered with the CRISPR components. Early methods used plasmid or viral vectors to make these components in the host cell, however newer approaches using recombinant Cas9 protein with synthetic guide RNAs introduced directly as an RNP complex into cells shows faster onset of action with fewer off-target effects. This approach also enables use of chemically modified synthetic guide RNAs that have improved nuclease stability and reduces the risk of triggering an innate immune response in the host cell. This article provides detailed methods for genome editing using the RNP approach with synthetic guide RNAs using lipofection or electroporation in mammalian cells or using microinjection in murine zygotes, with or without addition of a single-stranded HDR template DNA. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Attending to Nuanced Emotions: Fostering Supervisees' Emotional Awareness and Complexity

ERIC Educational Resources Information Center

Tangen, Jodi L.

2017-01-01

There is limited supervision research exploring how supervisees learn emotional awareness and complexity. In this article, the 5 levels of emotional awareness and 3 aspects of emotional complexity are explored in light of the supervision enterprise. In addition, 2 supervision intervention guides and a case example are provided.

Biotin-tagged platinum(iv) complexes as targeted cytostatic agents against breast cancer cells.

PubMed

Muhammad, Nafees; Sadia, Nasreen; Zhu, Chengcheng; Luo, Cheng; Guo, Zijian; Wang, Xiaoyong

2017-09-05

A biotin-guided platinum IV complex is highly cytotoxic against breast cancer cells but hypotoxic against mammary epithelial cells. The mono-biotinylated Pt IV complex is superior to the di-biotinylated one and hence a promising drug candidate for the targeted therapy of breast cancer.

Laughter, Power, and Motivation in Religious Education.

ERIC Educational Resources Information Center

Berryman, Jerome W.

1998-01-01

Investigates the connections among laughter, power, and motivation for religious education by reviewing the history of laughter and four models for laughter. Discusses complexity and the laughter of complexity. Concludes that the laughter of complexity can be a guide towards the appropriate use of power by using intrinsic motivation. (CMK)

The natural science underlying big history.

PubMed

Chaisson, Eric J

2014-01-01

Nature's many varied complex systems-including galaxies, stars, planets, life, and society-are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density-contrasting with information content or entropy production-is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated.

The Natural Science Underlying Big History

PubMed Central

Chaisson, Eric J.

2014-01-01

Nature's many varied complex systems—including galaxies, stars, planets, life, and society—are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density—contrasting with information content or entropy production—is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated. PMID:25032228

CAD/CAM-produced surgical guides: Optimizing the treatment workflow.

PubMed

Neugebauer, J; Kistler, F; Kistler, S; Züdorf, G; Freyer, D; Ritter, L; Dreiseidler, T; Kusch, J; Zöller, J E

2011-01-01

The increased availability of devices for 3D radiological diagnosis allows the more frequent use of CAD/CAM-produced surgical guides for implant placement. The conventional workflow requires a complex logistic chain which is time-consuming and costly. In a pilot study, the workflow of directly milled surgical guides was evaluated. These surgical guides were designed based on the fusion of an optical impression and the radiological data. The clinical use showed that the surgical guides could be accurately placed on the residual dentition without tipping movements. The conventional surgical guides were used as a control for the manual check of the deviation of the implant axis. The direct transfer of the digital planning data allows the fabrication of surgical guides in an external center without the need of physical transport, which reduces the logistic effort and expense of the central fabrication of surgical guides.

Photoreception in Phytoplankton.

PubMed

Colley, Nansi Jo; Nilsson, Dan-Eric

2016-11-01

In many species of phytoplankton, simple photoreceptors monitor ambient lighting. Photoreceptors provide a number of selective advantages including the ability to assess the time of day for circadian rhythms, seasonal changes, and the detection of excessive light intensities and harmful UV light. Photoreceptors also serve as depth gauges in the water column for behaviors such as diurnal vertical migration. Photoreceptors can be organized together with screening pigment into visible eyespots. In a wide variety of motile phytoplankton, including Chlamydomonas, Volvox, Euglena, and Kryptoperidinium, eyespots are light-sensitive organelles residing within the cell. Eyespots are composed of photoreceptor proteins and typically red to orange carotenoid screening pigments. This association of photosensory pigment with screening pigment allows for detection of light directionality, needed for light-guided behaviors such as positive and negative phototaxis. In Chlamydomonas, the eyespot is located in the chloroplast and Chlamydomonas expresses a number of photosensory pigments including the microbial channelrhodopsins (ChR1 and ChR2). Dinoflagellates are unicellular protists that are ecologically important constituents of the phytoplankton. They display a great deal of diversity in morphology, nutritional modes and symbioses, and can be photosynthetic or heterotrophic, feeding on smaller phytoplankton. Dinoflagellates, such as Kryptoperidinium foliaceum, have eyespots that are used for light-mediated tasks including phototaxis. Dinoflagellates belonging to the family Warnowiaceae have a more elaborate eye. Their eye-organelle, called an ocelloid, is a large, elaborate structure consisting of a focusing lens, highly ordered retinal membranes, and a shield of dark pigment. This complex eye-organelle is similar to multicellular camera eyes, such as our own. Unraveling the molecular makeup, structure and function of dinoflagellate eyes, as well as light-guided behaviors in phytoplankton can inform us about the selective forces that drove evolution in the important steps from light detection to vision. We show here that the evolution from simple photoreception to vision seems to have independently followed identical paths and principles in phytoplankton and animals, significantly strengthening our understanding of this important biological process. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

The Manipulative Complexity of Lower Paleolithic Stone Toolmaking

PubMed Central

Faisal, Aldo; Stout, Dietrich; Apel, Jan; Bradley, Bruce

2010-01-01

Background Early stone tools provide direct evidence of human cognitive and behavioral evolution that is otherwise unavailable. Proper interpretation of these data requires a robust interpretive framework linking archaeological evidence to specific behavioral and cognitive actions. Methodology/Principal Findings Here we employ a data glove to record manual joint angles in a modern experimental toolmaker (the 4th author) replicating ancient tool forms in order to characterize and compare the manipulative complexity of two major Lower Paleolithic technologies (Oldowan and Acheulean). To this end we used a principled and general measure of behavioral complexity based on the statistics of joint movements. Conclusions/Significance This allowed us to confirm that previously observed differences in brain activation associated with Oldowan versus Acheulean technologies reflect higher-level behavior organization rather than lower-level differences in manipulative complexity. This conclusion is consistent with a scenario in which the earliest stages of human technological evolution depended on novel perceptual-motor capacities (such as the control of joint stiffness) whereas later developments increasingly relied on enhanced mechanisms for cognitive control. This further suggests possible links between toolmaking and language evolution. PMID:21072164

High Selection Pressure Promotes Increase in Cumulative Adaptive Culture

PubMed Central

Vegvari, Carolin; Foley, Robert A.

2014-01-01

The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little attention has been paid to the role of natural selection in the evolution of cultural complexity. Here we use an agent-based simulation model to demonstrate that high selection pressure in the form of resource pressure promotes the accumulation of adaptive culture in spite of small population sizes and high innovation costs. We argue that the interaction of demography and selection is important, and that neither can be considered in isolation. We predict that an increase in cultural complexity is most likely to occur under conditions of population pressure relative to resource availability. Our model may help to explain why culture change can occur without major environmental change. We suggest that understanding the interaction between shifting selective pressures and demography is essential for explaining the evolution of cultural complexity. PMID:24489724

Knowing the Natural World: The Construction of Knowledge about Evolution in and out of the Classroom

ERIC Educational Resources Information Center

Perkins, Alison Emily Havard

2009-01-01

Evolution is a central underlying concept to a significant number of discourses in civilized society, but the complexity of understanding basic tenets of this important theory is just now coming to light. Knowledge about evolution is constructed from both formal and "free-choice" opportunities, like television. Nature programs are commonly…

The (Un)Lonely Planet Guide: Formation and Evolution of Planetary Systems from a ``Blue Dots'' Perspective

NASA Astrophysics Data System (ADS)

Meyer, M. R.

2010-10-01

In this contribution I summarize some recent successes, and focus on remaining challenges, in understanding the formation and evolution of planetary systems in the context of the Blue Dots initiative. Because our understanding is incomplete, we cannot yet articulate a design reference mission engineering matrix suitable for an exploration mission where success is defined as obtaining a spectrum of a potentially habitable world around a nearby star. However, as progress accelerates, we can identify observational programs that would address fundamental scientific questions through hypothesis testing such that the null result is interesting.

Epistasis analysis using artificial intelligence.

PubMed

Moore, Jason H; Hill, Doug P

2015-01-01

Here we introduce artificial intelligence (AI) methodology for detecting and characterizing epistasis in genetic association studies. The ultimate goal of our AI strategy is to analyze genome-wide genetics data as a human would using sources of expert knowledge as a guide. The methodology presented here is based on computational evolution, which is a type of genetic programming. The ability to generate interesting solutions while at the same time learning how to solve the problem at hand distinguishes computational evolution from other genetic programming approaches. We provide a general overview of this approach and then present a few examples of its application to real data.

Bioprosthetic Mesh in Abdominal Wall Reconstruction

PubMed Central

Baumann, Donald P.; Butler, Charles E.

2012-01-01

Mesh materials have undergone a considerable evolution over the last several decades. There has been enhancement of biomechanical properties, improvement in manufacturing processes, and development of antiadhesive laminate synthetic meshes. The evolution of bioprosthetic mesh materials has markedly changed our indications and methods for complex abdominal wall reconstruction. The authors review the optimal properties of bioprosthetic mesh materials, their evolution over time, and their indications for use. The techniques to optimize outcomes are described using bioprosthetic mesh for complex abdominal wall reconstruction. Bioprosthetic mesh materials clearly have certain advantages over other implantable mesh materials in select indications. Appropriate patient selection and surgical technique are critical to the successful use of bioprosthetic materials for abdominal wall repair. PMID:23372454

[The evolution of human cultural behavior: notes on Darwinism and complexity].

PubMed

Peric, Mikael; Murrieta, Rui Sérgio Sereni

2015-12-01

The article analyzes three schools that can be understood as central in studies of the evolution of human behavior within the paradigm of evolution by natural selection: human behavioral ecology (HBE), evolutionary psychology, and dual inheritance. These three streams of thought are used to depict the Darwinist landscape and pinpoint its strong suits and limitations. Theoretical gaps were identified that seem to reduce these schools' ability to account for the diversity of human evolutionary behavior. Their weak points include issues related to the concept of reproductive success, types of adaptation, and targets of selection. An interdisciplinary approach is proposed as the solution to this dilemma, where complex adaptive systems would serve as a source.

Language evolution and human-computer interaction

NASA Technical Reports Server (NTRS)

Grudin, Jonathan; Norman, Donald A.

1991-01-01

Many of the issues that confront designers of interactive computer systems also appear in natural language evolution. Natural languages and human-computer interfaces share as their primary mission the support of extended 'dialogues' between responsive entities. Because in each case one participant is a human being, some of the pressures operating on natural languages, causing them to evolve in order to better support such dialogue, also operate on human-computer 'languages' or interfaces. This does not necessarily push interfaces in the direction of natural language - since one entity in this dialogue is not a human, this is not to be expected. Nonetheless, by discerning where the pressures that guide natural language evolution also appear in human-computer interaction, we can contribute to the design of computer systems and obtain a new perspective on natural languages.

Emergence, reductionism and landscape response to climate change

NASA Astrophysics Data System (ADS)

Harrison, Stephan; Mighall, Tim

2010-05-01

Predicting landscape response to external forcing is hampered by the non-linear, stochastic and contingent (ie dominated by historical accidents) forcings inherent in landscape evolution. Using examples from research carried out in southwest Ireland we suggest that non-linearity in landform evolution is likely to be a strong control making regional predictions of landscape response to climate change very difficult. While uncertainties in GCM projections have been widely explored in climate science much less attention has been directed by geomorphologists to the uncertainties in landform evolution under conditions of climate change and this problem may be viewed within the context of philosophical approaches to reductionsim and emergence. Understanding the present and future trajectory of landform change may also guide us to provide an enhanced appreciation of how landforms evolved in the past.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

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

Reboredo, Fernando A.; Kim, Jeongnim

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspacemore » of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.« less

Geometry, packing, and evolutionary paths to increased multicellular size

NASA Astrophysics Data System (ADS)

Jacobeen, Shane; Graba, Elyes C.; Brandys, Colin G.; Day, Thomas C.; Ratcliff, William C.; Yunker, Peter J.

2018-05-01

The evolutionary transition to multicellularity transformed life on earth, heralding the evolution of large, complex organisms. Recent experiments demonstrated that laboratory-evolved multicellular "snowflake yeast" readily overcome the physical barriers that limit cluster size by modifying cellular geometry [Jacobeen et al., Nat. Phys. 14, 286 (2018), 10.1038/s41567-017-0002-y]. However, it is unclear why this route to large size is observed, rather than an evolved increase in intercellular bond strength. Here, we use a geometric model of the snowflake yeast growth form to examine the geometric efficiency of increasing size by modifying geometry and bond strength. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ˜13 times more effective than increasing bond strength at increasing the number of cells in a cluster. Modifying other geometric parameters, such as the geometric arrangement of mother and daughter cells, also had larger effects on cluster size than increasing bond strength. Simulations reveal that as cells reproduce, internal stress in the cluster increases rapidly; thus, increasing bond strength provides diminishing returns in cluster size. Conversely, as cells become more elongated, cellular packing density within the cluster decreases, which substantially decreases the rate of internal stress accumulation. This suggests that geometrically imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.

Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles.

PubMed

Tsao, Jean I

2009-01-01

Lyme borreliosis (LB) is caused by a group of pathogenic spirochetes - most often Borrelia burgdorferi, B. afzelii, and B. garinii - that are vectored by hard ticks in the Ixodes ricinus-persulcatus complex, which feed on a variety of mammals, birds, and lizards. Although LB is one of the best-studied vector-borne zoonoses, the annual incidence in North America and Europe leads other vector-borne diseases and continues to increase. What factors make the LB system so successful, and how can researchers hope to reduce disease risk - either through vaccinating humans or reducing the risk of contacting infected ticks in nature? Discoveries of molecular interactions involved in the transmission of LB spirochetes have accelerated recently, revealing complex interactions among the spirochete-tick-vertebrate triad. These interactions involve multiple, and often redundant, pathways that reflect the evolution of general and specific mechanisms by which the spirochetes survive and reproduce. Previous reviews have focused on the molecular interactions or population biology of the system. Here molecular interactions among the LB spirochete, its vector, and vertebrate hosts are reviewed in the context of natural maintenance cycles, which represent the ecological and evolutionary contexts that shape these interactions. This holistic system approach may help researchers develop additional testable hypotheses about transmission processes, interpret laboratory results, and guide development of future LB control measures and management.

Evolution of radiation resistance in a complex microenvironment

NASA Astrophysics Data System (ADS)

Kim, So Hyun; Austin, Robert; Mehta, Monal; Kahn, Atif

2013-03-01

Radiation treatment responses in brain cancers are typically associated with short progression-free intervals in highly lethal malignancies such as glioblastomas. Even as patients routinely progress through second and third line salvage therapies, which are usually empirically selected, surprisingly little information exists on how cancer cells evolve resistance. We will present experimental results showing how in the presence of complex radiation gradients evolution of resistance to radiation occurs. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

Irradiation-induced damage evolution in concentrated Ni-based alloys

DOE PAGES

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou; ...

2017-06-06

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

Irradiation-induced damage evolution in concentrated Ni-based alloys

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

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

AXONOMETRIC, LAUNCH DOOR AND DOOR CYLINDER, LAUNCH PLATFORM ROLLER GUIDE, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

AXONOMETRIC, LAUNCH DOOR AND DOOR CYLINDER, LAUNCH PLATFORM ROLLER GUIDE, CRIB SUSPENSION SHOCK STRUT, LAUNCH PLATFORM - Dyess Air Force Base, Atlas F Missle Site S-8, Launch Facility, Approximately 3 miles east of Winters, 500 feet southwest of Highway 1770, center of complex, Winters, Runnels County, TX

Attention Guiding in Multimedia Learning

ERIC Educational Resources Information Center

Jamet, Eric; Gavota, Monica; Quaireau, Christophe

2008-01-01

Comprehension of an illustrated document can involve complex visual scanning in order to locate the relevant information on the screen when this is evoked in spoken explanations. The present study examined the effects of two types of attention-guiding means (color change or step-by-step presentation of diagram elements synchronized with a spoken…

The Complexity-Adaptability Paradox: Issues for Combat Aircraft Development

DTIC Science & Technology

2011-02-16

to Darwin in many sources, including being engraved in stone on the floor of the California Academy of Science, it is most widely attributed to...showing laser -guided bombs guiding down elevator shafts. Observers have described this combination of precision and stealth as having a ―revolutionary

Examining the Forces That Guide Teaching Decisions

ERIC Educational Resources Information Center

Griffith, Robin; Massey, Dixie; Atkinson, Terry S.

2013-01-01

This study of two successful first grade teachers examines the forces that guide their instructional decisions. Findings reveal the complexities of forces that influence the moment-to-moment decisions made by these teachers. Teachers repeatedly attempted to balance their desires to be student-centered while addressing state standards and…

Humane Education: Resource Guide. A Guide for Elementary School Teachers.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn, NY. Div. of Curriculum and Instruction.

Humane education promotes responsible behavior and improves the quality of life for animals and humans. Teaching the humane treatment of animals is a complex, philosophical, and values-oriented subject. Lessons for each grade level have performance objectives, materials, and activities. Student activity sheets are provided for follow-up…

Internet Policy Handbook for Libraries. Neal-Schuman NetGuide Series.

ERIC Educational Resources Information Center

Smith, Mark

This book is intended to guide library administrators--directors and departmental managers in public, school, and academic libraries--through the many complex decisions inherent in managing public Internet access. The handbook systematically deals with each possible element of an Internet policy. It identifies the options available at each…

A Guide to Collaboration for IEP Teams

ERIC Educational Resources Information Center

Martin, Nicholas R. M.

2005-01-01

With so many complex, challenging, and emotionally charged decisions involved, participating in an IEP meeting can seem like navigating through a minefield. But now there is a practical guide to managing these meetings with a high level of awareness, safety, and confidence. Developed for administrators, teachers, resource professionals, and…

Evolution of the PWWP-domain encoding genes in the plant and animal lineages

PubMed Central

2012-01-01

Background Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations (‘promiscuous’ domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. Results Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements (‘cassettes’). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. Conclusion Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms. PMID:22734652

Nonlinear stochastic interacting dynamics and complexity of financial gasket fractal-like lattice percolation

NASA Astrophysics Data System (ADS)

Zhang, Wei; Wang, Jun

2018-05-01

A novel nonlinear stochastic interacting price dynamics is proposed and investigated by the bond percolation on Sierpinski gasket fractal-like lattice, aim to make a new approach to reproduce and study the complexity dynamics of real security markets. Fractal-like lattices correspond to finite graphs with vertices and edges, which are similar to fractals, and Sierpinski gasket is a well-known example of fractals. Fractional ordinal array entropy and fractional ordinal array complexity are introduced to analyze the complexity behaviors of financial signals. To deeper comprehend the fluctuation characteristics of the stochastic price evolution, the complexity analysis of random logarithmic returns and volatility are preformed, including power-law distribution, fractional sample entropy and fractional ordinal array complexity. For further verifying the rationality and validity of the developed stochastic price evolution, the actual security market dataset are also studied with the same statistical methods for comparison. The empirical results show that this stochastic price dynamics can reconstruct complexity behaviors of the actual security markets to some extent.

Star-Forming Regions in Orion as a Dust Evolution Laboratory

NASA Astrophysics Data System (ADS)

Wiebe, D.; Murga, M.; Sivkova, E.

2017-06-01

Star-forming regions (SFR) represent a convenient opportunity to study various processes related both to dust growth and to dust destruction. While extragalactic SFRs allow considering these processes in a wide range of metallicities, UV field intensities, etc., the Orion star-forming complex opens up a possibility to observe dust evolution with an unprecedented angular resolution. We review various observations related to dust evolution in some most prominent Orion regions, paying special attention to organic dust evolution, and introduce a new model of organic dust evolution.

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex.

PubMed

Konermann, Silvana; Brigham, Mark D; Trevino, Alexandro E; Joung, Julia; Abudayyeh, Omar O; Barcena, Clea; Hsu, Patrick D; Habib, Naomi; Gootenberg, Jonathan S; Nishimasu, Hiroshi; Nureki, Osamu; Zhang, Feng

2015-01-29

Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. We used these engineered Cas9 activation complexes to investigate single-guide RNA (sgRNA) targeting rules for effective transcriptional activation, to demonstrate multiplexed activation of ten genes simultaneously, and to upregulate long intergenic non-coding RNA (lincRNA) transcripts. We also synthesized a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that, upon activation, confer resistance to a BRAF inhibitor. The top hits included genes previously shown to be able to confer resistance, and novel candidates were validated using individual sgRNA and complementary DNA overexpression. A gene expression signature based on the top screening hits correlated with markers of BRAF inhibitor resistance in cell lines and patient-derived samples. These results collectively demonstrate the potential of Cas9-based activators as a powerful genetic perturbation technology.